@article {1601927, title = {Interactions between identical DNA double helices}, journal = {PHYSICAL REVIEW E}, volume = {101}, year = {2020}, month = {MAR 24}, abstract = {The molecular mechanism of specific interactions between double stranded DNA molecules has been investigated for many years. Problems remain in how confinement, ions, and condensing agents change the interactions. We consider how the orientational alignment of DNAs contributes to the interactions via free energy simulations. Here we report on the effective interactions between two parallel DNA double helices in 150-mM NaCl solution using all atom models. We calculate the potential of mean force (PMF) of DNA-DNA interactions as a function of two coordinates, interhelical separation of parallel double helices and relative rotation of a DNA molecule with respect to the other about the helical axis. We generate the two-dimensional PMF to better understand the effective interactions when a DNA molecule is in juxtaposition with another. The analysis of the ion and solvent distributions around the DNA and particularly in the interface region shows that certain alignments of the DNA pair enhance the interactions. At local free energy minima in distance and alignment, water molecules and Na+ ions form a hydrogen bonded network with the phosphates from each DNA. This network contributes an attractive energy component to the DNA-DNA interactions. Our results provide a molecular mechanism whereby local DNA-DNA interactions, depending on the helical orientation, give a potential mechanism for stabilizing pairing of much larger lengths of homologous DNA that have been seen experimentally. The study suggests an atomically detailed local picture of relevance to certain aspects of DNA condensation or aggregation.}, keywords = {ATTRACTION, B-DNA, BINDING, FORCES, HOMOLOGY, Ions, MOLECULAR-DYNAMICS, recognition, Sodium, Water}, isbn = {2470-00452470-0053 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.101.032414}, author = {Lai, C. L. and Chen, C. Y. and Ou, S. C. and Prentiss, M. and Pettitt, B. M.} } @article {1601934, title = {The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {47}, year = {2019}, month = {FEB 28}, pages = {1836-1846}, abstract = {Bacterial recombinational repair of double-strand breaks often begins with creation of initiating 3 single-stranded DNA (ssDNA) tails on each side of a double-strand break (DSB). Importantly, if the RecBCD pathway is followed, RecBCD creates a gap between the sequences at 3 ends of the initiating strands. The gap flanks the DSB and extends at least to the nearest Chi site on each strand. Once the initiating strands form ssDNA-RecA filaments, each ssDNA-RecA filament searches for homologous double-stranded DNA (dsDNA) to use as a template for the DNA synthesis needed to fill the gap created by RecBCD. Our experimental results show that the DNA synthesis requires formation of a heteroduplex dsDNA that pairs \>20 contiguous bases in the initiating strand with sequence matched bases in a strand from the original dsDNA. To trigger synthesis, the heteroduplex must be near the 3 end of the initiating strand. Those experimentally determined requirements for synthesis combined with the Chi site dependence of the function of RecBCD and the distribution of Chi sites in bacterial genomes could allow the RecBCD pathway to avoid some genomic rearrangements arising from directly induced DSBs; however, the same three factors could promote other rearrangements.}, keywords = {BREAK REPAIR, DNA STRAND EXCHANGE, ENZYME, ESCHERICHIA-COLI, Heterochromatin, Homologous Recombination, POLYMERASE IV, RECA, REPLICATION FORKS, REVEALS}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gky1252}, author = {C. Li and Danilowicz, C. and Tashjian, T. F. and Godoy, V. G. and Prevost, C. and Prentiss, M.} } @article {1601960, title = {Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair}, journal = {JOURNAL OF BIOLOGICAL CHEMISTRY}, volume = {294}, year = {2019}, month = {MAY 10}, pages = {7588-7600}, abstract = {The evolutionarily conserved Escherichia coli translesion DNA polymerase IV (DinB) is one of three enzymes that can bypass potentially deadly DNA lesions on the template strand during DNA replication. Remarkably, however, DinB is the only known translesion DNA polymerase active in RecA-mediated strand exchange during error-prone double-strand break repair. In this process, a single-stranded DNA (ssDNA)-RecA nucleoprotein filament invades homologous dsDNA, pairing the ssDNA with the complementary strand in the dsDNA. When exchange reaches the 3 end of the ssDNA, a DNA polymerase can add nucleotides onto the end, using one strand of dsDNA as a template and displacing the other. It is unknown what makes DinB uniquely capable of participating in this reaction. To explore this topic, we performed molecular modeling of DinB{\textquoteright}s interactions with the RecA filament during strand exchange, identifying key contacts made with residues in the DinB fingers domain. These residues are highly conserved in DinB, but not in other translesion DNA polymerases. Using a novel FRET-based assay, we found that DinB variants with mutations in these conserved residues are less effective at stabilizing RecA-mediated strand exchange than native DinB. Furthermore, these variants are specifically deficient in strand displacement in the absence of RecA filament. We propose that the amino acid patch of highly conserved residues in DinB-like proteins provides a mechanistic explanation for DinB{\textquoteright}s function in strand exchange and improves our understanding of recombination by providing evidence that RecA plays a role in facilitating DinB{\textquoteright}s activity during strand exchange.}, keywords = {ACCURATE BYPASS, COMPLEX, DinB, DNA Damage, DNA polymerase, DNA polymerase IV, DNA Repair, dna synthesis, HIGH-FIDELITY, Homologous Recombination, IN-VITRO, IV, MOLECULAR-DYNAMICS, Mutagenesis, RECA, RECA PROTEIN, RECBCD ENZYME}, isbn = {0021-92581083-351X J9 - J BIOL CHEM}, url = {https://www.doi.org/10.1074/jbc.RA118.006233}, author = {Tashjian, T. F. and Danilowicz, C. and Molza, A. E. and Nguyen, B. H. and Prevost, C. and Prentiss, M. and Godoy, V. G.} } @article {1601938, title = {Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology}, journal = {JOURNAL OF BIOLOGICAL CHEMISTRY}, volume = {294}, year = {2019}, month = {MAY 24}, pages = {8606-8616}, abstract = {DNA recombination resulting from RecA-mediated strand exchange aided by RecBCD proteins often enables accurate repair of DNA double-strand breaks. However, the process of recombinational repair between short DNA regions of accidental similarity can lead to fatal genomic rearrangements. Previous studies have probed how effectively RecA discriminates against interactions involving a short similar sequence that is embedded in otherwise dissimilar sequences but have not yielded fully conclusive results. Here, we present results of in vitro experiments with fluorescent probes strategically located on the interacting DNA fragments used for recombination. Our findings suggest that DNA synthesis increases the stability of the recombination products. Fluorescence measurements can also probe the homology dependence of the extension of invading DNA strands in D-loops formed by RecA-mediated strand exchange. We examined the slow extension of the invading strand in a D-loop by DNA polymerase (Pol) IV and the more rapid extension by DNA polymerase LF-Bsu. We found that when DNA Pol IV extends the invading strand in a D-loop formed by RecA-mediated strand exchange, the extension afforded by 82 bp of homology is significantly longer than the extension on 50 bp of homology. In contrast, the extension of the invading strand in D-loops by DNA LF-Bsu Pol is similar for intermediates with 50 bp of homology. These results suggest that fatal genomic rearrangements due to the recombination of small regions of accidental homology may be reduced if RecA-mediated strand exchange is immediately followed by DNA synthesis by a slow polymerase.}, keywords = {ALLOWS, cooperativity, DNA Damage, DNA polymerase, DNA recombination, double-strand break (DSB), ESCHERICHIA-COLI, EXCHANGE, fluorescence resonance energy transfer (FRET), heteroduplex formation, Hydrolysis, IV, mechanism, molecular dynamics, POLYMERASE, RECA, Repair, strand displacement synthesis}, isbn = {0021-92581083-351X J9 - J BIOL CHEM}, url = {https://www.doi.org/10.1074/jbc.RA119.007554}, author = {Lu, D. and Danilowicz, C. and Tashjian, T. F. and Prevost, C. and Godoy, V. G. and Prentiss, M.} } @article {1601878, title = {Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {47}, year = {2019}, month = {SEP 5}, pages = {7798-7808}, abstract = {Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.}, keywords = {CONFORMATIONAL-CHANGES, dynamics, ESCHERICHIA-COLI, EXCHANGE, INTERSUBUNIT COORDINATION, MOLECULAR-MECHANISM, MOTOR, PRESYNAPTIC FILAMENT, Protein, recognition}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkz667}, author = {Boyer, B. and Danilowicz, C. and Prentiss, M. and Prevost, C.} } @article {1601889, title = {ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {45}, year = {2017}, month = {AUG 21}, pages = {8448-8462}, abstract = {During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with \>100 base pair lengths occupy more than 1\% of bacterial genomes; however, commitment to strand exchange was believed to occur after testing similar to 20-30 bp. If that were true, pairings between different copies of long repeated sequences would usually become irreversible. Our experiments reveal that in the presence of ATP hydrolysis even 75 bp sequence-matched strand exchange products remain quite reversible. Experiments also indicate that when ATP hydrolysis is present, flanking heterologous dsDNA regions increase the reversibility of sequence matched strand exchange products with lengths up to similar to 75 bp. Results of molecular dynamics simulations provide insight into how ATP hydrolysis destabilizes strand exchange products. These results inspired a model that shows how pairings between long repeated sequences could be efficiently rejected even though most homologous pairings form irreversible products.}, keywords = {DNA-STRAND-EXCHANGE, dynamics, ESCHERICHIA-COLI, GENETIC-RECOMBINATION, Homologous Recombination, mechanism, NUCLEOPROTEIN FILAMENTS, RECA-PROTEIN, recognition, REGIONS}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkx582}, author = {Danilowicz, C. and Hermans, L. and Coljee, V. and Prevost, C. and Prentiss, M.} } @article {1601875, title = {Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA}, journal = {PLOS COMPUTATIONAL BIOLOGY}, volume = {13}, year = {2017}, month = {MAR}, abstract = {Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear. Here we consider a kinetic system, inspired by homology dependent pairing between double stranded DNA in bacteria. By considering a simplified tractable model, we identify different homology testing stages that naturally occur in the system. In particular, we first model dsDNA molecules as short rigid rods containing periodically spaced binding sites. The interaction begins when the centers of two rods collide at a random angle. For most collision angles, the interaction energy is weak because only a few binding sites near the collision point contribute significantly to the binding energy. We show that most incorrect pairings are rapidly rejected at this stage. In rare cases, the two rods enter a second stage by rotating into parallel alignment. While rotation increases the stability of matched and nearly matched pairings, subsequent rotational fluctuations reduce kinetic trapping. Finally, in vivo chromosome are much longer than the persistence length of dsDNA, so we extended the model to include multiple parallel collisions between long dsDNA molecules, and find that those additional interactions can greatly accelerate the searching.}, keywords = {EXCHANGE, HELICES, recognition, RECOMBINATION, yeast}, isbn = {1553-7358 J9 - PLOS COMPUT BIOL}, url = {https://www.doi.org/10.1371/journal.pcbi.1005421}, author = {Bitran, A. and Chiang, W. Y. and Levine, E. and Prentiss, M.} } @article {1601936, title = {Single molecule identification of homology-dependent interactions between long ssRNA and dsDNA}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {45}, year = {2017}, month = {JAN}, pages = {894-901}, abstract = {Long non-coding RNAs (lncRNAs) are prominently associated with chromosomes in an ever-increasing diversity of roles. To provide further insight into the potential nature of these associations, we have explored, for the first time, the interaction of long single-stranded (ss) RNAs with cognate homologous double-stranded (ds) DNA in vitro. Using magnetic tweezers, we measured the effects of ssRNA on force extension curves for dsDNA. We observe that the presence of ssRNA impedes the extension of dsDNA, specifically at low forces, dependent on homology between the RNA and DNA species, and dependent on ssRNA lengths (\>= 1 kb). The observed effect also depends on the concentration of ssRNA and is abolished by overstretching of the dsDNA. These findings show that significant homologous contacts can occur between long ssRNA and dsDNA in the absence of protein and that these contacts alter the mechanical properties of the dsDNA. We propose that long ssRNA interacts paranemically with long dsDNA via periodic short homologous interactions, e.g. mediated by RNA/DNA triplex-formation, and that dsDNA extension is impeded by formation of RNA secondary structure in the intervening unbound regions. Analogous interactions in vivo would permit lncRNAs to mediate the juxtaposition of two or more DNA regions on the same or different chromosomes.}, keywords = {DUPLEX DNA, GENE, HYBRIDS, LOCUS, NONCODING RNA, recognition, TRIPLE-HELIX}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkw758}, author = {Liu, C. L. and Danilowicz, C. and Kleckner, N. and Prentiss, M.