Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session R44: Nucleic Acids: Structure, Function, Protein Interactions |
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Sponsoring Units: DBIO Chair: Xiangyun Qiu, Physics department, George Washington University Room: Hilton Baltimore Holiday Ballroom 1 |
Wednesday, March 20, 2013 2:30PM - 2:42PM |
R44.00001: Stretching DNA molecules on a flexible substrate, a polarization-dependent fluorescence microscopy study Ke Zhu, John Mele, Julia Budassi, Jonathon Sokolov DNA molecules absorbed and stretched onto surfaces can be used to analyze DNA structure by imaging fluorescence of labeled hybridization probes or enzymes. A recently proposed method for sequencing by electron microscopy requires either adsorbed single-stranded DNAs or untwisted double-stranded DNA. In this experiment, studies were performed on the adsorption of isolated DNA molecules to a flexible PDMS substrate, which permits continuous stretching, until breakage of the DNA molecules. Lambda and T4 DNAs (48.5 and 165.6 kilobase pairs, respectively) were absorbed onto PDMS out of solution by withdrawing a submerged substrate at a rate of 2mm/s, producing linear molecules deposited on the surface. Incident light polarization was varied and fluorescence emission intensity measured as a function of polarization angle and degree of stretching of the DNA. The stretching and breakage properties of lambda and T-4 DNA on the PDMS substrate were determined. The amount of stretching before breakage occurred was found to be up to 40{\%} relative to the as-deposited length. Supported by NSF-DMR MRSEC program. [Preview Abstract] |
Wednesday, March 20, 2013 2:42PM - 2:54PM |
R44.00002: Controlled enzymatic cutting of DNA molecules adsorbed on surfaces using soft lithography Alyssa Auerbach, Julia Budassi, Emily Shea, Ke Zhu, Jonathan Sokolov The enzyme DNase I was applied to adsorbed and aligned DNA molecules (Lamda, 48.5 kilobase pairs (kbp), and T4, 165.6 kbp), stretched linearly on a surface, by stamping with a polydimethylsiloxane (PDMS) grating. The DNAs were cut by the enzyme into separated, micron-sized segments along the length of the molecules at positions determined by the grating dimensions (3-20 microns). Ozone-treated PDMS stamps were coated with DNase I solutions and placed in contact with surface-adsorbed DNA molecules deposited on a 750 polymethylmethacrylate (PMMA) film spun-cast onto a silicon substrate. The stamps were applied under pressure for times up to 15 minutes at 37 C. The cutting was observed by fluorescence microscopy imaging of DNA labeled with YOYO dye. Cutting was found to be efficient despite the steric hindrance due to surface attachment of the molecules. Methods for detaching and separating the cut segments for sequencing applications will be discussed. [Preview Abstract] |
Wednesday, March 20, 2013 2:54PM - 3:06PM |
R44.00003: Localizing the critical point of random RNA secondary structures William Baez, Ralf Bundschuh Previous numerical studies have found that below the denaturation temperature random RNA secondary structures can exist in one of two phases: a strongly disordered, low-temperature glass phase and a weakly disordered, high-temperature molten phase. The probability of two bases pairing in these phases have been shown to scale with the distance between the two bases as -3/2 and -4/3 in the molten and glass phases, respectively. In this study, we characterize the scaling behavior of various sub-strand lengths within the molecule for a range of temperatures both far from and near the critical point. We anticipate that this approach allows to more accurately determine the critical point and to measure the critical exponents of the system right at the phase transition. [Preview Abstract] |
Wednesday, March 20, 2013 3:06PM - 3:18PM |
R44.00004: Self-assembly of virus particles: The role of genome Gonca Erdemci-Tandogan, Jef Wagner, Rudolf Podgornik, Roya Zandi A virus is an infectious agent that inserts its genetic material into the cell and hijacks the cell's machinery to reproduce. The simplest viruses are made of a protein shell (capsid) that protects its genome (DNA or RNA). Many plant and animal viruses can be assembled spontaneously from a solution of proteins and genetic material in different capsid shapes and sizes. This work focuses on the role of genome in the assembly of spherical RNA viruses. The RNA, a highly flexible polymer, is modeled by mean field approximations. Two RNA models are discussed: (i) A linear polymer model including a pairing affinity between RNA base pairs, and (ii) a branched polymer model. Polymer density and electrostatic potential profiles are obtained, and the relevant free energies are calculated from these profiles. The optimal length of the encapsidated chain is examined as a function of the model parameters. The osmotic pressure of the system is also discussed. [Preview Abstract] |
