Publications

2007
A. Winkleman, R. Perez-Castillejos, K. L. Gudiksen, S. T. Phillips, M. Prentiss, and G. M. Whitesides. 2007. “Density-based diamagnetic separation: Devices for detecting binding events and for collecting unlabeled diamagnetic particles in paramagnetic solutions.” ANALYTICAL CHEMISTRY, 79, Pp. 6542-6550. Publisher's VersionAbstract
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.
E. Feinstein, E. Alsberg, D. Ingber, and M. Prentiss. 2007. “Development and micromechanical analysis of a self-assembled Tissue Engineered extracellular matrix analogue with defined nanostructure.” BIOPHYSICAL JOURNAL, Pp. 333A-333A. Web of Science Citation
K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss. 2007. “Direct measurements of the stabilization of single-stranded DNA under tension by single-stranded binding proteins.” PHYSICAL REVIEW E, 76. Publisher's VersionAbstract
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.
K. A. Hatch, C. Danilowicz, V. Cojee, and M. Prentiss. 2007. “Dynamics of unzipping and rezipping DNA.” BIOPHYSICAL JOURNAL, Pp. 165A-165A. Web of Science Citation
C. Danilowicz, C. H. Lee, V.W. Coljee, and M. Prentiss. 2007. “Effects of temperature on the mechanical properties of single stranded DNA.” PHYSICAL REVIEW E, 75. Publisher's VersionAbstract
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.
S. S. Shevkoplyas, A. C. Siegel, R. M. Westervelt, M. G. Prentiss, and G. M. Whitesides. 2007. “The force acting on a superparamagnetic bead due to an applied magnetic field.” LAB ON A CHIP, 7, Pp. 1294-1302. Publisher's VersionAbstract
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.
K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss. 2007. “Measurements of the hysteresis in unzipping and rezipping double-stranded DNA.” PHYSICAL REVIEW E, 75. Publisher's VersionAbstract
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.
C. Danilowicz, C. Limouse, V. Cojee, and M. Prentiss. 2007. “Overstretching dsDNA from different ends.” BIOPHYSICAL JOURNAL, Pp. 165A-165A. Google Scholar Citation
2006
C. H. Lee, C. Danilowicz, V.W. Coljee, and M. Prentiss. 2006. “Comparison of the measured phase diagrams in the force-temperature plane for the unzipping of two different natural DNA sequences.” EUROPEAN PHYSICAL JOURNAL E, 19, Pp. 339-344. Publisher's VersionAbstract
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.
C. H. Lee, C. Danilowicz, R. S. Conroy, V.W. Coljee, and M. Prentiss. 2006. “Impacts of magnesium ions on the unzipping of lambda-phage DNA.” JOURNAL OF PHYSICS-CONDENSED MATTER, 18, Pp. S205-S213. Publisher's VersionAbstract
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.
E. Alsberg, E. Feinstein, M. P. Joy, M. Prentiss, and D. E. Ingber. 2006. “Magnetically-guided self-assembly of fibrin matrices with ordered nano-scale structure for tissue engineering.” TISSUE ENGINEERING, 12, Pp. 3247-3256. Publisher's VersionAbstract
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.
C. H. Lee, C. Danilowicz, V.W. Coljee, and M. Prentiss. 2006. “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".” EUROPEAN PHYSICAL JOURNAL E, 19, Pp. 351-352. Publisher's Version
E. Feinstein and M. Prentiss. 2006. “Three-dimensional self-assembly of structures using the pressure due to a ferrofluid in a magnetic field gradient.” JOURNAL OF APPLIED PHYSICS, 99. Publisher's VersionAbstract
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.
2005
C. Danilowicz, D. Greenfield, and M. Prentiss. 2005. “Dissociation of ligand-receptor complexes using magnetic tweezers.” ANALYTICAL CHEMISTRY, 77, Pp. 3023-3028. Publisher's VersionAbstract
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.
C. H. Lee, C. Danilowicz, R. Conroy, A. Mignot, Y. Kafri, V.W. Coljee, and M. Prentiss. 2005. “Effect of magnesium ions and temperature on the unzipping of Lambda DNA.” BIOPHYSICAL JOURNAL, 88, Pp. 347A-347A.
M. Boncheva, S. A. Andreev, L. Mahadevan, A. Winkleman, D. R. Reichman, M. G. Prentiss, S. Whitesides, and G. M. Whitesides. 2005. “Magnetic self-assembly of three-dimensional surfaces from planar sheets.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102, Pp. 3924-3929. Publisher's VersionAbstract
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.
J.D. Weeks, J.B. Lucks, Y. Kafri, C. Danilowicz, D.R. Nelson, and M. Prentiss. 2005. “Pause point spectra in DNA constant-force unzipping.” BIOPHYSICAL JOURNAL, 88, Pp. 2752-2765. Publisher's VersionAbstract
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.
2004
C. Danilowicz, R. Conroy, Y. Kafri, V. Coljee, and M. Prentiss. 2004. “Measurement of the phase diagram of DNA unzipping as a function of temperature and force.” BIOPHYSICAL JOURNAL, 86, Pp. 324A-324A. Publisher's Version
C. Danilowicz, Y. Kafri, R. S. Conroy, V.W. Coljee, J. Weeks, and M. Prentiss. 2004. “Measurement of the phase diagram of DNA unzipping in the temperature-force plane.” PHYSICAL REVIEW LETTERS, 93. Publisher's VersionAbstract
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.
2003
Y. Lu, H. Xiong, X. C. Jiang, Y. N. Xia, M. Prentiss, and G. M. Whitesides. 2003. “Asymmetric dimers can be formed by dewetting half-shells of gold deposited on the surfaces of spherical oxide colloids.” JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 125, Pp. 12724-12725. Publisher's Version

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