Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session P31: Biopolymers: Molecules, Solutions and Networks I |
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Sponsoring Units: DPOLY DBP Chair: John Crocker, University of Pennsylvania Room: LACC 503 |
Wednesday, March 23, 2005 11:15AM - 11:51AM |
P31.00001: Nonlinear elasticity of semiflexible polymer networks Invited Speaker: Networks of filamentous proteins play a crucial role in cell mechanics. These cytoskeletal networks, together with various crosslinking and other associated proteins largely determine the (visco)elastic response of cells. Such biopolymers have also provided new insights into basic aspects of polymer physics. In contrast with conventional polymer materials, the response of these networks is highly non-linear, and their rheological properties can be tuned with small changes in density and local network connectivity. We discuss recent theoretical and experimental efforts to understand these essential materials of the cell. [Preview Abstract] |
Wednesday, March 23, 2005 11:51AM - 12:03PM |
P31.00002: RNA gels with negative Poisson ratio Amir Ahsan, Joseph Rudnick, Robijn Bruinsma We present a simple model for the elastic properties of very large single-stranded RNA molecules linked by partial complementary pairing, such as a viral RNA genome in solution. It shown that the sign of Poisson's Ratio is determined by the convexity of the force-extension curve of single-stranded RNA. The implications of negative Poisson Ratio's for viral genome encapsidation will be discussed. [Preview Abstract] |
Wednesday, March 23, 2005 12:03PM - 12:15PM |
P31.00003: DNA intercalation by ethidium bromide: A quantitative binding study using DNA stretching and force-induced melting Mark C. Williams, Ioana Vladescu, Micah McCauley, Ioulia Rouzina The interactions between single DNA molecules and the non- covalent binding agent ethidium bromide are investigated using an optical tweezers instrument and the effects of this intercalator on the structure and mechanical stability of DNA molecules are quantitatively analyzed using our model of force- induced melting. The DNA force-extension cycles in the presence and absence of drug are recorded. It is found that the drug binds preferentially to double-stranded DNA and stabilizes the double helix. There is clear evidence of the force induced melting transition at low concentrations of drug, while at higher concentrations the drug is able to prevent the melting transition. The DNA contour length is obtained as a function of ligand concentration directly from the stretching curves. From this data we obtain the complete ethidium bromide dsDNA binding isotherm, which is used to find the binding constant and the binding site size of the intercalator. Out data also allows us to quantify directly the effect of ethidium bromide on the free energy of the helix-coil transition in dsDNA. This single molecule study brings new insights into the molecular mechanisms which drive drug-DNA complex formation. [Preview Abstract] |
Wednesday, March 23, 2005 12:15PM - 12:27PM |
P31.00004: Stretching DNA by a Constant Field Yuko Hori, Ashok Prasad, Jane' Kondev We consider the problem of stretching DNA by a constant field, such as an electric field or a hydrodynamic flow field. We obtain analytical expressions for the elongation of DNA under both weak and strong applied fields, in two and three dimensions. In the weak field limit we consider the effect of self-avoidance, which leads to a 9-fold enhancement of the average end-to-end distance over the result obtained when self-avoidance is ignored in two dimensions, and 3-fold increase in three dimensions. In the strong stretching regime we obtain the exact force-extension relation by mapping the problem to the Schr\"{o}dinger equation for a simple harmonic oscillator in a time dependent potential. We use our theoretical results to comment on the experiment of Maier {\em et al.} \footnote{B. Maier, U. Seifert, and J. O. R\"{a}dler, {\it Europhys. Lett.}, {\bf 60}, 622 (2002).} on DNA adsorbed on a lipid bilayer in the presence of an in-plane electric field. In particular, we find that their estimate for the effective charge density of the DNA molecule, made on the basis of an approximate theory, requires significant corrections in light of our calculations. This work was supported by the NSF through grants DMR-9984471 and DMR-0403997. JK is a Cottrell Scholar of Research Corporation. [Preview Abstract] |
Wednesday, March 23, 2005 12:27PM - 12:39PM |
P31.00005: Beyond Wormlike Chain: An effective theory of mesoscale DNA mechanics Philip Nelson, Paul Wiggins, Rob Phillips The wormlike chain model has come to dominate physical discussions of DNA conformation, due in part to its spectacular success in modeling the force-extension of single molecules. This model rests upon an assumption of linear bending elasticity in a rod-like polymer chain. But we show that force-extension relations are actually rather insensitive to the details of the stress-strain relation, and in particular do not test the linear-elasticity hypothesis. A renormalization-group flow toward the linear-elastic model hides deviations from linear elasticity on length scales larger than a few helical turns. Our results can be seen as validating the wormlike chain model for the long-scale (small curvature) regime of DNA mechanics, but many important biological processes such as DNA looping operate on shorter scales. We will show how recent experiments on DNA cyclization, and DNA contour analysis by scanning force microscopy, imply a stress-strain relation on intermediate length scales that is quite different from the simple linear form [cond-mat/0409003, Phys Rev E in press]. This revision of DNA mechanics has implications for the structure and dynamics of DNA loops essential in gene regulation. [Preview Abstract] |
