Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session L40: Nucleic Acids: Structure, Function and Dynamics |
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Sponsoring Units: DBP Chair: Michael Poirier, Ohio State University Room: 412 |
Tuesday, March 17, 2009 2:30PM - 2:42PM |
L40.00001: Histone octamer acetylation affects the free energy of nucleosome formation Alex Mooney, Mridula Manohar, Annick Edon, Robin Nakkula, Jennifer Ottesen, Michael Poirier Nucleosomes, histone octamer-DNA complexes, form the fundamental repeating units of eukaryotic chromatin. Numerous post-translational modifications of histone octamers are found \emph{in vivo} and are known to play roles in gene regulation and DNA repair, but the molecular functions of these modifications are not well understood. In this study we consider the effects of acetylating histone protein H3 residues Lys$^{115}$ and Lys$^{122}$. These modifications reduce the positive surface charge of the histone octamer at contact points with the negatively charged DNA phosphate backbone and add steric bulk in the dyad region. We report results from competitive reconstitutions that show the free energy of nucleosome formation between wild-type and modified histone octamer binding to a strong nucleosome positioning sequence is reduced. These results suggest that these modifications may be involved in nucleosome assembly and disassembly. [Preview Abstract] |
Tuesday, March 17, 2009 2:42PM - 2:54PM |
L40.00002: Density fluctuations in confined and non-confined DNA Junhan Pan, Chunda Zhou, Robert Riehn DNA stretching in quasi one-dimensional nanochannels is an emerging technique for the analysis of genomic-sized DNA molecules. For formulating an optimal measurement strategy, the thermal fluctuations of confined molecules are of crucial importance. While previous measurements have concentrated only on the end-to-end length, we present here an experimental study of density fluctuations within the molecule, and find a good agreement with a model similar to a oscillator chain. We further discuss how such a model leads to a natural interpretation of the interesting intramolecular collapse of DNA that we recently under application of a.c. electric fields at frequencies of a few hundred Hertz. [Preview Abstract] |
Tuesday, March 17, 2009 2:54PM - 3:06PM |
L40.00003: Direct Observation of Multiple Pathways of DNA Stacking Using Single-Molecule AFM Ching-Hwa Kiang, Wei-Hung Chen During DNA interactions, single-stranded DNA (ssDNA) is often stretched and stabilized by coupling with ssDNA binding proteins to serve as an intermediate state. The conformational and energetic changes of stretched DNA are of great interest because of their relevance in biological functions. Direct manipulation of DNA has yielded much of the information about the mechanical properties of DNA without the complication of interacting molecules. Stretching ssDNA has provided direct measurement of the base stacking mechanics and energetics. For example, polydA has been shown to have two transitions during overstretching. Here we showed direct observation of two overstretching pathways during the second transition. We have observed ``hopping'' between these two pathways during constant-force measurements. We will discuss the implications of such transition and its significance in biological functions. [Preview Abstract] |
Tuesday, March 17, 2009 3:06PM - 3:18PM |
L40.00004: Stabilities of Constituent Hairpins Determine Whether RNA Folds via Ordered and/or Parallel Mechanisms Samuel Cho, Devarajan Thirumalai RNA molecules are increasing becoming seen as a set of critical players in numerous cellular processes, and a firm understanding of their folding energy landscapes is essential for understanding how they carry out their functions. While it might seem natural to assume that the simplicity of RNA molecules, with only four possible bases, dictate that they must fold via simple mechanisms, experiments continue to point to complex folding energy landscapes involving parallel mechanisms. In our present study, we address how even simple RNA molecules can give rise to very complex folding mechanisms. We begin by making the argument that the complexity observed for RNA folding are in fact fully expected because the lack of variability of the RNA subunits leads to a lack of specificity for folding to the native basin. To illustrate our point, we performed coarse-grained simulations of three RNA pseudoknots and a tRNA molecule, which each are all relatively simple RNA molecules that contain at least two hairpins. From our simulations, we find that the main determinant for how these RNA molecules fold is largely dependent on the relative stabilities of their constituent hairpins. Ordered mechanisms arise if the stabilities of the constituent hairpins are sufficiently dissimilar and parallel folding mechanisms occur if the stabilities of the hairpins are similar. [Preview Abstract] |
Tuesday, March 17, 2009 3:18PM - 3:30PM |
L40.00005: Structural basis of pathway-dependent force profiles in DNA Daniel Roe, Anne Chaka Since DNA must bend and/or stretch to perform many of its functions, it is important to understand the mechanical properties of DNA. Single molecule experiments have been able to study the response of DNA to applied forces. One interesting result of such studies is that at high loading rates a greater force is required to stretch DNA when pulling from the 3' ends as opposed to the 5' ends. While these experiments provide valuable insights into the stability of DNA, it is often difficult to relate the results to specific structural changes. We have used molecular dynamics simulation methods to study the structure and dynamics of DNA under a tensile load. Simulations were performed on a variety of fully solvated DNA sequences up to 30 base-pairs in length, and were conducted under both non-equilibrium and equilibrium conditions. Different stretched DNA structures are observed depending on whether pulling occurs from the 5' ends or 3' ends. Detailed analysis of these structures provides a direct structural explanation of the observed difference between 3' and 5' pulling. [Preview Abstract] |