} } @article {1601933, title = {Binding energies of nucleobase complexes: Relevance to homology recognition of DNA}, journal = {PHYSICAL REVIEW E}, volume = {93}, year = {2016}, month = {JUN 13}, abstract = {The binding energies of complexes of DNA nucleobase pairs are evaluated using quantum mechanical calculations at the level of dispersion corrected density functional theory. We begin with Watson-Crick base pairs of singlets, duplets, and triplets and calculate their binding energies. At a second step, mismatches are incorporated into theWatson-Crick complexes in order to evaluate the variation in the binding energy with respect to the canonical Watson-Crick pairs. A linear variation of this binding energy with the degree of mismatching is observed. The binding energies for the duplets and triplets containing mismatches are further compared to the energies of the respective singlets in order to assess the degree of collectivity in these complexes. This study also suggests that mismatches do not considerably affect the energetics of canonical base pairs. Our work is highly relevant to the recognition process in DNA promoted through the RecA protein and suggests a clear distinction between recognition in singlets, and recognition in duplets or triplets. Our work assesses the importance of collectivity in the homology recognition of DNA.}, keywords = {BASE-PAIRS, CRYSTAL-STRUCTURE, EXCHANGE, GEOMETRIC PARAMETERS, mechanism, MEIOTIC RECOMBINATION, MOLECULAR-STRUCTURE, NUCLEIC-ACIDS, RECA PROTEIN, SKIN-CANCER}, isbn = {2470-00452470-0053 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.93.062410}, author = {Leon, S. C. and Prentiss, M. and Fyta, M.} } @article {1601932, title = {Evidence of protein-free homology recognition in magnetic bead force-extension experiments}, journal = {PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES}, volume = {472}, year = {2016}, month = {JUL 1}, abstract = {Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data.}, keywords = {DNA, DOUBLE HELICES, homology recognition, macromolecular mechanics, molecular interactions, SEQUENCE, single-molecule force experiments}, isbn = {1364-50211471-2946 J9 - P ROY SOC A-MATH PHY}, url = {https://www.doi.org/10.1098/rspa.2016.0186}, author = {Lee, D. J. and Danilowicz, C. and Rochester, C. and Kornyshev, A. A. and Prentiss, M.} } @article {1601935, title = {Chromosomes Progress to Metaphase in Multiple Discrete Steps via Global Compaction/Expansion Cycles}, journal = {CELL}, volume = {161}, year = {2015}, month = {MAY 21}, pages = {1124-1137}, abstract = {Mammalian mitotic chromosome morphogenesis was analyzed by 4D live-cell and snapshot deconvolution fluorescence imaging. Prophase chromosomes, whose organization was previously unknown, are revealed to comprise co-oriented sister linear loop arrays displayed along a single, peripheral, regularly kinked topoisomerase II/cohesin/condensin II axis. Thereafter, rather than smooth, progressive compaction as generally envisioned, progression to metaphase is a discontinuous process involving chromosome expansion as well as compaction. At late prophase, dependent on topoisomerase II and with concomitant cohesin release, chromosomes expand, axes split and straighten, and chromatin loops transit to a radial disposition around now-central axes. Finally, chromosomes globally compact, giving the metaphase state. These patterns are consistent with the hypothesis that the molecular events of chromosome morphogenesis are governed by accumulation and release of chromosome stress, created by chromatin compaction and expansion. Chromosome state could evolve analogously throughout the cell cycle.}, keywords = {CHECKPOINT, CONDENSIN-II, dynamics, Interference, LIVING CELLS, MITOTIC CHROMOSOME, model, ORGANIZATION, SISTER-CHROMATID RESOLUTION, Synaptonemal Complex}, isbn = {0092-86741097-4172 J9 - CELL}, url = {https://www.doi.org/10.1016/j.cell.2015.04.030}, author = {Liang, Z. Y. and Zickler, D. and Prentiss, M. and Chang, F. S. and Witz, G. and Maeshima, K. and Kleckner, N.} } @article {1601977, title = {Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {43}, year = {2015}, month = {DEC 2}, pages = {10251-10263}, abstract = {RecA protein is the prototypical recombinase. Members of the recombinase family can accurately repair double strand breaks in DNA. They also provide crucial links between pairs of sister chromatids in eukaryotic meiosis. A very broad outline of how these proteins align homologous sequences and promote DNA strand exchange has long been known, as are the crystal structures of the RecA-DNA pre- and postsynaptic complexes; however, little is known about the homology searching conformations and the details of how DNA in bacterial genomes is rapidly searched until homologous alignment is achieved. By integrating a physical model of recognition to new modeling work based on docking exploration and molecular dynamics simulation, we present a detailed structure/function model of homology recognition that reconciles extremely quick searching with the efficient and stringent formation of stable strand exchange products and which is consistent with a vast body of previously unexplained experimental results.}, keywords = {ACCELERATED MOLECULAR-DYNAMICS, ATP HYDROLYSIS, BINDING, C-TERMINAL DOMAIN, DNA-STRAND-EXCHANGE, FREE-ENERGY, GENETIC-RECOMBINATION, LOOP L2, PROTEIN DOCKING, Real-time}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1080/07391102.2015.1032752}, author = {Yang, D. R. and Boyer, B. and Prevost, C. and Danilowicz, C. and Prentiss, M.} } @article {1601897, title = {The poor homology stringency in the heteroduplex allows strand exchange to incorporate desirable mismatches without sacrificing recognition in vivo}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {43}, year = {2015}, month = {JUL 27}, pages = {6473-6485}, abstract = {RecA family proteins are responsible for homology search and strand exchange. In bacteria, homology search begins after RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site, forming the presynaptic filament. Once the filament is formed, it interrogates double-stranded DNA (dsDNA). During the interrogation, bases in the dsDNA attempt to form Watson-Crick bonds with the corresponding bases in the initiating strand. Mismatch dependent instability in the base pairing in the heteroduplex strand exchange product could provide stringent recognition; however, we present experimental and theoretical results suggesting that the heteroduplex stability is insensitive to mismatches. We also present data suggesting that an initial homology test of 8 contiguous bases rejects most interactions containing more than 1/8 mismatches without forming a detectable 20 bp product. We propose that, in vivo, the sparsity of accidental sequence matches allows an initial 8 bp test to rapidly reject almost all non-homologous sequences. We speculate that once the initial test is passed, the mismatch insensitive binding in the heteroduplex allows short mismatched regions to be incorporated in otherwise homologous strand exchange products even though sequences with less homology are eventually rejected.}, keywords = {COLI RECA PROTEIN, DNA-BINDING SITE, FILAMENTS, GENETIC-RECOMBINATION, mechanism, MOLECULE, MUTL, Polymerization, Real-time, Repair}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkv610}, author = {Danilowicz, C. and Yang, D. and Kelley, C. and Prevost, C. and Prentiss, M.} } @article {1601978, title = {RecA mediated homology recognition offers lessons for sequence dependent protein recognition, protein folding, and artificial self-assembly}, journal = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS}, volume = {33}, year = {2015}, month = {MAY 18}, pages = {69-70}, isbn = {0739-11021538-0254 J9 - J BIOMOL STRUCT DYN}, url = {https://www.doi.org/10.1080/07391102.2015.1032744}, author = {Yang, D. R. and Danilowicz, C. and Boyer, B. and Prevost, C. and Prentiss, M.} } @article {1601942, title = {ssDNA Pairing Accuracy Increases When Abasic Sites Divide Nucleotides into Small Groups}, journal = {PLOS ONE}, volume = {10}, year = {2015}, month = {JUN 26}, abstract = {Accurate sequence dependent pairing of single-stranded DNA (ssDNA) molecules plays an important role in gene chips, DNA origami, and polymerase chain reactions. In many assays accurate pairing depends on mismatched sequences melting at lower temperatures than matched sequences; however, for sequences longer than similar to 10 nucleotides, single mismatches and correct matches have melting temperature differences of less than 3 degrees C. We demonstrate that appropriately grouping of 35 bases in ssDNA using abasic sites increases the difference between the melting temperature of correct bases and the melting temperature of mismatched base pairings. Importantly, in the presence of appropriately spaced abasic sites mismatches near one end of a long dsDNA destabilize the annealing at the other end much more effectively than in systems without the abasic sites, suggesting that the dsDNA melts more uniformly in the presence of appropriately spaced abasic sites. In sum, the presence of appropriately spaced abasic sites allows temperature to more accurately discriminate correct base pairings from incorrect ones.}, keywords = {DNA}, isbn = {1932-6203 J9 - PLOS ONE}, url = {https://www.doi.org/10.1371/journal.pone.0130875}, author = {Peacock-Villada, A. and Coljee, V. and Danilowicz, C. and Prentiss, M.} } @article {1601879, title = {Structural insights into the mechanism of homologous recombination}, journal = {JOURNAL OF BIOMOLECULAR STRUCTURE \& DYNAMICS}, volume = {33}, year = {2015}, month = {MAY 18}, pages = {72-72}, keywords = {CONFORMATIONAL DYNAMICS}, isbn = {0739-11021538-0254 J9 - J BIOMOL STRUCT DYN}, url = {https://www.doi.org/10.1080/07391102.2015.1032747}, author = {Boyer, B. and Yang, D. R. and Danilowicz, C. and Prentiss, M. and Prevost, C.} } @article {1601949, title = {Structure/function relationships in RecA protein-mediated homology recognition and strand exchange}, journal = {CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY}, volume = {50}, year = {2015}, month = {NOV 2}, pages = {453-476}, abstract = {RecA family proteins include RecA, Rad51, and Dmc1. These recombinases are responsible for homology search and strand exchange. Homology search and strand exchange occur during double-strand break repair and in eukaryotes during meiotic recombination. In bacteria, homology search begins when RecA binds an initiating single-stranded DNA (ssDNA) in the primary DNA-binding site to form the presynaptic filament. The filament is a right-handed helix, where the initiating strand is bound deep within the filament. Once the presynaptic filament is formed, it interrogates nearby double-stranded DNA (dsDNA) to find a homologous sequence; therefore, we provide a detailed discussion of structural features of the presynaptic filament that play important functional roles. The discussion includes many diagrams showing multiple filament turns. These diagrams illustrate interactions that are not evident in single turn structures. The first dsDNA interactions with the presynaptic filament are insensitive to mismatches. The mismatch insensitive interactions lead to dsDNA deformation that triggers a homology testing process governed by kinetics. The first homology test involves approximate to 8 bases. Almost all interactions are rejected by this initial rapid test, leading to a new cycle of homology testing. Interactions that pass the initial rapid test proceed to a slower testing stage. That slower stage induces nonhomologous dsDNA to reverse strand exchange and begin a new cycle of homology testing. In contrast, homologous dsDNA continues to extend the heteroduplex strand-exchange product until ATP hydrolysis makes strand exchange irreversible.}, keywords = {C-TERMINAL DOMAIN, DIFFUSION-DRIVEN MECHANISMS, DNA-BINDING SITE, Double-strand break repair, ESCHERICHIA-COLI RECA, FACILITATED TARGET LOCATION, GENETIC-RECOMBINATION, IN-VIVO, Meiosis, MEIOTIC RECOMBINATION, MISMATCH REPAIR, NUCLEOPROTEIN FILAMENTS, Rad51, recombinase, REGULATORY PROTEINS}, isbn = {1040-92381549-7798 J9 - CRIT REV BIOCHEM MOL}, url = {https://www.doi.org/10.3109/10409238.2015.1092943}, author = {Prentiss, M. and Prevost, C. and Danilowicz, C.} } @article {1601976, title = {Atomistic Studies Support a Detailed Model of RecA Mediated Homology Recognition and Strand Exchange}, journal = {BIOPHYSICAL JOURNAL}, volume = {106}, year = {2014}, month = {JAN 28}, pages = {691A-691A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2013.11.3820}, author = {Yang, D. and Prevost, C. and Prentiss, M.} } @article {1601896, title = {The differential extension in dsDNA bound to Rad51 filaments may play important roles in homology recognition and strand exchange}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {42}, year = {2014}, month = {JAN}, pages = {526-533}, abstract = {RecA and Rad51 proteins play an important role in DNA repair and homologous recombination. For RecA, X-ray structure information and single molecule force experiments have indicated that the differential extension between the complementary strand and its Watson-Crick pairing partners promotes the rapid unbinding of non-homologous dsDNA and drives strand exchange forward for homologous dsDNA. In this work we find that both effects are also present in Rad51 protein. In particular, pulling on the opposite termini (3{\textquoteright} and 5{\textquoteright}) of one of the two DNA strands in a dsDNA molecule allows dsDNA to extend along non-homologous Rad51-ssDNA filaments and remain stably bound in the extended state, but pulling on the 3{\textquoteright}5{\textquoteright} ends of the complementary strand reduces the strand-exchange rate for homologous filaments. Thus, the results suggest that differential extension is also present in dsDNA bound to Rad51. The differential extension promotes rapid recognition by driving the swift unbinding of dsDNA from non-homologous Rad51-ssDNA filaments, while at the same time, reducing base pair tension due to the transfer of the Watson-Crick pairing of the complementary strand bases from the highly extended outgoing strand to the slightly less extended incoming strand, which drives strand exchange forward.}, keywords = {DUPLEX DNA, ESCHERICHIA-COLI RECA, Meiosis, MOLECULE, RECOMBINATION PROTEINS, Repair, SEARCH}, isbn = {0305-10481362-4962 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkt867}, author = {Danilowicz, C. and Peacock-Villada, A. and Vlassakis, J. and Facon, A. and Feinstein, E. and Kleckner, N. and Prentiss, M.