Wednesday, March 23, 2005 12:39PM - 12:51PM |
P31.00006: Semiflexible Chain Networks Formed via Self-Assembly of Beta-Hairpin Molecules Bulent Ozbas, Darrin Pochan, Karthikan Rajagopal, Joel Schneider We present experimental results from a de novo designed oligopeptide that intermolecularly self-assembles into rigid hydrogel networks after an intramolecular folding event. The effect of ionic strength and beta hairpin peptide strand length on beta-sheet formation, self-assembly and resultant rheological properties were studied. The peptide molecules are locally amphiphilic with two linear strands of alternating hydrophobic valine and hydrophilic lysine amino acids flanking a central turn sequence. The beta-sheet formation of 24, 20, 16 and 12 amino acid long beta-hairpin molecules were studied by CD spectroscopy. The network properties and the nanostructure of the hydrogels were studied by rheology, TEM and SANS. The hydrogel network is composed of semiflexible fibrillar assemblies with viscoelastic behavior that follows the theoretical prediction for heavily crosslinked,semi-flexible polymer networks. SANS results show that the cross-sectional diameter of the fibrils, and thus, the bending modulus of the chains can be varied by changing the number of amino acids of strands of the molecules. Rheological measurements reveal that rigidity, creep and relaxation behavior of the hydrogels vary with the magnitude of stimulus and with the cross-section diameter of the chains. [Preview Abstract] |
Wednesday, March 23, 2005 12:51PM - 1:03PM |
P31.00007: The Rheological Properties of the Biopolymers in Synovial Fluid Wendy E. Krause, Rebecca R. Klossner, Julie Wetsch, Katherine M. N. Oates, Ralph H. Colby The polyelectrolyte hyaluronic acid (HA, hyaluronan), its interactions with anti-inflammatory drugs and other biopolymers, and its role in synovial fluid are being studied. We are investigating the rheological properties of sodium hyaluronate (NaHA) solutions and an experimental model of synovial fluid (comprised of NaHA, and the plasma proteins albumin and $\gamma $-globulins). Steady shear measurements on bovine synovial fluid and the synovial fluid model indicate that the fluids are highly viscoeleastic and rheopectic (stress increases with time under steady shear). In addition, the influence of anti-inflammatory agents on these solutions is being explored. Initial results indicate that D-penicillamine and hydroxychloroquine affect the rheology of the synovial fluid model and its components. The potential implications of these results will be discussed. [Preview Abstract] |
Wednesday, March 23, 2005 1:03PM - 1:15PM |
P31.00008: The nonlinear elasticity of alpha helical polypeptides: Analytical and Monte Carlo studies Buddhapriya Chakrabarti, Alex Levine We study a minimal extension of the worm-like chain model to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending modulus. Using this model we analytically compute the extensional compliance of an alpha-helix under tensile stress, the bending compliance of the molecule under externally imposed torques, and the nonlinear interaction of such torques and forces on the molecule. We find that, due to coupling of the ``internal'' secondary structure variables to the conformational degrees of freedom of the polymer, the molecule has a highly nonlinear response to applied stress and bending torques. In particular we demonstrate a sharp lengthening transition under applied force and a buckling transition under applied torque. We use perturbative calculations and a mean field analysis to obtain these results. We also carry out Monte Carlo simulations of this model. The numerical results agree well with the mean-field and perturbative calculations where they are expected to do so. The Monte Carlo simulations allow us to examine the response of the chain to large forces and torques where the perturbative approaches fail. In addition we extend our mean-field analysis by studying the fluctuation dominated regime at the force-induced denaturation transition. [Preview Abstract] |
Wednesday, March 23, 2005 1:15PM - 1:27PM |
P31.00009: Persistency of single-stranded DNA: the interplay between base sequences and base stacking Bae-Yeun Ha, Anirban Sain, Jeff Z.Y. Chen The chain persistency of single-stranded (ss) DNA at a high-salt limit mainly arises from the so called base-stacking interaction between consecutive bases along the strand; stacking is appreciable only for purine-purine (e.g., $A$-$A$) and purine- pyrimidine stacks (e.g., $A$-$T$), stiffening the strand, but is negligible for pyrimidine stacks ({\i.e.}, $T$-$T$, $T$-$C$, and $C$-$C$). We develop an exactly-solvable model for describing the stacking-induced persistency of heterogeneous ssDNA. Using this, we study the interplay between the heterogeneity of sequences and base stacking in determining the persistency. Our results demonstrate how the sequence information can influence the conformational properties of ssDNA. [Preview Abstract] |