Tuesday, March 17, 2009 3:30PM - 3:42PM |
L40.00006: Folding Kinetics of Riboswitch Transcriptional Terminators Benjamin Sauerwine, Michael Widom Riboswitches control the expression of genes in bacteria by halting gene transcription or allowing it to proceed based on the presence of ligands in solution. A key feature of every riboswitch is a transcriptional terminator in which the messenger RNA folds into a secondary structure with the stem-loop structure of a hairpin. Through kinetic Monte Carlo simulation we show that terminators have been naturally selected to fold with high reliability on the time-scale of gene transcription. This efficient folding behavior is preserved among two classes of riboswitch and among two species of bacteria. [Preview Abstract] |
Tuesday, March 17, 2009 3:42PM - 3:54PM |
L40.00007: First Principles Study of Nuclear Quadrupole Interactions in Single and Double Chain DNA and Solid Nucleobases T.P. Das, R.H. Pink, S.R. Badu, Archana Dubey, R.H. Scheicher, H.P. Saha, Lee Chow, M.B. Huang Nuclear Quadrupole Interactions (NQI) of $^{17}$O, $^{14}$N and $^{2}$H nuclei have been studied for free nucleobases and nucleobases in single strand and double strand DNA and in solid state. Our first-principles investigations were carried out using the Gaussian 2003 set of programs to implement the Hartree-Fock procedure combined with many-body effects included using many-body perturbation theory. As expected for NQI in general, many-body effects are found to be small. Results will be presented for the quadrupole coupling constants (e$^{2}$qQ) and asymmetry parameters ($\eta)$ for the nucleobases in the various environments. Trends in e$^{2}$qQ and $\eta $ in the different environments will be discussed. In the case of the solid nucleobases, comparisons will be made with available experimental data [1] for $^{17}$O nuclei.\\[3pt] [1] Gang Wu et al., J. Am. Chem. Soc. 124, 1768 (2002) [Preview Abstract] |
Tuesday, March 17, 2009 3:54PM - 4:06PM |
L40.00008: Optical control of DNA radio-sensitivity Ramin Abolfath We explore the manipulation of the radio-sensitivity of the DNA molecules driven by the spin blockade mechanism of diffusive free radicals. We propose a mechanism which uses the simultaneous application of circularly polarized light and an external magnetic field to control the polarization of the free radicals and create an $S=1$ electron-hole spin excitation (exciton) on DNA molecules. It allows us to manipulate and partially suppress the damage induced by ionizing radiation. We deploy an {\em ab-initio} molecular dynamics model to calculate the characteristic parameters of the light needed for optical transitions and investigate the effect of spin-injection on the formation of a free energy barrier in diffusion controlled chemical reaction pathways that controls radiation-induced DNA damage. As a specific example, we present the numerical results calculated for a nucleotide-base, e.g., Guanine, in the presence of an OH free radical. [Preview Abstract] |
Tuesday, March 17, 2009 4:06PM - 4:18PM |
L40.00009: Acetylated histone H3 increases nucleosome dissociation Marek Simon, Mridula Manohar, Jennifer Ottesen, Michael Poirier Chromatin's basic unit structure is the nucleosome, i.e. genomic DNA wrapped around a particular class of proteins -- histones -- which due to their physical hindrance, block vital biological processes, such as DNA repair, DNA replication, and RNA transcription. Histone post-translational modifications, which are known to exist \textit{in vivo}, are hypothesized to regulate these biological processes by directly altering DNA-histone interactions and thus nucleosome structure and stability. Using magnetic tweezers technique we studied the acetylation of histone H3 in the dyad region, i.e. at K115 and K122, on reconstituted arrays of nucleosomes under constant external force. Based on the measured increase in the probability of dissociation of modified nucleosomes, we infer that this double modification could facilitate histone chaperone mediated nucleosome disassembly \textit{in vivo}. [Preview Abstract] |
Tuesday, March 17, 2009 4:18PM - 4:30PM |
L40.00010: First Principles Study of Muonium Trapping and Associated Magnetic Hyperfine Interactions in Nucleobases in Single and Double Chain DNA and Solid Nucleobases S.R. Badu, R.H. Pink, Archana Dubey, R.H. Scheicher, H.P. Saha, K. Nagamine, E. Torikai, Lee Chow, M.B. Huang, T.P. Das The trapping of muonium (Mu) and muon hyperfine interactions (HFI) are studied for free nucleobases and nucleobases in single and double strand DNA and in solid nucleobases. For our investigations we have utilized the Hartree-Fock procedure with many-body effects included using many-body perturbation theory. Results for the muon magnetic contact and dipolar HFI will be presented for the various environments. The trends among the different environments is rather different from those for the nuclear quadrupole interactions in the corresponding systems because of the differences in geometry of the Mu trapping sites in the various systems. Quantitative comparison will be made between our theoretical results and experimentally measured\footnote{Penny L Hubbard et al., J. Phys. Chem. A108, 9302 (2004).} muon HFI properties in the solid nucleobases. [Preview Abstract] |
Tuesday, March 17, 2009 4:30PM - 4:42PM |