} } @article {1601922, title = {RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers}, journal = {PHYSICAL REVIEW E}, volume = {90}, year = {2014}, month = {AUG 7}, abstract = {Ideally, self-assembly should rapidly and efficiently produce stable correctly assembled structures. We study the tradeoff between enthalpic and entropic cost in self-assembling systems using RecA-mediated homology search as an example. Earlier work suggested that RecA searches could produce stable final structures with high stringency using a slow testing process that follows an initial rapid search of similar to 9-15 bases. In this work, we will show that as a result of entropic and enthalpic barriers, simultaneously testing all similar to 9-15 bases as separate individual units results in a longer overall searching time than testing them in groups and stages.}, keywords = {DNA-STRAND-EXCHANGE, dynamics, GENETIC-RECOMBINATION, INITIATION, Kinetics, mechanism, model, PAIRS, Protein, SYNAPSIS}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.90.022704}, author = {Jiang, L. L. and Prentiss, M.} } @article {1601908, title = {Four-Dimensional Imaging of E. coli Nucleoid Organization and Dynamics in Living Cells}, journal = {CELL}, volume = {153}, year = {2013}, month = {MAY 9}, pages = {882-895}, abstract = {Visualization of living E. coli nucleoids, defined by HupA-mCherry, reveals a discrete, dynamic helical ellipsoid. Three basic features emerge. (1) Nucleoid density coalesces into longitudinal bundles, giving a stiff, low-DNA-density ellipsoid. (2) This ellipsoid is radially confined within the cell cylinder. Radial confinement gives helical shape and directs global nucleoid dynamics, including sister segregation. (3) Longitudinal density waves flux back and forth along the nucleoid, with 5\%-10\% of density shifting within 5 s, enhancing internal nucleoid mobility. Furthermore, sisters separate end-to-end in sequential discontinuous pulses, each elongating the nucleoid by 5\%-15\%. Pulses occur at 20 min intervals, at defined cell-cycle times. This progression includes sequential installation and release of programmed tethers, implying cyclic accumulation and relief of intranucleoid mechanical stress. These effects could comprise a chromosome-based cell-cycle engine. Overall, the presented results suggest a general conceptual framework for bacterial nucleoid nnorphogenesis and dynamics.}, keywords = {Chromosome Segregation, COMPACTION, DIVISOME, DNA, ESCHERICHIA-COLI, Protein, Separation, SPATIAL-ORGANIZATION}, isbn = {0092-86741097-4172 J9 - CELL}, url = {https://www.doi.org/10.1016/j.cell.2013.04.006}, author = {Fisher, J. K. and Bourniquel, A. and Witz, G. and Weiner, B. and Prentiss, M. and Kleckner, N.} } @article {1601924, title = {Simplified biased random walk model for RecA-protein-mediated homology recognition offers rapid and accurate self-assembly of long linear arrays of binding sites}, journal = {PHYSICAL REVIEW E}, volume = {88}, year = {2013}, month = {JUL 3}, abstract = {Inspired by RecA-protein-based homology recognition, we consider the pairing of two long linear arrays of binding sites. We propose a fully reversible, physically realizable biased random walk model for rapid and accurate self-assembly due to the spontaneous pairing of matching binding sites, where the statistics of the searched sample are included. In the model, there are two bound conformations, and the free energy for each conformation is a weakly nonlinear function of the number of contiguous matched bound sites.}, keywords = {DNA-STRAND-EXCHANGE, dynamics, Kinetics, Real-time, RECOMBINATION, SEARCH}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.88.012702}, author = {Kates-Harbeck, J. and Tilloy, A. and Prentiss, M.} } @article {1601968, title = {Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange}, journal = {PHYSICAL REVIEW E}, volume = {87}, year = {2013}, month = {MAR 5}, abstract = {It is well known that during homology recognition and strand exchange the double-stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that calculates the distribution of tension in the extended dsDNA during strand exchange. The model suggests that the binding of additional dsDNA base pairs to the DNA/RecA filament alters the tension in dsDNA that was already bound to the filament, resulting in a nonlinear increase in the mechanical energy as a function of the number of bound base pairs. This collective mechanical response may promote homology stringency and underlie unexplained experimental results. DOI: 10.1103/PhysRevE.87.032702}, keywords = {ATP HYDROLYSIS, DNA, mechanism, PAIRS, Protein, Real-time, RECOMBINATION}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.87.032702}, author = {Vlassakis, J. and Feinstein, E. and Yang, D. and Tilloy, A. and Weiller, D. and Kates-Harbeck, J. and Coljee, V. and Prentiss, M.} } @article {1601966, title = {Analog modeling of Worm-Like Chain molecules using macroscopic beads-on-a-string}, journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS}, volume = {14}, year = {2012}, pages = {9041-9046}, abstract = {This paper describes an empirical model of polymer dynamics, based on the agitation of millimeter-sized polymeric beads. Although the interactions between the particles in the macroscopic model and those between the monomers of molecular-scale polymers are fundamentally different, both systems follow the Worm-Like Chain theory.}, keywords = {CRYSTALS, DNA, PERSISTENCE LENGTH, Single}, isbn = {1463-90761463-9084 J9 - PHYS CHEM CHEM PHYS}, url = {https://www.doi.org/10.1039/c2cp40593h}, author = {Tricard, S. and Feinstein, E. and Shepherd, R. F. and Reches, M. and Snyder, P. W. and Bandarage, D. C. and Prentiss, M. and Whitesides, G. M.} } @article {1601943, title = {Complementary strand relocation may play vital roles in RecA-based homology recognition}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {40}, year = {2012}, month = {NOV}, pages = {10441-10451}, abstract = {RecA-family proteins mediate homologous recombination and recombinational DNA repair through homology search and strand exchange. Initially, the protein forms a filament with the incoming single-stranded DNA (ssDNA) bound in site I. The RecA-ssDNA filament then binds double-stranded DNA (dsDNA) in site II. Non-homologous dsDNA rapidly unbinds, whereas homologous dsDNA undergoes strand exchange yielding heteroduplex dsDNA in site I and the leftover outgoing strand in site II. We show that applying force to the ends of the complementary strand significantly retards strand exchange, whereas applying the same force to the outgoing strand does not. We also show that crystallographically determined binding site locations require an intermediate structure in addition to the initial and final structures. Furthermore, we demonstrate that the characteristic dsDNA extension rates due to strand exchange and free RecA binding are the same, suggesting that relocation of the complementary strand from its position in the intermediate structure to its position in the final structure limits both rates. Finally, we propose that homology recognition is governed by transitions to and from the intermediate structure, where the transitions depend on differential extension in the dsDNA. This differential extension drives strand exchange forward for homologs and increases the free energy penalty for strand exchange of non-homologs.}, keywords = {ATP HYDROLYSIS, BINDING, DUPLEX DNA, ENERGY-TRANSFER, EXCHANGE, NUCLEOTIDE COMPLEXES, Protein, RECOMBINATION, SEARCH, SINGLE-MOLECULE}, isbn = {0305-1048 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gks769}, author = {Peacock-Villada, A. and Yang, D. and Danilowicz, C. and Feinstein, E. and Pollock, N. and McShan, S. and Coljee, V. and Prentiss, M.} } @article {1601903, title = {Mechanical Stress on Double Stranded DNA Drives Homology Recognition}, journal = {BIOPHYSICAL JOURNAL}, volume = {102}, year = {2012}, month = {JAN 31}, pages = {16A-16A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2011.11.110}, author = {Feinstein, E. and Danilowicz, C. and Prentiss, M.} } @article {1601906, title = {Organization and Dynamics of the Living E. Coli Nucleoid at High Resolution in Space and Time}, journal = {BIOPHYSICAL JOURNAL}, volume = {102}, year = {2012}, month = {JAN 31}, pages = {16A-16A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2011.11.109}, author = {Fisher, J. and Bourniquel, A. and Witz, G. and Prentiss, M. and Kleckner, N. E.} } @article {1601885, title = {RecA homology search is promoted by mechanical stress along the scanned duplex DNA}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {40}, year = {2012}, month = {FEB}, pages = {1717-1727}, abstract = {A RecA-single-stranded DNA (RecA-ssDNA) filament searches a genome for sequence homology by rapidly binding and unbinding double-stranded DNA (dsDNA) until homology is found. We demonstrate that pulling on the opposite termini (3{\textquoteright} and 5{\textquoteright}) of one of the two DNA strands in a dsDNA molecule stabilizes the normally unstable binding of that dsDNA to non-homologous RecA-ssDNA filaments, whereas pulling on the two 3{\textquoteright}, the two 5{\textquoteright}, or all four termini does not. We propose that the {\textquoteright}outgoing{\textquoteright} strand in the dsDNA is extended by strong DNA-protein contacts, whereas the {\textquoteright}complementary{\textquoteright} strand is extended by the tension on the base pairs that connect the {\textquoteright}complementary{\textquoteright} strand to the {\textquoteright}outgoing{\textquoteright} strand. The stress resulting from different levels of tension on its constitutive strands causes rapid dsDNA unbinding unless sufficient homology is present.}, keywords = {ATP HYDROLYSIS, BINDING, COMPLEXES, DOUBLE-STRANDED DNA, EXCHANGE, FILAMENTS, Polymerization, Protein, RECOMBINATION, SINGLE-MOLECULE}, isbn = {0305-1048 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkr855}, author = {Danilowicz, C. and Feinstein, E. and Conover, A. and Coljee, V.W. and Vlassakis, J. and Chan, Y. L. and Bishop, D. K. and Prentiss, M.} } @article {1601882, title = {Changes in the tension in dsDNA alter the conformation of RecA bound to dsDNA-RecA filaments}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {39}, year = {2011}, month = {NOV}, pages = {8833-8843}, abstract = {The RecA protein is an ATPase that mediates recombination via strand exchange. In strand exchange a single-stranded DNA (ssDNA) bound to RecA binding site I in a RecA/ssDNA filament pairs with one strand of a double-stranded DNA (dsDNA) and forms heteroduplex dsDNA in site I if homology is encountered. Long sequences are exchanged in a dynamic process in which initially unbound dsDNA binds to the leading end of a RecA/ssDNA filament, while heteroduplex dsDNA unbinds from the lagging end via ATP hydrolysis. ATP hydrolysis is required to convert the active RecA conformation, which cannot unbind, to the inactive conformation, which can unbind. If dsDNA extension due to RecA binding increases the dsDNA tension, then RecA unbinding must decrease tension. We show that in the presence of ATP hydrolysis decreases in tension induce decreases in length whereas in the absence of hydrolysis, changes in tension have no systematic effect. These results suggest that decreases in force enhance dissociation by promoting transitions from the active to the inactive RecA conformation. In contrast, increases in tension reduce dissociation. Thus, the changes in tension inherent to strand exchange may couple with ATP hydrolysis to increase the directionality and stringency of strand exchange.}, keywords = {ATP HYDROLYSIS, BINDING SITE, DNA-STRAND EXCHANGE, ESCHERICHIA-COLI, GENETIC-RECOMBINATION, Homologous Recombination, NUCLEOPROTEIN FILAMENTS, Protein, SINGLE-MOLECULE, STALLED REPLICATION FORKS}, isbn = {0305-1048 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkr561}, author = {Conover, A. J. and Danilowicz, C. and Gunaratne, R. and Coljee, V.W. and Kleckner, N. and Prentiss, M.} } @article {1601907, title = {Segregation of Sister Chromosomes in E. coli is Governed by the Shape of the Nucleoid and the Release of Inter-Sister "snaps"}, journal = {BIOPHYSICAL JOURNAL}, volume = {100}, year = {2011}, month = {FEB 2}, pages = {239-239}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.cell.com/biophysj/fulltext/S0006-3495(10)03027-4}, author = {Fisher, J. K. and Bourniquel, A. and Prentiss, M. and Kleckner, N.} } @article {1601902, title = {Single-molecule studies of the stringency factors and rates governing the polymerization of RecA on double-stranded DNA}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {39}, year = {2011}, month = {MAY}, pages = {3781-3791}, abstract = {RecA is a key protein in homologous recombination. During recombination, one single-stranded DNA (ssDNA) bound to site I in RecA exchanges Watson-Crick pairing with a sequence-matched ssDNA that was part of a double-stranded DNA molecule (dsDNA) bound to site II in RecA. After strand exchange, heteroduplex dsDNA is bound to site I. In vivo, direct polymerization of RecA on dsDNA through site I does not occur, though it does in vitro. The mechanisms underlying the difference have been unclear. We use single-molecule experiments to decouple the two steps involved in polymerization: nucleation and elongation. We find that elongation is governed by a fundamental clock that is insensitive to force and RecA concentration from 0.2 and 6 mu M, though rates depend on ionic conditions. Thus, we can probe nucleation site stability by creating nucleation sites at high force and then measuring elongation as a function of applied force. We find that in the presence of ATP hydrolysis a minimum force is required for polymerization. The minimum force decreases with increasing RecA or ATP concentrations. We propose that force reduces the off-rate for nucleation site binding and that nucleation site stability is the stringency factor that prevents in vivo polymerization.}, keywords = {ATP HYDROLYSIS, BINDING, DUPLEX DNA, dynamics, ESCHERICHIA-COLI, FILAMENTS, Homologous Recombination, mechanism, Protein, Real-time}, isbn = {0305-1048 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkr013}, author = {Feinstein, E. and Danilowicz, C. and Conover, A. and Gunaratne, R. and Kleckner, N. and Prentiss, M.} } @article {1601959, title = {Atom interferometry using wave packets with constant spatial displacements}, journal = {PHYSICAL REVIEW A}, volume = {81}, year = {2010}, month = {APR}, abstract = {A standing-wave light-pulse sequence is demonstrated that places atoms into a superposition of wave packets with precisely controlled displacements that remain constant for times as long as 1 s. The separated wave packets are subsequently recombined, resulting in atom interference patterns that probe energy differences of approximate to 10(-34) J and can provide acceleration measurements that are insensitive to platform vibrations.