Wednesday, March 20, 2013 3:18PM - 3:30PM |
R44.00005: Automated building of three-dimensional RNA structures Yunjie Zhao, Zhou Gong, Yangyu Huang, Yi Xiao, Chen Zeng RNAs have been found to be involved in many biological processes. Difficulties of experimental determination of tertiary structures of RNA limit our understanding of their biological functions. Therefore, some computational methods of building tertiary structures of RNA have been proposed. However, current algorithms of RNA tertiary structure prediction give satisfactory accuracy only for RNA of small size and simple topology, and most are not fully automatic. Here, we present an automated and efficient program, 3dRNA. Since the organization of RNA structure is largely defined by topological constraints in the secondary structure as well as the tertiary contacts, we build the RNA tertiary structure from the smallest secondary elements (SSEs) by using a two-step procedure. We first assemble the SSEs into hairpins or duplexes and then into complete structure since the tertiary structures of hairpins and duplexes usually can be built with a high accuracy. In a benchmark test with known structures, 3dRNA can give predictions with reasonable accuracy for RNAs of larger size and complex topology. [Preview Abstract] |
Wednesday, March 20, 2013 3:30PM - 3:42PM |
R44.00006: Ion concentration dependent tRNA folding energy landscapes Rongzhong Li, Samuel Cho The RNA folding is highly dependent on the ionic conditions of its environment in the cell because the surrounding ions electrostatically screen the charged phosphates that line the RNA backbone.~Recent studies (Cho, Pincus, and Thirumalai, PNAS, 2007; Biyun, Cho, and Thirumalai, JACS, 2011) demonstrated that the coarse-grained model we use accurately captures the RNA folding mechanisms by incorporating a Debye-Huckel potential to screen the electrostatics. We compare the ion-concentration dependent tRNA folding mechanism to the classical thermodynamic melting profiles of Crothers and co-workers, and we observe excellent agreement. We also supported our findings by performing empirical force field MD simulations with CHARMM and AMBER, and we observe remarkably comparable qualitative similarities between the average base-base distances from simulations and the empirically measured base-stacking potentials from the well-known Turner's Rules.~ [Preview Abstract] |
Wednesday, March 20, 2013 3:42PM - 3:54PM |
R44.00007: Determination of counterion distribution around DNA coated nanoparticles (DNA-AuNP) by small angle X-ray scattering (SAXS) Sumit Kewalramani, CheukYui Leung, Jos Zwanikken, Robert Macfarlane, Monica Olvera de la Cruz, Chad Mirkin, Michael Bedzyk The interactions between DNA-Au nanoparticles (AuNP) and the surrounding cationic counterion layer critically determine the melting behavior of DNA duplexes on isolated DNA-AuNP and in crystalline assemblies of DNA-AuNPs. Also, the counterion layer is speculated to cause the enhanced stability of DNA-AuNPs against nuclease degradation, as compared to isolated DNAs. This makes DNA-AuNPs attractive for bio-diagnostic and therapeutic applications. To probe the ion cloud around DNA-AuNPs, we apply the isomorphous heavy ion replacement SAXS approach. Specifically, the SAXS measurements are carried out on DNA-AuNPS dispersed in a series of solutions that contain different monovalent ions (Na$^{\mathrm{+}}$, K$^{\mathrm{+}}$, Rb$^{\mathrm{+}}$ or Cs$^{\mathrm{+}})$. The combined analysis of all four intensity profiles makes it possible to extract, in a model-independent manner, the cation profile contribution $I_{cat}$ ($q)$ from the SAXS intensity that is averaged over the polydispersity of AuNPs. The $I_{cat}$ ($q)$ is found to be consistent with the cation dependent SAXS intensities that are derived on the basis of classical DFT calculations for the counterion distribution around DNA-AuNPs. [Preview Abstract] |
Wednesday, March 20, 2013 3:54PM - 4:06PM |
