C. Danilowicz, D. Greenfield, and M. Prentiss. 2005. “
Dissociation of ligand-receptor complexes using magnetic tweezers.” ANALYTICAL CHEMISTRY, 77, Pp. 3023-3028.
Publisher's VersionAbstractWe 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 VersionAbstractThis 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 VersionAbstractUnder 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.