Bulletin of the American Physical Society
2013 Annual Fall Meeting of the APS New England Section
Volume 58, Number 11
Friday–Saturday, October 11–12, 2013; Bridgewater, Massachusetts
Session A1: Plenary Talks: Biophysics and Optics |
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Chair: Ed Deveney, Bridgewater State University Room: Science and Mathematics Auditorium CON120 |
Friday, October 11, 2013 1:10PM - 2:00PM |
A1.00001: Optical Trapping: From Ultrastable Measurements to Simple Biophysical Experiments Ashley Carter It has been about thirty years since Ashkin and colleagues first used a focused laser to optically trap micron-sized particles, ushering in a new era of precision measurement. Today, the most fascinating applications of optical traps are in biophysics where we can use these systems to sort cancerous cells, to measure individual molecular motors walking along protein filaments, to watch DNA or proteins fold and unfold, or to observe single ribosomes translate mRNA into protein. I'll discuss the physics of optical trapping and some of these exciting experiments, including a recent measurement of a helicase, RecBCD, that is able to miraculously open multiple base-pairs of double-stranded DNA at once. Measurements at this scale require an ultrastable optical trapping system that is state of the art. Then I'll move on to discussing measurements of DNA condensation, some of which can easily be done in the undergraduate laboratory. [Preview Abstract] |
Friday, October 11, 2013 2:00PM - 2:50PM |
A1.00002: Force-induced DNA interactions: From polymer elasticity to protein dynamics Mark Williams As DNA is stretched with optical tweezers, the force-extension curve is strongly altered in the presence of ligands that bind to double- and single-stranded forms of DNA. These ligands can alter the length of the molecule, its elasticity, and the relative stability of the two forms of DNA. Small molecules that intercalate between the DNA base pairs increase the length of DNA, and this length increase can be used to precisely quantify the ligand-DNA binding energy. For complex small molecules such as Actinomycin D, slow binding kinetics can be directly measured, allowing complete characterization of the energy landscape for DNA-ligand binding. DNA bending proteins such as eukaryotic HMGB proteins alter the flexibility of the molecule, and the change in DNA persistence length can also be used to quantify DNA-protein binding affinity. In addition, these measurements allow protein-DNA interaction kinetics to be measured. In the case of HMGB proteins, I will show how we can independently measure microscopic and macroscopic dissociation events. We find that these proteins dissociate rapidly from local DNA binding sites, while remaining associated overall to the DNA molecule for a longer time. This result has important implications for protein-DNA interactions in the cell. [Preview Abstract] |
Friday, October 11, 2013 2:50PM - 3:40PM |
A1.00003: Coordination of individual and ensemble molecular motors studied using tools from DNA Nanotechnology Nathan Derr Cytoplasmic dynein and kinesin-1 are cytoskeletal molecular motor proteins that move in opposing directions on intracellular microtubules. These motors are responsible for many functions in eukaryotic cells, including primary roles in cargo transport, cell division and the maintenance of sub-cellular spatial organization. These motors are homodimeric and move in discrete increments, averaging 8 nm perstep and outputting forces in the piconewton range. Moving processively on their microtubule tracks,they can take hundreds or thousands of consecutive steps. To better understand how individual dynein motors achieve this processive motion, we created orthogonally labeled dynein heterodimers joined by DNA base paring and observed their steps using two-color, single-molecule microscopy with high-precision, two-dimensional tracking. Additionally, to investigate the biophysical mechanisms that govern the collective behavior of motor ensembles, we built a programmable synthetic cargo using the techniques of three-dimensional DNA origami. This allowed us to precisely control the number, spacing and type of motors within the ensemble. [Preview Abstract] |
Friday, October 11, 2013 3:40PM - 4:30PM |
A1.00004: Electric-field driven translocation of colloidal wild and mutant fd viruses through a solid-state nanopore Invited Speaker: (Katherine) Miao Wang Research on DNA translocation through nanopore has drawn much attention because of its potential in DNA sequencing and biosensing. A lot of issues about translocation process have been found in recent years, such as capture kinetics, thermal fluctuations, electro-osmotic flow, etc. Due to the flexibility of DNA molecules, there are many complicated folded translocation events, which makes the task of data analysis difficult. Here we use semi-flexible fd virus particles as a model system for studying translocation dynamics. The fd particles have persistent length of $\sim$3 m, much larger than the diameter of a nanopore, making folded translocation unlikely. In our study, we can observe the subtle difference in their translocation dynamics of wild and mutant types of fd particles due to their different degrees of flexibility measured by their persistent lengths, fd at $\sim$3 $\mu$m and mutant Y21M at $\sim$10 $\mu$m. This work is done in collaboration with Anna Lu, Liping Liu, and Hongwen Wu in Sean Ling's group at Brown University. [Preview Abstract] |
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