Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session M7: Kinked States of DNA: From Physical Measurement to Functional Significance |
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Sponsoring Units: DBP Chair: Philip Nelson, University of Pennsylvania Room: LACC 408B |
Tuesday, March 22, 2005 5:30PM - 6:06PM |
M7.00001: Multiscale Models of DNA Minicircles Invited Speaker: I will describe various numerical and analytical approaches to multi-scale modelling of the configurations of DNA minicircles. One approach that exhibits localized ``kinking" of the DNA double helix involves full atomistic simulation (via Molecular Dynamics with explicit solvent) of 94 base pair minicircles of different Links. For full citations see the web page http://lcvmwww.epfl.ch [Preview Abstract] |
Tuesday, March 22, 2005 6:06PM - 6:42PM |
M7.00002: Macroscopic Mechanisms of DNA Flexibility Invited Speaker: In recent experiments Cloutier and Widom found that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds the theoretical expectations by 3 orders of value. Is it possible to revise the theoretical model of DNA bending, based on harmonic potential for the bend angle between adjacent base pairs, to fit these unexpected results? We investigated the effect of the bend angle distribution on the cyclization efficiency. Different modifications of the angle distribution, extracted from the DNA-Protein Data Bank, were tested. We found that incorporating non-quadratic terms in the potential can provide increase of the short fragment cyclization efficiency by about one order of value. The computations showed that only incorporating a possibility of sharp kinks in the distribution is capable to provide the desired increase of the cyclization efficiency. The frequency of such kinks should be about one per thousand base pairs. The kink model does not allow, however, fitting all cyclization data for DNA fragments of different lengths. Trying to resolve this problem we reinvestigated the cyclization of 100 bp DNA fragments experimentally. [Preview Abstract] |
Tuesday, March 22, 2005 6:42PM - 7:18PM |
M7.00003: Localized single-stranded bubble mechanism for cyclization of short DNAs Invited Speaker: Recent experiments (T.E. Cloutier, J. Widom, Mol. Cell 14, 355-62 2004) indicate that double-stranded DNA molecules of approximately 100 base pairs in length have a probability of cyclization which is up to $10^5$ times larger than that expected based on the known bending modulus of the double helix. We argue that for short molecules, formation of small (few base pair) regions of single-stranded DNA can provide `flexible hinges' that facilitate loop formation. A statistical-mechanical calculation using a transfer-matrix approach, which treats disordered double helix regions as thermally excited, highly flexible joints, indicates that this mechanism can explain the experimental data. Applications of this type of model and calculation to other situations where localized double helix structural defects may play a important role in DNA higher-order structure will also be discussed. This research was supported by NSF Grant DMR-0203963. [Preview Abstract] |
Tuesday, March 22, 2005 7:18PM - 7:54PM |
M7.00004: DNA Flexibility Invited Speaker: Classic experimental and theoretical analyses led to a unified view of DNA as a semiflexible polymer, characterized by a bending persistence length, P, $\sim $50 nm ($\sim $150 bp). In this view, DNA lengths that are greater than P are, on average, spontaneously gently bent, and require relatively little force to bend significantly, while DNA lengths that are shorter than P are nearly straight, and require great force to bend significantly. Nevertheless, sharply bent DNA plays important roles in biology. We used the method of ligase catalyzed DNA cyclization to investigate the spontaneous looping of short DNAs. Remarkably, DNAs as short as 84 bp spontaneously bend into circles, and 94 bp DNA sequences cyclize up to 10$^{5}$ times more easily than predicted from classic theories of DNA bending. In subsequent studies we find that the twistability of sharply looped DNAs exceeds the prediction of classic theories by up to 400-fold. These results can only be understood by greatly enhanced DNA flexibility, not by permanent bends. Our results provide striking support for two new theories of DNA mechanics based on local melted or kinked regions, and they establish DNA as an active participant in the formation and function of looped regulatory complexes \textit{in vivo}. [Preview Abstract] |
Tuesday, March 22, 2005 7:54PM - 8:30PM |
M7.00005: What's Wrong with the Wormlike Chain Invited Speaker: DNA bending on length scales shorter than a persistence length (50 nm) plays an essential role in the translation of genetic information from DNA to cellular function. Although the Wormlike Chain model successfully describes the bending of DNA on length scales longer than a persistence length, recent DNA cyclization experiments reveal that this model underestimates the probability of spontaneous sharp bending. Indeed, at the scales most relevant for biological processes, recent experiments give cyclization rates three orders of magnitude greater than that predicted by the Wormlike Chain model.\\ \\ In this talk, we reconcile the successes of the Wormlike Chain model in describing the long-length-scale mechanics of DNA, with its failure to describe bending on biologically relevant length scales. We present an exact statistical mechanics model for a polymer which can undergo a kinking transition and explicitly show that this high-curvature softening of the polymer constitutive relation can dramatically increase the probability of high curvature configurations while leaving the long-length-scale mechanics of the polymer virtually unchanged [P. Wiggins, R. Phillips, \& P. Nelson: cond- mat/0409003, Phys Rev E in press]. Next, we present a new technique for describing stiff polymers which can be exploited to compute near-exact result for many polymer observables. We use these techniques and short-length-scale AFM measurements to construct a quantitative model for DNA bending mechanics applicable on the length scales relevant for many biological processes. This new model predicts the softening observed in short-contour-length cyclization measurements. [Preview Abstract] |
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