}, keywords = {MATTER-WAVE, OPTICS, TIME-DOMAIN}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.81.043631}, author = {Su, E. J. and Wu, S. J. and Prentiss, M. G.} } @article {1601877, title = {The E.coli Chromosome is an Internally-Organized, Springy, Helical Ellipsoid, the Shape and Dynamics of Which, Through the Cell Cycle, are Determined by the Mechanical Constraints Associated with Replication-Driven Extrusion of DNA/chromatin into a Confin}, journal = {BIOPHYSICAL JOURNAL}, volume = {98}, year = {2010}, month = {JAN}, pages = {658A-658A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2009.12.3611}, author = {Bourniquel, A. A. and Ho, B. T. and Prentiss, M. and Kleckner, N. E.} } @article {1601910, title = {A Magnetic Force Micropiston for Analysis of Chromosome Expansive and Compressive Forces and their Effects on Structure and Function}, journal = {BIOPHYSICAL JOURNAL}, volume = {98}, year = {2010}, month = {JAN}, pages = {477A-477A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2009.12.2597}, author = {Fisher, J. K. and Koszul, R. and Prentiss, M. and Kleckner, N.} } @inbook {1601969, title = {An optical tweezers study of nanosecond duration DNA conformations through DNA-surface binding distance measurements}, booktitle = {OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION VII}, volume = {7762}, year = {2010}, abstract = {Optical tweezers have been widely used to study DNA properties including time dependent changes in conformation; however, such studies have emphasized direct fluorescent observation of the conformations of dyed DNA molecules. In this work we explore DNA conformations that allow undyed DNA to link to spatially separated surfaces. In one set of experiments, we used optical tweezers to hold a polystyrene bead at a fixed distance from the sample capillary wall and measured the probability of the binding as a function of the separation between the polystyrene bead and the capillary, where the beads were fully confined in liquid. In a separate magnetic crystal experiment, we used magnetic forces to control the separation between magnetic beads in a hexagonal lattice at an air-water interface and measured the probability of linking to beads in the crystal. In both types of experiments peak binding occurs at a surface separation several times longer than the radius of gyration of the DNA. These experiments provide fundamental information on elusive, but significant DNA conformations, as well as technologically useful information on the probability of the DNA binding that will link two surfaces.}, keywords = {DNA conformations, DNA dynamics, DNA radius of gyration, DNA-surface binding, dynamics, end-to-end distance of DNA, MOLECULES, optical tweezers and DNA, self-avoiding random walks, Shape}, isbn = {0277-786X1996-756X978-0-8194-8258-7 J9 - PROC SPIE}, url = {https://www.doi.org/10.1117/12.868284}, author = {Vlassakis, J. and Tyle, S. and Crawford, T. and Williams, J. and Weeks, J. and Kodger, T. and Feinstein, E. and Danilowicz, C. and Coljee, V. and Prentiss, M.}, editor = {Dholakia, K. and Spalding, G. C.} } @article {1601963, title = {Straight macroscopic magnetic guide for cold atom interferometer}, journal = {JOURNAL OF APPLIED PHYSICS}, volume = {108}, year = {2010}, month = {NOV 1}, abstract = {We demonstrate a macroscopic magnetic guide for cold atom interferometry, where the magnetic guiding field is generated by a symmetrical array of racetrack coils of copper tape. This system represents a conceptual advance over previous guided atom interferometers based on nonsymmetrical geometries because the symmetry provides a much lower magnetic field curvature per fixed length than equivalent nonsymmetrical geometries, permitting a decrease in system length without increasing the decoherence rate associated with field curvature. We realized a magnetic guide a few cm away from each coil, where smooth translation of the guided atoms is achieved by changing the currents in second array of the multiple-conductor tape. (c) 2010 American Institute of Physics. [doi:10.1063/1.3506685]}, keywords = {CHIP, CONVEYOR, Manipulation, NEUTRAL ATOMS, Wires}, isbn = {0021-89791089-7550 J9 - J APPL PHYS}, url = {https://www.doi.org/10.1063/1.3506685}, author = {Tonyushkin, A. and Prentiss, M.} } @article {1601887, title = {Study of force induced melting of dsDNA as a function of length and conformation}, journal = {JOURNAL OF PHYSICS-CONDENSED MATTER}, volume = {22}, year = {2010}, month = {OCT 20}, abstract = {We measure the constant force required to melt double-stranded (ds) DNA as a function of length for lengths from 12 to 100 000 base pairs, where the force is applied to the 3{\textquoteright}3{\textquoteright} or 5{\textquoteright}5{\textquoteright} ends of the dsDNA. Molecules with 32 base pairs or fewer melt before overstretching. For these short molecules, the melting force is independent of the ends to which the force is applied and the shear force as a function of length is well described by de Gennes theory with a de Gennes length of less than 10 bp. Molecules with lengths of 500 base pairs or more overstretch before melting. For these long molecules, the melting force depends on the ends to which the force is applied. The melting force as a function of length increases even when the length exceeds 1000 bp, where the length dependence is inconsistent with de Gennes theory. Finally, we expand de Gennes melting theory to 3{\textquoteright}5{\textquoteright} pulling and compare the predictions with experimental results.}, keywords = {DEPENDENCE, DOUBLE-STRANDED DNA, ENERGY, EXCHANGE, MOLECULE, OVERSTRETCHING TRANSITION, RECA}, isbn = {0953-8984 J9 - J PHYS-CONDENS MAT}, url = {https://www.doi.org/10.1088/0953-8984/22/41/414106}, author = {Danilowicz, C. and Hatch, K. and Conover, A. and Ducas, T. and Gunaratne, R. and Coljee, V. and Prentiss, M.} } @article {1601905, title = {Using Magnetic Fluids as a Versatile Method for Manipulating and Sorting Unlabeled Nonmagnetic Particles in a Flow}, journal = {BIOPHYSICAL JOURNAL}, volume = {98}, year = {2010}, month = {JAN}, pages = {605A-605A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1016/j.bpj.2009.12.3297}, author = {Feinstein, E. and Striehl, P. and Shivers, J. and Prentiss, M.} } @article {1601964, title = {Demonstration of a multipulse interferometer for quantum kicked-rotor studies}, journal = {PHYSICAL REVIEW A}, volume = {79}, year = {2009}, month = {MAY}, abstract = {We implemented a multipulse interferometer scheme that allows us to study a quantum kicked rotor by observing dephasing of momentum coherence. Our study shows that momentum coherence can be nearly perfectly preserved under conditions where the mean energy as a function of the kick number is known to increase without bound. The accompanying width narrowing of these coherences may provide a new method for accurate measurement of the recoil frequency.}, keywords = {AMPLITUDE NOISE, DYNAMICAL LOCALIZATION, interferometers, Quantum Theory, resonance}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.79.051402}, author = {Tonyushkin, A. and Wu, S. and Prentiss, M.} } @article {1601956, title = {DNA unzipping phase diagram calculated via replica theory}, journal = {PHYSICAL REVIEW E}, volume = {79}, year = {2009}, month = {MAY}, abstract = {We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). Toward this end, we study a statistical-mechanics model for the fluctuating structure of a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under applied force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c. We include stacking interactions, hydrogen bonds, and main-chain entropy. We include sequence heterogeneity at the level of random sequences; in particular, there is no correlation in the base-pairing (bp) energy from one sequence position to the next. We present heuristic arguments to demonstrate that the low-temperature macrostate does not exhibit degenerate ergodicity breaking. We use this claim to understand the results of our replica-theoretic calculation of the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical-force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a double helix versus the region where the molecule exists as two separate strands. We compare our random-sequence model to magnetic tweezer experiments performed on the 48 502 bp genome of bacteriophage lambda. We find good agreement with the experimental data, which is restricted to temperatures between 24 and 50 degrees C. At higher temperatures, the critical-force curve of our random-sequence model is very different for that of the homogeneous-sequence version of our model. For both sequence models, the critical force falls to zero at the melting temperature T-c like parallel to T-T-c parallel to(alpha). For the homogeneous-sequence model, alpha=1/2 almost exactly, while for the random-sequence model, alpha approximate to 0.9. Importantly, the shape of the critical-force curve is connected, via our theory, to the manner in which the helix fraction falls to zero at T-c. The helix fraction is the property that is used to classify the melting transition as a type of phase transition. In our calculation, the shape of the critical-force curve holds strong evidence that the zero-force melting transition of long natural dsDNA should be classified as a higher-order (continuous) phase transition. Specifically, the order is 3rd or greater.}, keywords = {BACTERIOPHAGE-LAMBDA, critical points, DENATURATION, dissociation energies, DNA, Entropy, equilibrium, HELIX-COIL TRANSITION, hydrogen bonds, model, molecular biophysics, molecular configurations, NUCLEIC-ACIDS, phase diagrams, STATISTICAL-MECHANICS, THERMAL-STABILITY}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.79.051923}, author = {Roland, C. B. and Hatch, K. A. and Prentiss, M. and Shakhnovich, E. I.} } @article {1601925, title = {Dynamic Conformation Fluctuations of lambda-Phage DNA in an Optical Trap}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {577A-577A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508032499?via\%3Dihub}, author = {Kodger, T. E. and Williams, J. and Tyle, S. and Prentiss, M.} } @article {1601979, title = {Formation Of RecA Filament During The Mechanical Unzipping Of dsDNA To ssDNA: Competition With SSB Differentially Controls RecA Mediated SOS Response And Replication Repair}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {59A-59A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508003287?via\%3Dihub}, author = {Zambonelli, C. and Danilowicz, C. and Kleckner, N. and Prentiss, M.} } @article {1601888, title = {Manipulating Single dsDNA Molecules To Study Force Induced Phase Transitions}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {345A-345A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508019516?via\%3Dihub}, author = {Danilowicz, C. and Hatch, K. and Limouse, C. and Gunaratne, R. and Vlassakis, J. and Williams, J. and Coljee, V. and Prentiss, M.} } @article {1601901, title = {A Novel Self-Assembled, Self-Healing, Ordered Biomaterial}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {635A-635A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508035960?via\%3Dihub}, author = {Feinstein, E. and Alsberg, E. and Ingber, D. and Prentiss, M.} } @article {1601974, title = {Observation of Saturation of Fidelity Decay with an Atom Interferometer}, journal = {PHYSICAL REVIEW LETTERS}, volume = {103}, year = {2009}, month = {JUL 17}, abstract = {We use an atom interferometer to investigate the dynamics of matter waves in a periodically pulsed optical standing wave: an atom optics realization of the quantum kicked rotor that exhibits chaotic classical dynamics. We experimentally show that a measure of the coherence between the interferometer diffraction orders can revive after a quick initial loss, and can approach a finite asymptote as the number of kicks increases. This observation demonstrates that quantum fidelity of a classically chaotic system can survive strong perturbations over long times without decay.}, keywords = {dynamics, ECHOES, KICKED ROTOR, MATTER-WAVE, OPTICS, SYSTEMS, WAVE INTERFEROMETRY}, isbn = {0031-90071079-7114 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.103.034101}, author = {Wu, S. J. and Tonyushkin, A. and Prentiss, M. G.} } @article {1601909, title = {Photonic and Magnetic Force Micro-piston: An integrated force/microfluidic device for investigating expansion and compression stress in chromatin/chromosomes and their roles in chromosome function}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {54A-54A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508003020?via\%3Dihub}, author = {Fisher, J. K. and Koszul, R. and Prentiss, M. and Kleckner, N.} } @article {1601899, title = {Quantifying Colorimetric Assays in Paper-Based Microfluidic Devices by Measuring the Transmission of Light through Paper}, journal = {ANALYTICAL CHEMISTRY}, volume = {81}, year = {2009}, month = {OCT 15}, pages = {8447-8452}, abstract = {This article describes a point-of-care (POC) system-comprising a microfluidic, paper-based analytical device (mu-PAD) and a hand-held optical colorimeter-for quantifying the concentration of analytes in biological fluids. The mu-PAD runs colorimetric assays, and consists of paper that has been (i) patterned to expose isolated regions of hydrophilic zones and (ii) wet with an index-matching fluid (e.g., vegetable oil) that is applied using a disposable, plastic sleeve encasement. Measuring transmittance through paper represents a new method of quantitative detection that expands the potential functionality of mu-PADs. This prototype transmittance colorimeter is inexpensive, rugged, and fully self-contained, and thus potentially attractive for use in resource-limited environments and developing countries.}, keywords = {Health, LOW-COST}, isbn = {0003-27001520-6882 J9 - ANAL CHEM}, url = {https://www.doi.org/10.1021/ac901307q}, author = {Ellerbee, A. K. and Phillips, S. T. and Siegel, A. C. and Mirica, K. A. and Martinez, A. W. and Striehl, P. and Jain, N. and Prentiss, M. and Whitesides, G. M.