R44.00008: Ion Competition in Ordered DNA arrays in the Attractive Regime Xiangyun Qiu, John Giannini, Kurt Andresen Quantitative knowledge of electrostatic interactions is of fundamental importance for many classes of biomolecules and biological processes. Acquiring such knowledge is challenged by inherent complexities such as the long-range nature of electrostatic forces, the non-linear screening of ubiquitous ions, and the involvement of a large number of solvent molecules. Here we report our recent work to address some of the key questions by interrogating electrostatics-governed ordered nucleic acids arrays and bringing together a set of quantitative tools to elucidate the role of each of the electrostatic factors: ion, water, and charged surface. Specifically, we will present measurements and modeling of the spacings between DNA strands and the numbers of interstitial competing ions in the attractive regime. Our results indicate a linear relation between the partition of interstitial ions and the magnitude of inter-DNA attraction, which will be discussed in the context of current theories of electrostatic interactions. [Preview Abstract] |
Wednesday, March 20, 2013 4:06PM - 4:18PM |
R44.00009: Modeling spatial correlation of DNA deformations: Allosteric effects of DNA protein binding Xinliang Xu, Jianshu Cao We report a study of DNA deformations by a coarse grained mechanical model. Recent single molecule experimental studies show that when DNA molecule is deformed by its binding to a protein, the binding affinity of a second protein at distance $L$ away from the first binding site is altered. To explain this observation, the relaxation of deformation along the DNA chain is examined. Our method predicts a general exponentially decaying behavior for differenct deformation modes. As an example, inter-helical distance deformation is studied in details, and is found to decay at a previously unknown lengthscale of 10 base pairs as a result of the balance between inter and intra DNA strand energy. This lengthscale is in good agreement with the said single molecule experimental observation. This model of local deformation relaxation helps us better understand many important issues in DNA such as the enhanced flexibility of DNA at short lengthscales and DNA repair mechanism inside cells. [Preview Abstract] |
Wednesday, March 20, 2013 4:18PM - 4:30PM |
R44.00010: Molecular dynamics simulation of DNA base-pair opening by sharp bending Peiwen Cong, Liang Dai, Johan R.C. van der Maarel, Jie Yan Many biological processes require sharp bending of DNA. According to worm-like chain model, the bending energy dominates the free energy cost of those processes containing DNA loops shorter than 40 nm, such as DNA wrapping around histones, Lac repressor looping and virus DNA packaging . However, several recent experimental observations suggest that the WLC model s not applicable under tight bending conditions. In full atom molecular dynamics simulations, a double stranded, 20 base-pairs DNA fragment is forced to bend by an external spring. It is found that one or two AT-rich regions are disrupted for sufficiently small end-to-end distance. The disrupted DNA base-pairs separate and usually stack with the neighbouring base-pairs to form a defect. It is shown that these defects are more bendable than the bending rigidity of the duplex in the regular B-form. The simulation suggests a curvature dependent, non-harmonic bending elasticity of the DNA backbone is necessary to describe the DNA conformation under tight bending conditions. [Preview Abstract] |
Wednesday, March 20, 2013 4:30PM - 4:42PM |
R44.00011: Looping of anisotropic, short double-stranded DNA Harold Kim, Tung Le Bending of double-stranded DNA (dsDNA) is associated with fundamental biological processes such as genome packaging and gene regulation, and therefore studying sequence-dependent dsDNA bending is a key to understanding biological impact of DNA sequence beyond the genetic code. Average mechanical behavior of long dsDNA is well described by the wormlike chain model, but sequence-dependent anisotropic bendability and bendedness of dsDNA can in principle lead to abnormally high looping probability at short length scales. Here, we measured the looping probability density (J factor) and kinetics of dsDNA as a function of length and curvature using single-molecule FRET (F\"{o}rster Resonance Energy Transfer). For theoretical comparison, we calculated the J-factor using a discrete dinucleotide chain model, and also simulated it by Monte Carlo methods. We provide evidences that even when the intrinsic shape of dsDNA is accounted for, the wormlike chain model fails to describe looping dynamics of dsDNA below 200-bp length scale. [Preview Abstract] |
Wednesday, March 20, 2013 4:42PM - 4:54PM |
R44.00012: DNA looping by a ligase under nanoconfinement Maedeh Heidarpour-Roushan, Robert Riehn DNA looping is essential for the function and maintenance of genetic information. We have investigated the kinetic evolution of DNA loops (48500 bp) induced by T4 ligase inside a nanofabricated channel system with a channel cross-section of 100x100 nm2, and a few hundred microns channel length. We found that addition of the ligase profoundly alters the behavior of DNA. In particular, ligase acts to stabilize hairpin geometries in which the extended forward and backward arms of the hairpin scan past each other. From the linear density of DNA inside the channel, we deduce that the effective excluded volume vanishes upon addition of T4 ligase and ATP. We conclude that the two strands are effectively stapled together through a large number of weak bonds involving T4 ligase. [Preview Abstract] |