L40.00011: Modeling nucleic acid structure in the presence of single-stranded binding proteins Robert Forties, Ralf Bundschuh There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV, the RecA DNA repair protein in bacteria, and all proteins involved in mRNA splicing and translation. We extend the Vienna Package for quantitatively modeling the secondary structure of nucleic acids to include proteins which bind to unpaired portions of the nucleic acid. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously measured. This leaves the footprint and sequence dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid, and FRET distributions for fluorophores attached to the nucleic acid. [Preview Abstract] |
Tuesday, March 17, 2009 4:42PM - 4:54PM |
L40.00012: A theoretical investigation of the interconversion between B and Z-DNA using the Adaptively Biased and Steered Molecular Dynamics methods Mahmoud Moradi, Chistopher Roland, Volodymyr Babin, Celeste Sagui The transition between right-handed B-DNA and left-handed Z-DNA in an implicit solvent environment was investigated via the free energy landscape of DNA as a function of the collective variables of handedness and radius of gyration, using the recently developed Adaptively Biased Molecular Dynamics (ABMD) method. The ABMD method, which belongs to the general category of umbrella sampling methods with a time-dependent potential, allows for an efficient and accurate estimation of the free energy barriers associated with the transition, especially when combined with multiple-walker and umbrella correction runs. The ABMD results are compared to those obtained using the Steered Molecular Dynamics (SMD) method. The implication of all these free energy results on the microscopics of the B to Z-DNA transition is to be discussed. [Preview Abstract] |
Tuesday, March 17, 2009 4:54PM - 5:06PM |
L40.00013: End-monomer dynamics in semiflexible polymers Michael Hinczewski, Xaver Schlagberger, Michael Rubinstein, Oleg Krichevsky, Roland Netz Precise experimental observations over the last few years of end-monomer dynamics in the diffusion of double-stranded DNA have given conflicting results: one study indicated an unexpected Rouse-like scaling of the mean squared displacement (MSD) $\langle r^2(t) \rangle \sim t^{1/2}$ at intermediate times, corresponding to fluctuations at length scales larger than the persistence length but smaller than the coil size; another study claimed the more conventional Zimm scaling $\langle r^2(t)\rangle \sim t^{2/3}$ in the same time range. Spurred by this experimental controversy, we investigate the end-monomer dynamics of semiflexible polymers through Brownian hydrodynamic simulations, an improved dynamic mean-field theory, and a heuristic scaling argument [1]. Both theory and simulation point to a novel intermediate dynamical regime where the effective local exponent of the end-monomer MSD, $\alpha(t) = d\log\langle r^2(t) \rangle /d\log t$, drops below the Zimm value of 2/3 for sufficiently long chains. This deviation increases with chain length (though it does not reach the Rouse limit of 1/2), and is related to hydrodynamic effects in the slow crossover from dynamics on length scales smaller than the persistence length to dynamics on larger scales. [1] arXiv:0809.0667v1, Macromolecules {\it in press} (2008). [Preview Abstract] |
Tuesday, March 17, 2009 5:06PM - 5:18PM |
L40.00014: Hydration effect on optical property of a DNA fiber: A first-principles study Takenori Yamamoto, Tsuyoshi Uda, Takahisa Ohno We present a first-principles study for salvation effects on properties of a deoxyribonucleic acid (DNA) double helix fiber. The first-principles electronic structure and the molecular dynamics simulations reveal that the electronic structure of the DNA fiber is varied by the hydration amount and the deformation. The electrostatic interaction in the DNA fiber is screened by the hydration water. The screened electrostatic interaction determines the electronic structure of the DNA fiber, while the electronic structure of the water is determined by its polarized change as the result of the electrostatic response. We show that the optical conductivity is influenced by the hydration and the deformation, and that our findings agree with other theoretical results and experimental observations. In conclusion, we really stress that the solvation must be carefully taken account for simulating electronic structures and properties of DNA's. [Preview Abstract] |
Tuesday, March 17, 2009 5:18PM - 5:30PM |
L40.00015: Supercoil Formation During DNA Melting Mehmet Sayar, Baris Avsaroglu, Alkan Kabakcioglu Supercoil formation plays a key role in determining the structure-function relationship in DNA. Biological and technological processes, such as protein synthesis, polymerase chain reaction, and microarrays relys on separation of the two strands in DNA, which is coupled to the unwinding of the supercoiled structure. This problem has been studied theoretically via Peyrard-Bishop and Poland-Scheraga type models, which include a simple representation of the DNA structural properties. In recent years, computational models, which provide a more realtistic representaion of DNA molecule, have been used to study the melting behavior of short DNA chains. Here, we will present a new coarse-grained model of DNA which is capable of simulating sufficiently long DNA chains for studying the supercoil formation during melting, without sacrificing the local structural properties. Our coarse-grained model successfully reproduces the local geometry of the DNA molecule, such as the 3'-5' directionality, major-minor groove structure, and the helical pitch. We will present our initial results on the dynamics of supercoiling during DNA melting. [Preview Abstract] |
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