} } @article {1601918, title = {Realization of coherent optically dense media via buffer-gas cooling}, journal = {PHYSICAL REVIEW A}, volume = {79}, year = {2009}, month = {JAN}, abstract = {We demonstrate that buffer-gas cooling combined with laser ablation can be used to create coherent optical media with high optical depth and low Doppler broadening that offers metastable states with low collisional and motional decoherence. Demonstration of this generic technique opens pathways to coherent optics with a large variety of atoms and molecules. We use helium buffer gas to cool Rb-87 atoms to below 7 K and slow atom diffusion to the walls. Electromagnetically induced transparency in this medium allows for 50\% transmission in a medium with initial optical depth D\>70 and for slow pulse propagation with large delay-bandwidth products. In the high-D regime, we observe high-contrast spectrum oscillations due to efficient four-wave mixing.}, keywords = {ATOMIC ENSEMBLES, ELECTROMAGNETICALLY INDUCED TRANSPARENCY, GROUP-VELOCITY, Helium, Interference, laser ablation, laser cooling, light coherence, metastable states, multiwave mixing, Photons, quantum optics, Rubidium, self-induced transparency}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.79.013806}, author = {Hong, T. and A.V. Gorshkov and D. Patterson and Zibrov, A. S. and Doyle, J. M. and M. D. Lukin and Prentiss, M. G.} } @article {1601893, title = {Single molecule detection of direct, homologous, DNA/DNA pairing}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {106}, year = {2009}, month = {NOV 24}, pages = {19824-19829}, abstract = {Using a parallel single molecule magnetic tweezers assay we demonstrate homologous pairing of two double-stranded (ds) DNA molecules in the absence of proteins, divalent metal ions, crowding agents, or free DNA ends. Pairing is accurate and rapid under physiological conditions of temperature and monovalent salt, even at DNA molecule concentrations orders of magnitude below those found in vivo, and in the presence of a large excess of nonspecific competitor DNA. Crowding agents further increase the reaction rate. Pairing is readily detected between regions of homology of 5 kb or more. Detected pairs are stable against thermal forces and shear forces up to 10 pN. These results strongly suggest that direct recognition of homology between chemically intact B-DNA molecules should be possible in vivo. The robustness of the observed signal raises the possibility that pairing might even be the "default" option, limited to desired situations by specific features. Protein-independent homologous pairing of intact dsDNA has been predicted theoretically, but further studies are needed to determine whether existing theories fit sequence length, temperature, and salt dependencies described here.}, keywords = {ATTRACTION, Cells, Chromosomes, DNA, dsDNA, dynamics, Magnesium, recognition, sequence-dependent, SITE, stability, Transcription}, isbn = {0027-8424 J9 - P NATL ACAD SCI USA}, url = {https://www.doi.org/10.1073/pnas.0911214106}, author = {Danilowicz, C. and Lee, C. H. and Kim, K. and Hatch, K. and Coljee, V.W. and Kleckner, N. and Prentiss, M.} } @article {1601895, title = {The structure of DNA overstretched from the 5 {\textquoteright} 5 {\textquoteright} ends differs from the structure of DNA overstretched from the 3 {\textquoteright} 3 {\textquoteright} ends}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {106}, year = {2009}, month = {AUG 11}, pages = {13196-13201}, abstract = {It has been suggested that the structure that results when double-stranded DNA (dsDNA) is pulled from the 3{\textquoteright}3{\textquoteright} ends differs from that which results when it is pulled from the 5{\textquoteright}5{\textquoteright} ends. In this work, we demonstrate, using lambda phage dsDNA, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. For 3{\textquoteright}3{\textquoteright} pulling versus 5{\textquoteright}5{\textquoteright} pulling, the following differences are observed: (i) the forces at which half of the molecules in the ensemble have made a complete force-induced transition to single stranded DNA are 141 +/- 3 pN and 122 +/- 4 pN, respectively; (ii) the extension vs. force curve for overstretched DNA has a marked change in slope at 127 +/- 3 pN for 3{\textquoteright}3{\textquoteright} and 110 +/- 3 pN for 5{\textquoteright}5{\textquoteright}; (iii) the hysteresis (H) in the extension vs. force curves at 150 mM NaCl is 0.3 +/- 0.8 pN mu m for 3{\textquoteright}3{\textquoteright} versus 13 +/- 8 pN for 5{\textquoteright}5{\textquoteright}; and (iv) 3{\textquoteright}3{\textquoteright} and 5{\textquoteright}5{\textquoteright} molecules show different changes in hysteresis due to interactions with beta-cyclodextrin, a molecule that is known to form stable host-guest complexes with rotated base pairs, and glyoxal that is known to bind stably to unpaired bases. These differences and additional findings are well-accommodated by the corresponding structures predicted on theoretical grounds.}, keywords = {BASE, CONSTANT, DEPENDENCE, Entropy, Force, MOLECULE, TRANSITION}, isbn = {0027-8424 J9 - P NATL ACAD SCI USA}, url = {https://www.doi.org/10.1073/pnas.0904729106}, author = {Danilowicz, C. and Limouse, C. and Hatch, K. and Conover, A. and Coljee, V.W. and Kleckner, N. and Prentiss, M.} } @article {1601892, title = {Study Of Sequence Dependent Homolog Pairing With A Single Molecule Assay}, journal = {BIOPHYSICAL JOURNAL}, volume = {96}, year = {2009}, month = {FEB}, pages = {345A-346A}, isbn = {0006-34951542-0086 J9 - BIOPHYS J}, url = {https://www-sciencedirect-com.ezp-prod1.hul.harvard.edu/science/article/pii/S0006349508019528?via\%3Dihub}, author = {Danilowicz, C. and Lee, C. H. and Hatch, K. and Coljee, V.W. and Kleckner, N. and Prentiss, M.} } @article {1601914, title = {Demonstration that the shear force required to separate short double-stranded DNA does not increase significantly with sequence length for sequences longer than 25 base pairs}, journal = {PHYSICAL REVIEW E}, volume = {78}, year = {2008}, month = {JUL}, abstract = {We have measured the shear force for short double-stranded DNA sequences pulled by either the 3{\textquoteright}3{\textquoteright} or 5{\textquoteright}5{\textquoteright} ends and find that the shear force is independent of the pulling technique. For the 50\% GC sequences examined, the force is a linear function of DNA length up to 20 base pairs (bp); however, we show that, as predicted by deGennes, the shear force approaches an asymptotic value in the limit where the number of base pairs approaches infinity, where the shear force for a 32 bp sequence is within 5\% of the asymptotic value of 61.4 pN. Fits to deGennes{\textquoteright} theory suggest that the shear force is distributed over fewer than 10 bp at the end of the sequence, with the rest of the sequence experiencing negligible shear force. The single base pair rupture force and the ratio of the backbone spring constant to the base pair spring constant determined from fits of the data to deGennes{\textquoteright} theory are consistent with ab initio predictions.}, keywords = {ADHESION, DUPLEX}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.78.011920}, author = {Hatch, K. and Danilowicz, C. and Coljee, V. and Prentiss, M.} } @article {1601915, title = {Measurement of the salt-dependent stabilization of partially open DNA by Escherichia coli SSB protein}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {36}, year = {2008}, month = {JAN}, pages = {294-299}, abstract = {The rezipping force of two complementary DNA strands under tension has been measured in the presence of Escherichia coli single-stranded-binding proteins under salt conditions ranging from 10 to 400 mM NaCl. The effectiveness of the binding protein in preventing rezipping is strongly dependent on salt concentration and compared with the salt dependence in the absence of the protein. At concentrations less than 50 mM NaCl, the protein prevents complete rezipping of lambda-phage on the 2-s timescale of the experiment, when the ssDNA is under tensions as low as 3.5 +/- 1 pN. For salt concentrations greater than 200 mM NaCl, the protein inhibits rezipping but cannot block rezipping when the tension is reduced below 6 +/- 1.8 pN. This change in effectiveness as a function of salt concentration may correspond to salt-dependent changes in binding modes that were previously observed in bulk assays.}, keywords = {BINDING-PROTEIN, COMPLEXES, Kinetics, MOLECULES, MULTIPLE, NUCLEIC-ACIDS, SINGLE-STRANDED-DNA, specificity, stability, UNWINDING PROTEIN}, isbn = {0305-1048 J9 - NUCLEIC ACIDS RES}, url = {https://www.doi.org/10.1093/nar/gkm1014}, author = {Hatch, K. and Danilowicz, C. and Coljee, V. and Prentiss, M.} } @article {1601926, title = {Meiotic chromosomes move by linkage to dynamic actin cables with transduction of force through the nuclear envelope}, journal = {CELL}, volume = {133}, year = {2008}, month = {JUN 27}, pages = {1188-1201}, abstract = {Chromosome movement is prominent during meiosis. Here, using a combination of in vitro and in vivo approaches, we elucidate the basis for dynamic mid-prophase telomere-led chromosome motion in budding yeast. Diverse findings reveal a process in which, at the pachytene stage, individual telomere/nuclear envelope (NE) ensembles attach passively to, and then move in concert with, nucleus-hugging actin cables that are continuous with the global cytoskeletal actin network. Other chromosomes move in concert with lead chromosome(s). The same process, in modulated form, explains the zygotene "bouquet{\textquoteright}{\textquoteright} configuration in which, immediately preceding pachytene, chromosome ends colocalize dynamically in a restricted region of the NE. Mechanical properties of the system and biological roles of mid-prophase movement for meiosis, including recombination, are discussed.}, keywords = {BOUQUET FORMATION, BUDDING YEAST, FISSION YEAST, Meiosis, ORGANIZATION, Prophase, RECOMBINATION, SACCHAROMYCES-CEREVISIAE, SYNAPSIS, TRANSITION}, isbn = {0092-8674 J9 - CELL}, url = {https://www.doi.org/10.1016/j.cell.2008.04.050}, author = {Koszul, R. and Kim, K. P. and Prentiss, M. and Kleckner, N. and Kameoka, S.} } @article {1601940, title = {Nanomagnetic actuation of receptor-mediated signal transduction}, journal = {NATURE NANOTECHNOLOGY}, volume = {3}, year = {2008}, month = {JAN}, pages = {36-40}, abstract = {Complex cell behaviours are triggered by chemical ligands that bind to membrane receptors and alter intracellular signal transduction. However, future biosensors, medical devices and other microtechnologies that incorporate living cells as system components will require actuation mechanisms that are much more rapid, robust, non-invasive and easily integrated with solid-state interfaces. Here we describe a magnetic nanotechnology that activates a biochemical signalling mechanism normally switched on by binding of multivalent chemical ligands. Superparamagnetic 30-nm beads, coated with monovalent ligands and bound to transmembrane receptors, magnetize when exposed to magnetic fields, and aggregate owing to bead-bead attraction in the plane of the membrane. Associated clustering of the bound receptors acts as a nanomagnetic cellular switch that directly transduces magnetic inputs into physiological cellular outputs, with rapid system responsiveness and non-invasive dynamic control. This technique may represent a new actuator mechanism for cell-based microtechnologies and man-machine interfaces.}, keywords = {Cells, DEGRANULATION, Integrins}, isbn = {1748-3387 J9 - NAT NANOTECHNOL}, url = {https://www.doi.org/10.1038/nnano.2007.418}, author = {Mannix, R. J. and Kumar, S. and Cassiola, F. and Montoya-Zavala, M. and Feinstein, E. and Prentiss, M. and Ingber, D. E.} } @book {1601975, title = {Observation of fidelity saturation in a delta-kicked rotor potential}, series = {2008 CONFERENCE ON LASERS AND ELECTRO-OPTICS \& QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE, VOLS 1-9}, year = {2008}, pages = {2075-2076}, abstract = {We experimentally investigate the effect of atomic delta-kicked rotor potentials on the mutual coherence between wavepackets in an atom interferometer, and demonstrate fidelity saturation in phase-space displacement echoes at quantum resonance. (C) 2008 Optical Society of America}, isbn = {978-1-55752-859-9}, url = {https://ieeexplore-ieee-org.ezp-prod1.hul.harvard.edu/document/4572226}, author = {Wu, S. J. and Tonyushkin, A. and Prentiss, M. G. and Ieee,} } @article {1601965, title = {Perfect Coherence Preservation in an Atom Interferometer Perturbed by Optical Standing Wave Pulses Acting as a Kicked Rotor}, journal = {2008 CONFERENCE ON LASERS AND ELECTRO-OPTICS \& QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE, VOLS 1-9}, year = {2008}, pages = {3349-3350}, abstract = {We experimentally studied the effect of standing wave pulses on an atom interferometer. Despite the external field perturbations the coherence is perfectly preserved for the conditions similar to quantum resonances of a quantum kicked rotor. (C) 2008 Optical Society of America}, isbn = {978-1-55752-859-9}, url = {https://ieeexplore-ieee-org.ezp-prod1.hul.harvard.edu/document/4572867}, author = {Tonyushkin, A. and Wu, S. and Prentiss, M. and Ieee,} } @article {1601970, title = {Probing the mechanical stability of DNA in the presence of monovalent cations}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {130}, year = {2008}, month = {APR 16}, pages = {5004-+}, abstract = {We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depends on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar foe all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.}, keywords = {B-DNA, BINDING, CRYSTAL-STRUCTURES, Ions, K+, MINOR-GROOVE, NA+, simulations, STABILIZATION, STRANDED-DNA}, isbn = {0002-78631520-5126 J9 - J AM CHEM SOC}, url = {https://www.doi.org/10.1021/ja0776576}, author = {Vlassakis, J. and Williams, J. and Hatch, K. and Danilowicz, C. and Coljee, V.W. and Prentiss, M.} } @article {1601962, title = {Selective manipulation of degenerate interferometer loops by an atom-optics kicked rotor}, journal = {PHYSICAL REVIEW A}, volume = {78}, year = {2008}, month = {NOV}, abstract = {We experimentally demonstrate that an atom-optics kicked rotor can remove the interference signal due to chosen interferometer paths in a four-pulse de Broglie wave atom interferometer. The interferometer output is dominated by two degenerate spatial loops: the nonreciprocal "trapezoid" loop and the reciprocal "figure-8" loop. By applying the kicked rotor sequence at a particular time we suppressed the contribution of the "trapezoid" loop to the interferometer signal while preserving the contribution due to the "figure-8" loop. When the degeneracy is present, the interferometer is sensitive to both rotation and linear acceleration. When the degeneracy is lifted the interferometer is insensitive to linear acceleration, but still sensitive to rotation. The suppression of nonreciprocal loops in an atom interferometer is valuable for rotation sensing.