Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session V40: Thesis Award Session: Nucleic Acids -- Structure, Function, and the Genome |
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Sponsoring Units: DBP Chair: Aihua Xie, Oklahoma State University Room: A122/123 |
Thursday, March 24, 2011 8:00AM - 8:36AM |
V40.00001: 2010 Award for Outstanding Doctoral Thesis Research in Biological Physics Talk: How the Genome Folds Invited Speaker: I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes. [Preview Abstract] |
Thursday, March 24, 2011 8:36AM - 8:48AM |
V40.00002: Recognition Tunneling towards Next Generation Single Molecule DNA Sequencing Shuo Huang A novel approach has been developed to trap and sequence DNA within a molecular junction formed by a pair of functionalized Au electrodes so individual DNA nucleotides could be recognized on small pieces of DNA with single base resolution. The cost of labeling reagents is totally eliminated since different nucleotides are recognized through their intrinsic physical properties. Unexpectedly long residence time of DNA (on the order of a second) in the molecular gap is observed which indicates that a pN force is required to achieve the sequencing speed as fast as 10 bases/Sec. Providing such ionic driving force, a nanopore device incorporated with recognition tunneling reader will provide a revolutionary way for fast, accurate and economic next generation DNA sequencing. [Preview Abstract] |
Thursday, March 24, 2011 8:48AM - 9:00AM |
V40.00003: Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap Shuai Chang New approaches to DNA sequencing are required to reduce costs and increase the availability of personalized genomics. Using Scanning Tunneling Microscope as a tool, we report measurements of the current signals generated as free nucleosides diffuse into a tunnel junction in which both electrodes are functionalized with a reagent that presents a hydrogen bond donor and acceptor to the nucleosides. This functionalization serves to both limit the range of molecular orientations in the tunnel gap and reduce the contact resistance, increasing the selectivity of the tunneling signal, so that a direct readout may be possible with a few repeated reads. [Preview Abstract] |
Thursday, March 24, 2011 9:00AM - 9:12AM |
V40.00004: Gel electrophoresis of partially denatured DNA: split-ends, bubbles, and squids David Sean, Gary W. Slater Gel electrophoresis separates partially denatured DNA fragments based on chemical sequence. Upon an increase in temperature, AT-rich regions melt into two strands which is thought to be the main contributor to the rapid reduction of the fragment's mobility. The reduction in mobility is often predicted from the average number of denatured bases regardless of their positions. We re-visit the theoretical basis of this approach and determine that the analysis only holds for denatured domains that occur at the ends. Langevin Dynamics simulations are used to study the effect that the placement of the melted regions has on the mobility by discriminating between denatured domains which occur in the middle of the fragment (bubbles) and at the ends (split-ends). It is found that the split-ends dominate the blocking mechanism. In addition, we find a novel conformation (the ``squid'') which seems to be responsible for the blocking at high fields. [Preview Abstract] |
Thursday, March 24, 2011 9:12AM - 9:24AM |
V40.00005: Temperature dependence of two distinct DNA overstretching transitions Xinghua Zhang, Hongxia Fu, Patrick Doyle, Jie Yan Recent experiments show that two distinct transitions are involved in the DNA overstretching that occurs at around 65 pN: a strand-unpeeling transition leading to strand separation from free DNA ends or nicks, and a B to S transition leading to an overstretched double-stranded DNA called ``S-DNA.'' Here we show that the two transitions have distinct temperature dependence: in the strand-unpeeling transition, the transition force decreases when the temperature increases; while in the B to S transition, the temperature dependence of the transition force is opposite. Our results are in agreement with the notion that the two transitions involve distinct types of double-helix reorganization. [Preview Abstract] |
Thursday, March 24, 2011 9:24AM - 9:36AM |
V40.00006: An Analytic Theory for Single Molecule Manipulation of DNA Cristiano Nisoli We introduce a minimal, analytically solvable model for thermomechanical behavior of DNA under tension and torque, and predict critical temperature for denaturation at unwinding and overwinding, phase diagrams for stable b--DNA, and supercoling-elongation curves as functions of applied torque, tension and temperature. Our results are in agreement with experimental data from experiments in single molecule manipulation. We also propose simple thermodynamical formulae for temperature, tension, torque, and supercoiling at criticality. [Preview Abstract] |
Thursday, March 24, 2011 9:36AM - 9:48AM |
V40.00007: Multimerization of DNA Origami Structures in Two Dimensions Daniel Schiffels, Deborah Fygenson, Tim Liedl DNA nanotechnology, here in particular DNA origami, is based on self-assembly and can be used to construct arbitrary three-dimensional structures with nanometer precision. The dimensions of such DNA origami structures are typically on the order of a hundred nanometers or smaller. To achieve large-scale two-dimensional lattices that could be employed as scaffolds for crystalline arrangement of biomolecules and proteins, individual DNA origami tiles need to be assembled hierarchically. We work on the multimerization of DNA origami structures into extended one- and two- dimensional lattices that can cover areas of several square micrometers. This is achieved by complementary single stranded DNAs (sticky ends) at specific positions on the DNA origami objects that we intend to grow into periodic structures. We study the effect of varying multimerization conditions such as annealing temperatures, length of sticky ends and salt concentration on the quality and size of the resulting lattice. [Preview Abstract] |
Thursday, March 24, 2011 9:48AM - 10:00AM |
