Publications
Corrigendum to "Sequence-dependent Kinetic Model for Transcription Elongation by RNA Polymerase" [J. Mol. Biol. 344 (2004) 335-349] (DOI:10.1016/j.jmb.2004.08.107)
A biophysicist marvels at the idea of grabbing microscopic particles with light by tweaking its phase.
Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules
The response of single DNA molecules to externally applied forces and torques was directly measured using an angular optical trap. Upon overwinding, DNA buckled abruptly as revealed by a sharp extension drop followed by a torque plateau. When the DNA was held at the buckling transition, its extension hopped rapidly between two distinct states. Furthermore, the initial plectonemic loop absorbed approximately twice as much extension as was absorbed into the plectoneme upon each additional turn.
Single-Molecule Studies Reveal Dynamics of DNA Unwinding by the Ring-Shaped T7 Helicase
Helicases are molecular motors that separate DNA strands for efficient replication of genomes. We probed the kinetics of individual ring-shaped T7 helicase molecules as they unwound double-stranded DNA (dsDNA) or translocated on single-stranded DNA (ssDNA). A distinctive DNA sequence dependence was observed in the unwinding rate that correlated with the local DNA unzipping energy landscape. The unwinding rate increased ∼10-fold (approaching the ssDNA translocation rate) when a destabilizing force on the DNA fork junction was increased from 5 to 11 pN.
Nanofabricated quartz cylinders for angular trapping: DNA supercoiling torque detection
We designed and created nanofabricated quartz cylinders well suited for torque application and detection in an angular optical trap. We made the cylinder axis perpendicular to the extraordinary axis of the quartz crystal and chemically functionalized only one end of each cylinder for attachment to a DNA molecule. We directly measured the torque on a single DNA molecule as it underwent a phase transition from B-form to supercoiled P-form.
Mechanochemical kinetics of transcription elongation
The mechanochemical kinetics of transcription elongation was examined with a combination of theoretical and experimental approaches. The predictive power of a sequence-dependent thermal ratchet model for transcription elongation was tested by establishing model parameters based solely on measurements under chemical perturbations and then directly predicting responses under mechanical perturbations without additional model parameters. Agreement between predicted and measured force-velocity curves provides strong support for a simple mechanochemical coupling mechanism.
Measurements of superfluid 4He flow through Sub-15 nm aperture arrays
We have constructed an experiment designed to study Josephson phenomena in 4He. Motivated by reports and our ideas for novel silicon nanofabrication techniques, we designed the experiment to study the possibility of a transition from stochastic to coherent phase slippage. Here we briefly describe the nanofabrication of sub-15 nm aperture arrays and show preliminary data. For temperatures below 2 K, these data show temperature dependence of the superfluid critical velocity through the weak link which is characteristic of phase-slip limited flow. © 2006 American Institute of Physics.
Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules
Chromatin-remodeling enzymes can overcome strong histone-DNA interactions within the nucleosome to regulate access of DNA-binding factors to the genetic code. By unzipping individual DNA duplexes, each containing a uniquely positioned nucleosome flanked by long segments of DNA, we directly probed histone-DNA interactions. The resulting disruption-force signatures were characteristic of the types and locations of interactions and allowed measurement of the positions of nucleosomes with 2.6-base-pair (bp) precision.
Single-molecule analysis of RNA polymerase transcription
The kinetics and mechanisms of transcription are now being investigated by a repertoire of single-molecule techniques, including optical and magnetic tweezers, high-sensitivity fluorescence techniques, and atomic force microscopy.
Detection of forces and displacements along the axial direction in an optical trap
We present measurements of the forces on, and displacements of, an optically trapped bead along the propagation direction of the trapping laser beam (the axial direction). In a typical experimental configuration, the bead is trapped in an aqueous solution using an oil-immersion, high-numerical-aperture objective. This refractive index mismatch complicates axial calibrations due to both a shift of the trap center along the axial direction and spherical aberrations.