}, keywords = {CONSTANT, GRAVITATIONAL ACCELERATION, QUANTUM RESONANCE}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.78.053625}, author = {Tonyushkin, A. and Prentiss, M.} } @article {1601973, title = {Demonstration of an area-enclosing guided-atom interferometer for rotation sensing}, journal = {PHYSICAL REVIEW LETTERS}, volume = {99}, year = {2007}, month = {OCT 26}, abstract = {We demonstrate area-enclosing atom interferometry based on a moving guide. Light pulses along the free-propagation direction of a magnetic guide are applied to split and recombine the confined atomic matter-wave, while the atoms are translated back and forth along a second direction in 50 ms. The interferometer is estimated to resolve 10 times the earth rotation rate per interferometry cycle. We demonstrate a "folded figure 8{\textquoteright}{\textquoteright} interfering configuration for creating a compact, large-area atom gyroscope with multiple-turn interfering paths.}, keywords = {BROGLIE WAVE INTERFEROMETRY, GYROSCOPE, TIME-DOMAIN}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.99.173201}, author = {Wu, S. and Su, E. and Prentiss, M.} } @article {1601972, title = {Density-based diamagnetic separation: Devices for detecting binding events and for collecting unlabeled diamagnetic particles in paramagnetic solutions}, journal = {ANALYTICAL CHEMISTRY}, volume = {79}, year = {2007}, month = {SEP 1}, pages = {6542-6550}, abstract = {This paper describes the fabrication of a fluidic device for detecting and separating diamagnetic materials that differ in density. The basis for the separation is the balance of the magnetic and gravitational forces on diamagnetic materials suspended in a paramagnetic medium. The paper demonstrates two applications of separations involving particles suspended in static fluids for detecting the following: (i) the binding of streptavidin to solid-supported biotin and (ii) the binding of citrate-capped gold nanoparticles to amine-modified polystyrene spheres. The paper also demonstrates a microfluidic device in which polystyrene particles that differ in their content of CH2Cl groups are continuously separated and collected in a flowing stream of an aqueous solution of GdCl3. The procedures for separation and detection described in this paper require only gadolinium salts, two NdFeB magnets, and simple microfluidic devices fabricated from poly(dimethylsiloxane). This device requires no power, has no moving parts, and may be suitable for use in resource-poor environments.}, keywords = {BEADS, Blood, Cells, Levitation, MAGNETIC PARTICLES, MAGNETOPHORESIS, ON-CHIP}, isbn = {0003-27001520-6882 J9 - ANAL CHEM}, url = {https://www.doi.org/10.1021/ac070500b}, author = {Winkleman, A. and Perez-Castillejos, R. and Gudiksen, K. L. and Phillips, S. T. and Prentiss, M. and Whitesides, G. M.} } @article {1601900, title = {Development and micromechanical analysis of a self-assembled Tissue Engineered extracellular matrix analogue with defined nanostructure}, journal = {BIOPHYSICAL JOURNAL}, year = {2007}, month = {JAN}, pages = {333A-333A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www-webofscience-com.ezp-prod1.hul.harvard.edu/wos/woscc/full-record/WOS:000243972402108}, author = {Feinstein, E. and Alsberg, E. and Ingber, D. and Prentiss, M.} } @article {1601912, title = {Direct measurements of the stabilization of single-stranded DNA under tension by single-stranded binding proteins}, journal = {PHYSICAL REVIEW E}, volume = {76}, year = {2007}, month = {AUG}, abstract = {The unzipping and rezipping of a double-stranded DNA molecule is carried out in the presence of two single-stranded binding proteins T4 gp32 and E. Coli SSB protein to determine the effect of the proteins on the stability of single- and double-stranded DNA. The proteins do not have a significant effect on unzipping, indicating that the two proteins do not destabilize the double-stranded DNA; however, both proteins inhibit rezipping. At protein concentrations where the rezipping force response is saturated, E. Coli SSB protein reduces the rezipping force to 5.5 +/- 1.5 pN, while T4 gp32 completely blocks rezipping on the time scale of the experiment.}, keywords = {COMPLEXES, HELIX, Kinetics, NUCLEIC-ACIDS, specificity, stability, T4 GENE-32 PROTEIN, UNZIPPING DNA}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.76.021916}, author = {Hatch, K. and Danilowicz, C. and Coljee, V. and Prentiss, M.} } @article {1601916, title = {Dynamics of unzipping and rezipping DNA}, journal = {BIOPHYSICAL JOURNAL}, year = {2007}, month = {JAN}, pages = {165A-165A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www-webofscience-com.ezp-prod1.hul.harvard.edu/wos/woscc/full-record/WOS:000243972400767}, author = {Hatch, K. A. and Danilowicz, C. and Cojee, V. and Prentiss, M.} } @article {1601891, title = {Effects of temperature on the mechanical properties of single stranded DNA}, journal = {PHYSICAL REVIEW E}, volume = {75}, year = {2007}, month = {MAR}, abstract = {We present the first measurements of the temperature dependent extension of single stranded DNA. At forces between 2 and 10 pN the extension increases with temperature. This increase in extension is consistent with the disruption of hairpins, and a simple theory that includes hairpin formation shows good agreement with the data at these low forces. In contrast, at forces above 10 pN and temperatures higher than 40 degrees C, the extension decreases rapidly with temperature in a manner not consistent with predictions.}, keywords = {MOLECULE}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.75.030902}, author = {Danilowicz, C. and Lee, C. H. and Coljee, V.W. and Prentiss, M.} } @article {1601958, title = {The force acting on a superparamagnetic bead due to an applied magnetic field}, journal = {LAB ON A CHIP}, volume = {7}, year = {2007}, pages = {1294-1302}, abstract = {This paper describes a model of the motion of superparamagnetic beads in a microfluidic channel under the influence of a weak magnetic field produced by an electric current passing through a coplanar metal wire. The model based on the conventional expression for the magnetic force experienced by a superparamagnetic bead ( suspended in a biologically relevant medium) and the parameters provided by the manufacturer failed to match the experimental data. To fit the data to the model, it was necessary to modify the conventional expression for the force to account for the non-zero initial magnetization of the beads, and to use the initial magnetization and the magnetic susceptibility of the beads as adjustable parameters. The best-fit value of susceptibility deviated significantly from the value provided by the manufacturer, but was in good agreement with the value computed using the magnetization curves measured independently for the beads from the same vial as those used in the experiment. The results of this study will be useful to researchers who need an accurate prediction of the behavior of superparamagnetic beads in aqueous suspensions under the influence of weak magnetic fields. The derivation of the force on a magnetic bead due to a magnetic field also identifies the correct treatment to use for this interaction, and resolves discrepancies present throughout the literature.}, keywords = {Biological cells, Blood, FORMAT, LIVING CELLS, Separation, system}, isbn = {1473-0197 J9 - LAB CHIP}, url = {https://www.doi.org/10.1039/b705045c}, author = {Shevkoplyas, S. S. and Siegel, A. C. and R. M. Westervelt and Prentiss, M. G. and Whitesides, G. M.} } @article {1601913, title = {Measurements of the hysteresis in unzipping and rezipping double-stranded DNA}, journal = {PHYSICAL REVIEW E}, volume = {75}, year = {2007}, month = {MAY}, abstract = {Complete unzipping and rezipping of lambda-phage double-stranded DNA is achieved by applying a constant force. A strong hysteresis is observed at all tested time scales and temperatures. Hysteresis also occurs for partial unzipping, indicating stability for the partially open state over a force range of 2-5 pN. Results are compared to nearest-neighbor model simulations, and reasonable agreement is found.}, keywords = {Force, KINETIC BARRIERS, SEQUENCE}, isbn = {1539-37551550-2376 J9 - PHYS REV E}, url = {https://www.doi.org/10.1103/PhysRevE.75.051908}, author = {Hatch, K. and Danilowicz, C. and Coljee, V. and Prentiss, M.} } @article {1601894, title = {Overstretching dsDNA from different ends}, journal = {BIOPHYSICAL JOURNAL}, year = {2007}, month = {JAN}, pages = {165A-165A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://scholar.google.ca/citations?view_op=view_citation\&hl=en\&user=NtjiZPIAAAAJ\&cstart=200\&pagesize=100\&citation_for_view=NtjiZPIAAAAJ:p__nRnzSRKYC}, author = {Danilowicz, C. and Limouse, C. and Cojee, V. and Prentiss, M.} } @article {1601928, title = {Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences}, journal = {EUROPEAN PHYSICAL JOURNAL E}, volume = {19}, year = {2006}, month = {MAR}, pages = {339-344}, abstract = {In this work, we consider the critical force required to unzip two different naturally occurring sequences of double-stranded DNA (dsDNA) at temperatures ranging from 20 degrees C to 50 degrees C, where one of the sequences has a 53\% average guanine-cytosine (GC) content and the other has a 40\% GC content. We demonstrate that the force required to separate the dsDNA of the 53\% GC sequence into single-stranded DNA (ssDNA) is approximately 0.5 pN, or approximately 5\% greater than the critical force required to unzip the 40\% GC sequence at the same temperature. In the temperature range between 20 and 40 degrees C the measured critical forces correspond reasonably well to predictions based on a simple theoretical homopolymeric model, but at temperatures above 40 degrees C the measured critical forces are much smaller than the predicted forces. The correspondence between theory and experiment is not improved by using Monte Carlo simulations that consider the heteropolymeric nature of the sequences.}, keywords = {DUPLEX STABILITY}, isbn = {1292-8941 J9 - EUR PHYS J E}, url = {https://www.doi.org/10.1140/epje/i2005-10051-5}, author = {Lee, C. H. and Danilowicz, C. and Coljee, V.W. and Prentiss, M.} } @article {1601931, title = {Impacts of magnesium ions on the unzipping of lambda-phage DNA}, journal = {JOURNAL OF PHYSICS-CONDENSED MATTER}, volume = {18}, year = {2006}, month = {APR 12}, pages = {S205-S213}, abstract = {We used magnetic tweezers to exert a constant force to separate double stranded lambda-phage DNA as a function of temperature and buffer content. The separation was performed at temperatures ranging from 20 to 50 degrees C in various Mg2+ buffers, including a T4 ligase buffer and a PCR buffer. At 30 degrees C and pH 7.4 (10 mM Tris), we measured the unzipping force as a function of concentration for Mg2+ concentrations between 0.2 and 50 mM, and determined that the unzipping force is proportional to the logarithm of concentration. For comparison, we performed the analogous experiment as a function of Na+ concentration and found that the unzipping force is also proportional to the log of concentration, but requires a much higher cation concentration to achieve the same unzipping force as in Mg2+ buffer. We also constructed the phase diagram in the force-temperature plane for the unzipping in 10 and 50 mM MgCl2 at pH 7.4 (10 mM Tris). The phase diagram for 10 mM Mg2+ is similar to the one measured previously for phosphate buffer saline (PBS) but the phase diagram for 50 mM Mg2+ deviates significantly from those for 10 MM Mg2+ and PBS at temperatures between 20 and 35 degrees C.}, keywords = {Cations, CURVATURE, DUPLEX STABILITY, Force, METAL COMPLEXES, MG2+, RAMAN-SPECTROSCOPY}, isbn = {0953-89841361-648X J9 - J PHYS-CONDENS MAT}, url = {https://www.doi.org/10.1088/0953-8984/18/14/S05}, author = {Lee, C. H. and Danilowicz, C. and Conroy, R. S. and Coljee, V.W. and Prentiss, M.} } @article {1601868, title = {Magnetically-guided self-assembly of fibrin matrices with ordered nano-scale structure for tissue engineering}, journal = {TISSUE ENGINEERING}, volume = {12}, year = {2006}, month = {NOV}, pages = {3247-3256}, abstract = {The development of effective biological scaffold materials for tissue engineering and regenerative medicine applications hinges on the ability to present precise environmental cues to specific cell populations to guide their position and function. Natural extracellular matrices have an ordered nano-scale structure that can modulate cell behaviors critical for developmental control, including directional cell motility. Here we describe a method for fabricating fibrin gels with defined architecture on the nanometer scale in which magnetic forces are used to position thrombin-coated magnetic micro-beads in a defined 2-dimensional array and thereby guide the self-assembly of fibrin fibrils through catalytic cleavage of soluble fibrinogen substrate. Time-lapse and confocal microscopy confirmed that fibrin fibrils nucleate near the surface of the thrombin-coated beads and extend out in a radial direction to form these gels. When controlled magnetic fields were used to position the beads in hexagonal arrays, the fibrin nano-fibrils that polymerized from the beads oriented preferentially along the bead-bead axes in a geodesic ( minimal path) pattern. These biocompatible scaffolds supported adhesion and spreading of human microvascular endothelial cells, which exhibited co-alignment of internal actin stress fibers with underlying fibrin nano-fibrils within some membrane extensions at the cell periphery. This magnetically-guided, biologically-inspired microfabrication system is unique in that large scaffolds may be formed with little starting material, and thus it may be useful for in vivo tissue engineering applications in the future.}, keywords = {ARCHITECTURE, BLOOD-VESSEL, Cells, COLLAGEN GELS, CONTACT GUIDANCE, Migration, Repair}, isbn = {1076-3279 J9 - TISSUE ENG}, url = {https://www.doi.org/10.1089/ten.2006.12.3247}, author = {Alsberg, E. and Feinstein, E. and Joy, M. P. and Prentiss, M. and Ingber, D. E.} } @article {1601929, title = {Response to the two comments on the paper "Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences"}, journal = {EUROPEAN PHYSICAL JOURNAL E}, volume = {19}, year = {2006}, month = {MAR}, pages = {351-352}, isbn = {1292-8941 J9 - EUR PHYS J E}, url = {https://www.doi.org/10.1140/epje/i2006-10002-8}, author = {Lee, C. H. and Danilowicz, C. and Coljee, V.W. and Prentiss, M.