V40.00008: Fluctuation Pressure Assisted Ejection of DNA From Bacteriophage Michael J. Harrison The role of thermal pressure fluctuations excited within tightly packaged DNA while it is ejected from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of parallel segments that forms an equilibrium conformation at minimum free energy, which presses tightly against capsid walls. Using a canonical ensemble at temperature T we calculate internal pressure fluctuations against a slowly moving or static capsid mantle for an elastic continuum model of the folded DNA bundle. It is found that fluctuating pressures on the capsid from thermal excitation of longitudinal acoustic vibrations in the bundle whose wavelengths are exceeded by the bend persistence length may have root-mean-square values that are several tens of atmospheres for typically small phage dimensions. Comparisons are given with measured data on three mutants of lambda phage with different base pair lengths and total genome ejection pressures. [Preview Abstract] |
Thursday, March 24, 2011 10:00AM - 10:12AM |
V40.00009: Effects of sequence on DNA wrapping around histones Vanessa Ortiz A central question in biophysics is whether the sequence of a DNA strand affects its mechanical properties. In epigenetics, these are thought to influence nucleosome positioning and gene expression. Theoretical and experimental attempts to answer this question have been hindered by an inability to directly resolve DNA structure and dynamics at the base-pair level. In our previous studies we used a detailed model of DNA to measure the effects of sequence on the stability of naked DNA under bending. Sequence was shown to influence DNA's ability to form kinks, which arise when certain motifs slide past others to form non-native contacts. Here, we have now included histone-DNA interactions to see if the results obtained for naked DNA are transferable to the problem of nucleosome positioning. Different DNA sequences interacting with the histone protein complex are studied, and their equilibrium and mechanical properties are compared among themselves and with the naked case. [Preview Abstract] |
Thursday, March 24, 2011 10:12AM - 10:24AM |
V40.00010: A quantitative model of nucleosome dynamics Robert Forties, Justin North, Sarah Javaid, Omar Tabbaa, Richard Fishel, Michael Poirier, Ralf Bundschuh The expression, replication and repair of eukaryotic genomes require the fundamental organizing unit of chromatin, the nucleosome, to be unwrapped and/or disassembled. We have developed a quantitative model of nucleosome dynamics which provides a fundamental understanding of these DNA processes. We calibrated this model using results from high precision single molecule nucleosome unzipping experiments, and then tested its predictions for experiments in which nucleosomes are disassembled by the DNA mismatch recognition complex hMSH2-hMSH6. We found that this calibrated model quantitatively describes hMSH2-hMSH6 induced disassembly rates of nucleosomes with two separate DNA sequences and four distinct histone modification states. In addition, this model provides mechanistic insight into nucleosome disassembly by hMSH2-hMSH6 and the influence of histone modifications on this disassembly reaction. This model's precise agreement with current experiments suggests that it can be applied more generally to provide important mechanistic understanding of the numerous nucleosome alterations that occur during DNA processing. [Preview Abstract] |
Thursday, March 24, 2011 10:24AM - 10:36AM |
V40.00011: Fitness and structure landscapes for pre-miRNA processing Ralf Bundschuh, Juliette de Meaux, Michael Lassig The processing from pre-miRNA to mature miRNA in plants involves a mechanism, which depends on an extended stem in the secondary structure of the pre-miRNA. Here, we show how natural selection acts on this secondary structure to produce evolutionary conservation of the processing mechanism together with modularity of the pre-miRNA molecules, making this molecular function independent of others. Our main results are: 1. Selection on miRNA processing can be described by a fitness landscape which depends directly on the secondary structure of the pre-miRNA. 2. This fitness landscape predicts the divergence of the phenotype between orthologous pre-miRNA molecules from different species. 3. Actual pre-miRNA structures are modular: their phenotype is significantly less affected by deleterious mutations in the remainder of the molecule than for random RNA molecules. [Preview Abstract] |
Thursday, March 24, 2011 10:36AM - 10:48AM |
V40.00012: DNA-damage by free radicals in solution P.K. Biswas, Ramin Abolfath, R. Rajnarayanam, K. Cho, T. Brabec, L. Papiez We employ a molecular simulation based on GROMACS-CPMD QM/MM method to study the initial damage to a fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the diatomic OH-radicals that are primary product of megavoltage ionizing radiation in water-based systems form a network of hydrogen bonds with the nearby water molecules. Our molecular simulation illustrates that the Hydrogen bonds strongly alter the relative orientation of the OH-radicals and DNA molecule. This results to an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen abstraction mechanisms than previously anticipated for identical system in the vacuum. We illustrate that the thermal fluctuations of the water molecules in the solution strongly compete with the H-abstraction that shows more energitically favorable in solution than in vacuum. As a result the chemical reaction takes place with slower rate in solution than in vacuum. [Preview Abstract] |
Thursday, March 24, 2011 10:48AM - 11:00AM |
V40.00013: Transport properties of nucleotides in a graphene nanogap for DNA sequencing J. Prasongkit, A. Grigoriev, R.H. Scheicher, R. Ahuja The application of graphene nanogaps for DNA sequencing has been proposed [H. W. Ch. Postma, Nano Lett. 10, 420 (2010)]. We used density functional theory and the non-equilibrium Green's function method to study the electron transport properties of nucleotides located inside a graphene nanogap. Our setup considered different positions and orientations of the bases with respect to the graphene electrodes, and we analyzed how the transmission spectra depend on such shifts and rotations. Even when taking into account current changes due to base fluctuations, we find that each nucleotide possesses a different characteristic current magnitude, owing to its distinctive electronic properties. Based on our results, it thus seems that the electrical readout from a graphene nanogap could in principle be sufficiently sensitive to distinguish between the four nucleotides, and thus achieve the goal of rapid and economical whole-genome sequencing. [Preview Abstract] |
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