Wednesday, March 20, 2013 4:54PM - 5:06PM |
R44.00013: Loops determine the mechanical properties of mitotic chromosomes Yang Zhang, Dieter W. Heermann In mitosis, chromosomes undergo a condensation into highly compacted, rod-like objects. Many models have been put forward for the higher-order organization of mitotic chromosomes including radial loop and hierarchical folding models. Additionally, mechanical properties of mitotic chromosomes under different conditions were measured. However, the internal organization of mitotic chromosomes still remains unclear. Here we present a polymer model for mitotic chromosomes and show how chromatin loops play a major role for their mechanical properties. The key assumption of the model is the ability of the chromatin fibre to dynamically form loops with the help of binding proteins. Our results show that looping leads to a tight compaction and significantly increases the bending rigidity of chromosomes. Moreover, our qualitative prediction of the force elongation behaviour is close to experimental findings. This indicates that the internal structure of mitotic chromosomes is based on self-organization of the chromatin fibre. We also demonstrate how number and size of loops have a strong influence on the mechanical properties. We suggest that changes in the mechanical characteristics of chromosomes can be explained by an altered internal loop structure. [Preview Abstract] |
Wednesday, March 20, 2013 5:06PM - 5:18PM |
R44.00014: New insights into nucleosome unwrapping Razvan Chereji, Alexandre Morozov Eukaryotic genomes are organized into arrays of nucleosomes, in which stretches of 147 base-pairs (bp) of DNA are wrapped around octameric histones. Recently, a new approach for direct mapping of nucleosome centers at bp resolution was developed [Brogaard et al., Nature 486, 496-501 (2012)] and some intriguing results appeared. About 40\% of the inter-dyad distances are smaller than 147 bp, which imply massive nucleosome unwrapping, genome-wide, in vivo. The histogram of the inter-dyad distances presents small oscillations which indicate a step-wise unwrapping of the nucleosomal DNA from the histone. We present a statistical mechanics model for the nucleosome unwrapping, which is able to take into account sequence-dependent binding energies, sequence-independent potential barriers and wells, effective two-body interactions between the nucleosomes, competition between different species, cooperative-binding, and other important factors which dictate the nucleosome distribution along the DNA. We are able to reproduce the distribution of the inter-dyad distances, which cannot be obtained if there is no nucleosome unwrapping. The nucleosome unwrapping model can explain also the variable DNA accessibility and the nucleosome-induced cooperativity, which were observed experimentally. [Preview Abstract] |
Wednesday, March 20, 2013 5:18PM - 5:30PM |
R44.00015: Mechanisms for enhanced protein dissociation driven by nucleosomes Ralf Bundschuh, Cai Chen When a transcription factor binding site is located within a nucleosome, the DNA in the nucleosome has to unwrap in order for the transcription factor to bind. Thus, it is not surprising that the rate of transcription factor binding is slowed significantly in the presence of a nucleosome. The resulting change in transcription factor binding site occupancy has been known for quite a while as a mechanism for regulation of gene expression via chromatin structure. More surprisingly, recent single molecule experiments have pointed out that not only is the on-rate of transcription factors reduced by the presence of a nucleosome but also is the off-rate increased. There are two possible explanations short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) the nucleosome can change the equilibrium between binding at the specific binding site and nonspecific binding to the surrounding DNA or (ii) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding. We explicitly model both scenarios and find that the first mechanism cannot be reconciled with experimental findings. However, we show that the second mechanism can indeed explain increases in off-rate by a factor as high as $100$. [Preview Abstract] |
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