} } @article {1601904, title = {Three-dimensional self-assembly of structures using the pressure due to a ferrofluid in a magnetic field gradient}, journal = {JOURNAL OF APPLIED PHYSICS}, volume = {99}, year = {2006}, month = {MAR 15}, abstract = {We developed an inexpensive and simple system for three-dimensional self-assembly of micron-sized nonmagnetic particles into millimeter-scale structures using the differential pressure exerted by ferrofluids in the presence of magnetic field gradients. We demonstrate it by assembling separate individual 5, 10, and 21 mu m diam polystyrene beads into millimeter-sized spherical and ellipsoidal structures. The system can also self-organize its smaller components by volume and provide compressive forces of hundreds of piconewtons on millimeter-scale structures. Extensions of this method have assembled multicellular systems. (c) 2006 American Institute of Physics.}, keywords = {MATRIX, PARTICLES}, isbn = {0021-8979 J9 - J APPL PHYS}, url = {https://www.doi.org/10.1063/1.2179196}, author = {Feinstein, E. and Prentiss, M.} } @article {1601886, title = {Dissociation of ligand-receptor complexes using magnetic tweezers}, journal = {ANALYTICAL CHEMISTRY}, volume = {77}, year = {2005}, month = {MAY 15}, pages = {3023-3028}, abstract = {We present a new tool for measuring ligand-receptor complex bonds at the single-molecule level using magnetic tweezers. Our apparatus allows massively parallel (100 - 1000) measurements on many single complexes perturbed by constant forces. Compared to other single-molecule techniques, our method is simple, inexpensive, robust, and widely compatible with other techniques. We immobilized specific receptor molecules on the surface of superparamagnetic beads and corresponding ligand molecules on a fixed surface. The beads were allowed to contact the surface so that ligand-receptor binding occurred. A permanent magnet then generated a constant force that pulled the receptors away from the ligands. The rates at which bound species separated at various forces allowed us to characterize the potential energy landscape of the bond and extrapolate bulk solution kinetic rates and transition-state distances. These values agreed with those obtained using bulk and single-molecule methods.}, keywords = {ADHESION, BINDING, BONDS, DNA, Force, SINGLE-MOLECULE, TRANSITION}, isbn = {0003-27001520-6882 J9 - ANAL CHEM}, url = {https://www.doi.org/10.1021/ac050057+}, author = {Danilowicz, C. and Greenfield, D. and Prentiss, M.} } @article {1601930, title = {Effect of magnesium ions and temperature on the unzipping of Lambda DNA}, journal = {BIOPHYSICAL JOURNAL}, volume = {88}, year = {2005}, month = {JAN}, pages = {347A-347A}, isbn = {0006-3495 J9 - BIOPHYS J}, author = {Lee, C. H. and Danilowicz, C. and Conroy, R. and Mignot, A. and Kafri, Y. and Coljee, V.W. and Prentiss, M.} } @article {1601876, title = {Magnetic self-assembly of three-dimensional surfaces from planar sheets}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {102}, year = {2005}, month = {MAR 15}, pages = {3924-3929}, abstract = {This report describes the spontaneous folding of flat elastomeric sheets, patterned with magnetic dipoles, into free-standing, 3D objects that are the topological equivalents of spherical shells. The path of the self-assembly is determined by a competition between mechanical and magnetic interactions. The potential of this strategy for the fabrication of 3D electronic devices is demonstrated by generating a simple electrical circuit surrounding a spherical cavity.}, keywords = {3D structure, folding, microfabrication, Semiconductors, soft, soft electronics, soft lithography}, isbn = {0027-8424 J9 - P NATL ACAD SCI USA}, url = {https://www.doi.org/10.1073/pnas.0500807102}, author = {Boncheva, M. and Andreev, S. A. and Mahadevan, L. and Winkleman, A. and D. R. Reichman and Prentiss, M. G. and Whitesides, S. and Whitesides, G. M.} } @article {1601971, title = {Pause point spectra in DNA constant-force unzipping}, journal = {BIOPHYSICAL JOURNAL}, volume = {88}, year = {2005}, month = {APR}, pages = {2752-2765}, abstract = {Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. A simple theoretical model of DNA constant-force unzipping is presented, which generates theoretical pause point spectra through Monte Carlo simulation of the unzipping process. The locations of peaks in the experimental and theoretical pause point spectra are found to be nearly coincident below 6000 basepairs for unzipping the bacteriophage lambda-genome. The model only requires the sequence, temperature, and a set of empirical basepair binding and stacking energy parameters, and the good agreement with experiment suggests that pause point locations are primarily determined by the DNA sequence. The model is also used to predict pause point spectra for the bacteriophage phi X174 genome. The algorithm for extracting the pause point spectrum might also be useful for studying related systems which exhibit pausing behavior such as molecular motors.}, keywords = {MOLECULAR MOTORS, RNA-POLYMERASE, SINGLE-MOLECULE, TWEEZERS}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.doi.org/10.1529/biophysj.104.047340}, author = {Weeks, J.D. and Lucks, J.B. and Kafri, Y. and Danilowicz, C. and Nelson, D.R. and Prentiss, M.} } @article {1601884, title = {Measurement of the phase diagram of DNA unzipping as a function of temperature and force}, journal = {BIOPHYSICAL JOURNAL}, volume = {86}, year = {2004}, month = {JAN}, pages = {324A-324A}, isbn = {0006-3495 J9 - BIOPHYS J}, url = {https://www.researchgate.net/publication/265050643_Measurement_of_the_phase_diagram_of_DNA_unzipping_as_a_function_of_temperature_and_force}, author = {Danilowicz, C. and Conroy, R. and Kafri, Y. and Coljee, V. and Prentiss, M.} } @article {1601890, title = {Measurement of the phase diagram of DNA unzipping in the temperature-force plane}, journal = {PHYSICAL REVIEW LETTERS}, volume = {93}, year = {2004}, month = {AUG 13}, abstract = {We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15 to 50 degreesC, and measure the minimum force required to separate the two strands. The measurements also offer information on the free energy of double stranded DNA (dsDNA) at temperatures where dsDNA does not thermally denature in the absence of force. While parts of the phase diagram can be explained using existing models and free energy parameters, others deviate significantly. Possible reasons for the deviations between theory and experiment are considered.}, keywords = {DOUBLE HELIX, MOLECULES, Optical Tweezers, stability}, isbn = {0031-90071079-7114 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.93.078101}, author = {Danilowicz, C. and Kafri, Y. and Conroy, R. S. and Coljee, V.W. and Weeks, J. and Prentiss, M.} } @article {1601939, title = {Asymmetric dimers can be formed by dewetting half-shells of gold deposited on the surfaces of spherical oxide colloids}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {125}, year = {2003}, month = {OCT 22}, pages = {12724-12725}, keywords = {Arrays, Crystallization, Fabrication, photonic crystals, POLYMER PARTICLES, SHAPES, SPHERES, Templates, WELL-DEFINED SIZES}, isbn = {0002-7863 J9 - J AM CHEM SOC}, url = {https://www.doi.org/10.1021/ja0373014}, author = {Lu, Y. and Xiong, H. and Jiang, X. C. and Xia, Y. N. and Prentiss, M. and Whitesides, G. M.} } @article {1601883, title = {DNA unzipped under a constant force exhibits multiple metastable intermediates}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {100}, year = {2003}, month = {FEB 18}, pages = {1694-1699}, abstract = {Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the unzipped length as a function of time is characterized by jumps during which the strands separate rapidly, followed by long pauses where the number of separated base pairs remains constant. Here, we report previously uncharacterized observations of this striking behavior carried out on a number of identical single molecules simultaneously. When several single X phage molecules are subject to the same applied force, the pause positions are reproducible in each. This reproducibility shows that the positions and durations of the pauses in unzipping provide a sequence-dependent molecular fingerprint. For small forces, the DNA remains in a partially unzipped state for at least several hours. For larger forces, the separation is still characterized by jumps and pauses, but the double-stranded DNA will completely unzip in less than 30 min.}, keywords = {dynamics, Mechanics, SINGLE-MOLECULE, TWEEZERS}, isbn = {0027-8424 J9 - P NATL ACAD SCI USA}, url = {https://www.doi.org/10.1073/pnas.262789199}, author = {Danilowicz, C. and Coljee, V.W. and Bouzigues, C. and D.K. Lubensky and Nelson, D.R. and Prentiss, M.} } @article {1601881, title = {Self-assembled monolayers exposed to metastable argon beams undergo thiol exchange reactions}, journal = {LANGMUIR}, volume = {19}, year = {2003}, month = {MAR 18}, pages = {2201-2205}, abstract = {Self-assembled monolayers (SAMs) formed from alkanethiols on thin films of gold were exposed to a beam of metastable argon atoms through a stencil mask. The changes in the organizational structure of the alkyl chains in the SAM that resulted from exposure were characterized using reflection-absorption infrared spectroscopy. All spectroscopic evidence suggested that the SAM become disordered after exposure to metastable argon atoms and that no apparent oxidation of the alkane chain occurred. The alkanethiolates in the regions of a SAM of dodecanethiolate damaged by the atom beam Exchanged readily upon immersion in a solution of 16-mercaptohexadecanoic acid. The exchange reaction was selective for the regions of the SAM exposed to metastable argon atoms with patterns containing critical dimensions of \< 50 nm. A thin (\<5 nm) polymeric multilayer was covalently linked to the carboxylic acid groups in the exposed regions of the SAM. The polymeric layer served as an improved resist against a commercial KI/I-2-based etchant used to transfer the pattern into the thin film of gold.}, keywords = {ELECTRON-SPECTROSCOPY, ETCH RESISTS, FILMS, Gold, INDUCED DAMAGE, NANOSTRUCTURE FABRICATION, NEUTRAL-ATOM LITHOGRAPHY, Silicon, SURFACES}, isbn = {0743-7463 J9 - LANGMUIR}, url = {https://www.doi.org/10.1021/la026495i}, author = {Chabinyc, M. L. and Love, J. C. and Thywissen, J. H. and Cervelli, F. and Prentiss, M. G. and Whitesides, G. M.} } @article {1601898, title = {Single molecule DNA unzipping under constant force using magnetic tweezers}, journal = {BIOPHYSICAL JOURNAL}, volume = {84}, year = {2003}, month = {FEB}, pages = {301A-301A}, isbn = {0006-3495 J9 - BIOPHYS J}, author = {Danilowicz, C. B. and Coljee, V. and Bouzig, C. and Conroy, R. S. and Lubensky, D. and Sarkar, A. and Nelson, D.R. and Prentiss, M.} } @article {1601967, title = {Sub-100 nm confinement of magnetic nanoparticles using localized magnetic field gradients}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {125}, year = {2003}, month = {OCT 22}, pages = {12704-12705}, keywords = {Chemistry, GIANT MAGNETORESISTANCE, nanowires}, isbn = {0002-7863 J9 - J AM CHEM SOC}, url = {https://www.doi.org/10.1021/ja0378308}, author = {Urbach, A. R. and Love, J. C. and Prentiss, M. G. and Whitesides, G. M.} } @article {1601937, title = {Three-dimensional self-assembly of metallic rods with submicron diameters using magnetic interactions}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {125}, year = {2003}, month = {OCT 22}, pages = {12696-12697}, keywords = {OBJECTS}, isbn = {0002-78631520-5126 J9 - J AM CHEM SOC}, url = {https://www.doi.org/10.1021/ja037642h}, author = {Love, J. C. and Urbach, A. R. and Prentiss, M. G. and Whitesides, G. M.} } @article {1601921, title = {Massively parallel single biomolecule measurements using magnetic tweezers}, journal = {BIOPHYSICAL JOURNAL}, volume = {82}, year = {2002}, month = {JAN}, pages = {40A-41A}, isbn = {0006-3495 J9 - BIOPHYS J}, author = {Jenks, R. A. and Assi, F. and Zabow, G. and Prentiss, M.} } @article {1601869, title = {Massively parallel adhesion and reactivity measurements using simple and inexpensive magnetic tweezers}, journal = {JOURNAL OF APPLIED PHYSICS}, volume = {92}, year = {2002}, month = {NOV 1}, pages = {5584-5586}, abstract = {Single molecule techniques to measure biological molecules and reactions have provided an alternative way to probe and visualize bond characteristics and reaction dynamics. However, these techniques, such as atomic force microscopy, optical tweezers, and micropipettes often require expensive and complicated equipment and are very time intensive, because each measurement gives the results of one-single reaction or a property of one-single molecule. Here, we report on a technique that allows for massively parallel measurements on many individual single molecules in microfluidic systems. We demonstrate the effectiveness of a simple, robust, inexpensive apparatus, by using it to differentiate between deoxyribonucleic acid (DNA) assemblies that are merely annealed from others that are ligated, and by measuring the rate at which annealed DNA denatures as function of temperature. (C) 2002 American Institute of Physics.}, keywords = {DNA, FORCES}, isbn = {0021-8979 J9 - J APPL PHYS}, url = {https://www.doi.org/10.1063/1.1509086}, author = {Assi, F. and Jenks, R. and J. Yang and Love, C. and Prentiss, M.} } @article {1601870, title = {Massively parallel measurements of molecule/surface binding forces}, journal = {BIOPHYSICAL JOURNAL}, volume = {80}, year = {2001}, month = {JAN}, pages = {155A-155A}, isbn = {0006-3495 J9 - BIOPHYS J}, author = {Assi, P. and Jenks, R. and Zabow, G. and Prentiss, M.} } @article {1601941, title = {de Broglie wave-front engineering}, journal = {PHYSICAL REVIEW A}, volume = {62}, year = {2000}, month = {SEP}, abstract = {We propose a simple method for the deterministic generation of an arbitrary continuous quantum state of the center-of-mass of an atom. The method{\textquoteright}s spatial resolution gradually increases with the interaction time with no apparent fundamental limitations. Such de Broglie wave-front engineering of the atomic density can find applications in Atom Lithography, and we discuss possible implementations of our scheme in atomic beam experiments.}, keywords = {ATOM, FIELD, QUANTUM STATES, TRAPPED ION}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.62.033612}, author = {Olshanii, M. and Dekker, N. and Herzog, C. and Prentiss, M.} } @article {1601920, title = {Three-dimensional metallic microstructures fabricated by soft lithography and microelectrodeposition}, journal = {LANGMUIR}, volume = {15}, year = {1999}, month = {FEB 2}, pages = {826-836}, abstract = {Soft lithography offers a convenient set of methods for the transfer of patterns to planar and nonplanar substrates. Microelectrodeposition can transform thin metal patterns into self-supporting microstructures, weld components together, and strengthen microstructures after deformations. Together, soft lithography and electrochemistry provide synergistic technologies and the basis for a strategy for converting planar patterns into three-dimensional (3D) microstructures with complex topologies. This strategy is illustrated in the formation of folded tetrahedra, square-based pyramids, cylinders with joints, "pop-up" cubes, and linked chains and knots.}, keywords = {COMPONENTS, DEPOSITION, FEATURES, LIGA, MICROCOILS, microfabrication, MICROMETER}, isbn = {0743-7463 J9 - LANGMUIR}, url = {https://www.doi.org/10.1021/la980857y}, author = {Jackman, R. J. and Brittain, S. T. and Adams, A. and Wu, H. K. and Prentiss, M. G. and Whitesides, S. and Whitesides, G. M.} } @article {1601919, title = {Design and fabrication of topologically complex, three-dimensional microstructures}, journal = {SCIENCE}, volume = {280}, year = {1998}, month = {JUN 26}, pages = {2089-2091}, abstract = {Two concepts for use in the fabrication of three-dimensional (3D) microstructures with complex topologies are described. Both routes begin with a two-dimensional (2D) pattern and transform it into a 3D microstructure, The concepts are illustrated by use of soft lithographic techniques to transfer 2D patterns to cylindrical (pseudo-3D) substrates. Subsequent steps-application of uniaxial strain, connection of patterns on intersecting surfaces-transform these patterns into free-standing, 3D, noncylindrically symmetrical microstructures. Microelectrodeposition provides an additive method that strengthens thin metal designs produced by patterning, welds nonconnected structures, and enables the high-strain deformations required in one method to be carried out successfully.}, keywords = {laser, MEMS, microfabrication, Silicon}, isbn = {0036-8075 J9 - SCIENCE}, url = {https://www.doi.org/10.1126/science.280.5372.2089}, author = {Jackman, R. J. and Brittain, S. T. and Adams, A. and Prentiss, M. G. and Whitesides, G. M.} } @article {1601923, title = {Localization of metastable atom beams with optical standing waves: Nanolithography at the Heisenberg limit}, journal = {SCIENCE}, volume = {280}, year = {1998}, month = {JUN 5}, pages = {1583-1586}, abstract = {The spatially dependent de-excitation of a beam of metastable argon atoms, traveling through an optical standing wave, produced a periodic array of localized metastable atoms with position and momentum spreads approaching the limit stated by the Heisenberg uncertainty principle. Silicon and silicon dioxide substrates placed in the path of the atom beam were patterned by the metastable atoms. The de-excitation of metastable atoms upon collision with the surface promoted the deposition of a carbonaceous film from a vapor-phase hydrocarbon precursor, The resulting patterns were imaged both directly and after chemical etching. Thus, quantum-mechanical steady-state atom distributions can be used for sub-0.1-micrometer lithography.}, keywords = {DEPOSITION, Lithography}, isbn = {0036-8075 J9 - SCIENCE}, url = {https://www.doi.org/10.1126/science.280.5369.1583}, author = {Johnson, K. S. and Thywissen, J. H. and Dekker, N. H. and Berggren, K. K. and Chu, A. P. and Younkin, R. and Prentiss, M.} } @article {1601871, title = {MICROLITHOGRAPHY BY USING NEUTRAL METASTABLE ATOMS AND SELF-ASSEMBLED MONOLAYERS}, journal = {SCIENCE}, volume = {269}, year = {1995}, month = {SEP 1}, pages = {1255-1257}, abstract = {Lithography can be performed with beams of neutral atoms in metastable excited states to pattern self-assembled monolayers (SAMs) of alkanethiolates on gold. An estimated exposure of a SAM of dodecanethiolate (DDT) to 15 to 20 metastable argon atoms per DDT molecule damaged the SAM sufficiently to allow penetration of an aqueous solution of ferricyanide to the surface of the gold. This solution etched the gold and transformed the patterns in the SAMs into structures of gold; these structures had edge resolution of less than 100 nanometers. Regions of SAMs as large as 2 square centimeters were patterned by exposure to a beam of metastable argon atoms. these observations suggest that this system may be useful in new forms of micro- and nanolithography.}, keywords = {Beam, SURFACES}, isbn = {0036-8075 J9 - SCIENCE}, url = {https://www.doi.org/10.1126/science.7652572}, author = {Berggren, K. K. and Bard, A. and Wilbur, J.L. and Gillaspy, J. D. and Helg, A. G. and McClelland, J. J. and Rolston, S. L. and Phillips, W. D. and Prentiss, M. and Whitesides, G. M.} } @article {1601951, title = {BOUND BY LIGHT}, journal = {SCIENCE}, volume = {260}, year = {1993}, month = {MAY 21}, pages = {1078-1080}, keywords = {ATOMS, Motion, Radiation}, isbn = {0036-8075 J9 - SCIENCE}, url = {https://www.doi.org/10.1126/science.260.5111.1078}, author = {Prentiss, M. G.} } @article {1601917, title = {1ST OBSERVATION OF FORCES ON 3-LEVEL ATOMS IN RAMAN RESONANT STANDING-WAVE OPTICAL-FIELDS}, journal = {PHYSICAL REVIEW LETTERS}, volume = {68}, year = {1992}, month = {MAY 25}, pages = {3148-3151}, abstract = {A sodium atomic beam is deflected by two optical standing-wave fields which excite near resonance Raman transitions. Observed deflections are consistent with theoretical predictions of a long-range dc component of the force on a three-level atom in the LAMBDA-configuration. The low laser intensities (and small detunings) used, combined with observed evidence of damping in the three-level LAMBDA-system, may ultimately lead to the design of high-density, all optical traps wherein the atoms would be mostly in the dark state.}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.68.3148}, author = {Hemmer, P. R. and Shahriar, M. S. and Prentiss, M. G. and Katz, D. P. and Berggren, K. and Mervis, J. and Bigelow, N. P.} } @article {1601911, title = {CALCULATION OF ENHANCED SLOWING AND COOLING DUE TO THE ADDITION OF A TRAVELING-WAVE TO AN INTENSE OPTICAL STANDING WAVE}, journal = {PHYSICAL REVIEW A}, volume = {46}, year = {1992}, month = {JUL 1}, pages = {356-363}, abstract = {We investigate the force on a two-level atom interacting with intense monochromatic laser fields which are combinations of standing and traveling waves. We present a continued-fraction solution to the optical Bloch equations. Using this solution to calculate the force on an atom, we have examined the slowing and cooling of a thermal Na atomic beam. We find that the addition of a traveling wave to an intense standing wave can significantly improve the slowing rate and simultaneously decrease the final velocity of the cooled beam.}, keywords = {ATOMIC-BEAM, Motion, RESONANCES}, isbn = {1050-29471094-1622 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.46.356}, author = {Gottesman, D. and Mervis, J. and Prentiss, M. and Bigelow, N. P.} } @article {1601961, title = {USING LIGHT AS A LENS FOR SUBMICRON, NEUTRAL-ATOM LITHOGRAPHY}, journal = {PHYSICAL REVIEW LETTERS}, volume = {69}, year = {1992}, month = {SEP 14}, pages = {1636-1639}, abstract = {We show that light can be used as a lens to focus a collimated neutral atomic beam to submicron dimensions during deposition onto a substrate. We have used an optical standing wave at 589 nm as an array of cylindrical lenses to focus a perpendicular sodium beam into a grating on a substrate, with a periodicity of 294.3 +/- 0.3 nm. This result is the first direct evidence of submicron focusing of atoms by light, and represents a fundamentally new scheme for submicron lithography.}, keywords = {RESONANCE-RADIATION PRESSURE, STANDING-WAVE}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.69.1636}, author = {Timp, G. and Behringer, R. E. and Tennant, D. M. and Cunningham, J. E. and Prentiss, M. and Berggren, K. K.} } @article {1601950, title = {USING LIGHT AS A STENCIL}, journal = {APPLIED PHYSICS LETTERS}, volume = {60}, year = {1992}, month = {FEB 24}, pages = {1027-1029}, abstract = {A new method for laterally manipulating the morphology of a thin film is presented, which uses the force exerted by light to deflect neutral atoms in an atomic beam during deposition. We have evaluated the dependence of the thickness of a thin metal film on the frequency, intensity, and the spatial structure of the light field, and find that the stimulated component of the force is suitable for laterally organizing atoms from centimeter to submicron dimensions.}, keywords = {ATOMS, STANDING-WAVE}, isbn = {0003-6951 J9 - APPL PHYS LETT}, url = {https://www.doi.org/10.1063/1.106488}, author = {Prentiss, M. and Timp, G. and Bigelow, N. and Behringer, R. E. and Cunningham, J. E.} } @article {1601872, title = {DECREASED DAMPING OF ULTRACOLD ATOMS IN OPTICAL MOLASSES - PREDICTIONS AND A POSSIBLE SOLUTION}, journal = {OPTICS LETTERS}, volume = {15}, year = {1990}, month = {DEC 15}, pages = {1479-1481}, abstract = {We derive expressions for the damping rate for a two-level atom trapped in the antinodes of an optical interference pattern. We find that the decay rate is much slower than the rate for untrapped atoms in optical molasses. Although the velocity of untrapped atoms decays exponentially in time, the velocity of trapped atoms decays only as t-1/2. We show that the slow damping rate can be circumvented by the addition of a traveling-wave component to the molasses standing wave and discuss how these results can be extended to multilevel atoms.}, keywords = {Motion, Radiation}, isbn = {0146-9592 J9 - OPT LETT}, url = {https://www.doi.org/10.1364/OL.15.001479}, author = {Bigelow, N. P. and Prentiss, M.} } @article {1601873, title = {DIRECT OBSERVATION OF THE INFLUENCE OF DOPPLER-INDUCED RESONANCES ON ATOMIC VELOCITIES}, journal = {PHYSICAL REVIEW LETTERS}, volume = {65}, year = {1990}, month = {JUL 30}, pages = {555-558}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.65.555}, author = {Bigelow, N. P. and Prentiss, M. G.} } @article {1601874, title = {OBSERVATION OF CHANNELING OF ATOMS IN THE 3-DIMENSIONAL INTERFERENCE PATTERN OF OPTICAL STANDING WAVES}, journal = {PHYSICAL REVIEW LETTERS}, volume = {65}, year = {1990}, month = {JUL 2}, pages = {29-32}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.65.29}, author = {Bigelow, N. P. and Prentiss, M. G.} } @article {1601880, title = {OBSERVATIONS OF SODIUM ATOMS IN A MAGNETIC MOLASSES TRAP LOADED BY A CONTINUOUS UNCOOLED SOURCE}, journal = {OPTICS LETTERS}, volume = {15}, year = {1990}, month = {MAY 1}, pages = {507-509}, isbn = {0146-9592 J9 - OPT LETT}, url = {https://www.doi.org/10.1364/OL.15.000507}, author = {Cable, A. and Prentiss, M. and Bigelow, N. P.} } @article {1601947, title = {EFFECT OF TRANSVERSE GUIDING ON THE VELOCITY DISTRIBUTION OF AN ATOMIC-BEAM}, journal = {JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS}, volume = {6}, year = {1989}, month = {NOV}, pages = {2155-2158}, isbn = {0740-3224 J9 - J OPT SOC AM B}, url = {https://www.doi.org/10.1364/JOSAB.6.002155}, author = {Prentiss, M. and Cable, A. and Bigelow, N. P.} } @article {1601946, title = {SLOWING AND COOLING AN ATOMIC-BEAM USING AN INTENSE OPTICAL STANDING WAVE}, journal = {PHYSICAL REVIEW LETTERS}, volume = {62}, year = {1989}, month = {MAR 20}, pages = {1354-1357}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.62.1354}, author = {Prentiss, M. and Cable, A.} } @article {1601948, title = {ATOMIC-DENSITY-DEPENDENT LOSSES IN AN OPTICAL TRAP}, journal = {OPTICS LETTERS}, volume = {13}, year = {1988}, month = {JUN}, pages = {452-454}, isbn = {0146-9592 J9 - OPT LETT}, url = {https://www.doi.org/10.1364/OL.13.000452}, author = {Prentiss, M. and Cable, A. and Bjorkholm, J. E. and S. Chu and Raab, E. L. and Pritchard, D. E.} } @article {1601953, title = {INFLUENCE OF ATOMIC RECOIL ON THE SPECTRUM OF RESONANCE FLUORESCENCE FROM A 2-LEVEL ATOM}, journal = {PHYSICAL REVIEW A}, volume = {35}, year = {1987}, month = {JAN 15}, pages = {922-925}, isbn = {1050-2947 J9 - PHYS REV A}, url = {https://www.doi.org/10.1103/PhysRevA.35.922}, author = {Prentiss, M. G. and Ezekiel, S.} } @article {1601955, title = {TRAPPING OF NEUTRAL SODIUM ATOMS WITH RADIATION PRESSURE}, journal = {PHYSICAL REVIEW LETTERS}, volume = {59}, year = {1987}, month = {DEC 7}, pages = {2631-2634}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.59.2631}, author = {Raab, E. L. and Prentiss, M. and Cable, A. and S. Chu and Pritchard, D. E.} } @article {1601952, title = {OBSERVATION OF INTENSITY-DEPENDENT FLUORESCENCE LINE-SHAPE ASYMMETRY FOR 2-LEVEL ATOMS IN A STANDING-WAVE FIELD}, journal = {PHYSICAL REVIEW LETTERS}, volume = {56}, year = {1986}, month = {JAN 6}, pages = {46-49}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.56.46}, author = {Prentiss, M. G. and Ezekiel, S.} } @article {1601954, title = {INTENSITY DEPENDENCE OF RESONANT LIGHT-DIFFRACTION BY AN ATOMIC-BEAM}, journal = {JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION}, volume = {1}, year = {1984}, pages = {1307-1307}, isbn = {0740-3232 J9 - J OPT SOC AM A}, author = {Prentiss, M. G. and Peuse, B. W. and Ezekiel, S.} } @article {1601945, title = {ELIMINATION OF LINE-SHAPE DISTORTION IN LASER-ABSORPTION SPECTROSCOPY IN ATOMIC-BEAMS}, journal = {OPTICS LETTERS}, volume = {8}, year = {1983}, pages = {154-156}, isbn = {0146-9592 J9 - OPT LETT}, url = {https://www.doi.org/10.1364/OL.8.000154}, author = {Peuse, B. W. and Prentiss, M. G. and Ezekiel, S.} } @article {1601944, title = {OBSERVATION OF RESONANT LIGHT-DIFFRACTION BY AN ATOMIC-BEAM}, journal = {PHYSICAL REVIEW LETTERS}, volume = {49}, year = {1982}, pages = {269-272}, isbn = {0031-9007 J9 - PHYS REV LETT}, url = {https://www.doi.org/10.1103/PhysRevLett.49.269}, author = {Peuse, B. W. and Prentiss, M. G. and Ezekiel, S.} } @article {1601957, title = {PASSIVE RING RESONATOR METHOD FOR SENSITIVE INERTIAL ROTATION MEASUREMENTS IN GEOPHYSICS AND RELATIVITY}, journal = {OPTICS LETTERS}, volume = {6}, year = {1981}, pages = {569-571}, isbn = {0146-9592 J9 - OPT LETT}, url = {https://www.doi.org/10.1364/OL.6.000569}, author = {Sanders, G. A. and Prentiss, M. G. and Ezekiel, S.} }