Wednesday, March 23, 2005 1:27PM - 1:39PM |
P31.00010: Unzipping DNA from the condensed globule state--effects of unraveling Pui-Man Lam We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force F$_{c}$ and the number of unzipped monomers M goes as M$\sim $(F$_{c}$-F)$^{-3}$, for both the homogeneous and heterogeneous double stranded DNA sequence. This is different from the case of unzipping from an extended coil state in which the number of unzipped monomers M goes as M$\sim $( F$_{c}$-F)$^{\chi }$, where the exponent $\chi $ is either 1 or 2 depending on whether the double stranded DNA sequence is homogeneous or heterogeneous respectively. In the case of unzipping at constant extension, we find that for a double stranded DNA with a very large number N of base pairs, the force remains almost constant as a function of the extension, before the unraveling transition, at which the force drops abruptly to zero. Right at the unraveling transition, the number of base pairs remaining in the condensed globule state is still very large and goes as N$^{3/4}$, in agreement with theoretical predictions of the unraveling transition of polymers stretched by an external force. [Preview Abstract] |
Wednesday, March 23, 2005 1:39PM - 1:51PM |
P31.00011: Distance measurement along DNA molecules using fluorecent quantum dots Helmut Strey To create and design better micro- and nanofluidic devices, we need to understand how macromolecules behave when squeezed by lateral barriers to create pseudo-two-dimensional confinement. We present experiments in which we visualize DNA molecules of varying sizes (2 kbp - 50 kbp) trapped in 10 micrometer wide slits, the slit height varying from the radius of gyration of the unconfined molecule (micrometer) down to 25 nm (half the persistence length of DNA). We present data on the diffusion coefficient and electrophoretic mobility (no electroosmotic flow) of SYBR-gold labeled DNA molecules as a function of slit height. Simultaneously, we have assessed the DNA conformation by examining molecules that are end-labeled with differently colored fluorescent quantum dots. By determining the distance between labels, we measure directly the end-to-end distance - a conformational measure much discussed but rarely measured. Using the same approach but turning the problem around, we determined if contour length can be estimated from visualization experiments. The answer to this question becomes important when the distance between specific binding sites on the DNA backbone must be measured. One such application, for example, is the determination of haplotypes (genetic variability due to blocks of single nucleotide polymorphisms (SNP)) in diploid individuals. [Preview Abstract] |
Wednesday, March 23, 2005 1:51PM - 2:03PM |
P31.00012: AFM Imaging of F-actin Network Formation on a photopolymer surface Taiji Ikawa, Osamu Watanabe, Youli Li, Cyrus R. Safinya We investigated the network formation of cytoskeltal filamentous (F-) actin in the presence of divalent cations by atomic force microscopy using a novel protein immobilization technique. The F-actin network was immobilized on the surface of a unique nonionic photopolymer containing azo-dyes (azopolymer), which upon photo-irradiation deforms along the contour of the proteins thus physically immobilizes them. Two-dimensional F-actin networks were formed and immobilized by spotting F-actin solutions on the azopolymer surface, which was then irradiated using an array of blue light emitting diodes. The structure of the F-actin network, which consists of multiple X-, Y-, T-shaped junctions, was influenced by the concentration of the divalent cations in the spotting solution. We observed that the angle between two crossing F-actins at a junction decreases with increasing concentration of divalent cations. Above a certain ionic concentration, the cross-linked networks of F-actin transform into close-packed parallel rafts and bundles. The results show promise in the fabrication of two-dimensional aligned F-actin sheets. [Preview Abstract] |
Wednesday, March 23, 2005 2:03PM - 2:15PM |
P31.00013: Microtubule Bundling and Shape Transitions Daniel Needleman, Miguel Ojeda-Lopez, Uri Raviv, Kai Ewert, Janya Jones, Herbert Miller, Leslie Wilson, Cyrus Safinya Microtubules (MTs) are hollow cylindrical polymers composed of heterodimers of the protein tubulin that align end-to-end in the MT wall, forming linear protofilaments that interact laterally. Placing MTs under osmotic pressure causes them to reversibly buckle to a noncircular shape and pack into rectangular bundles at a critical osmotic pressure; further increases in pressure continue to distort MTs elastically. At higher osmotic pressures stressing polymers may be forced into the MT lumen causing the MTs to revert to a circle cross-section and pack into hexagonal bundles. This SAXRD-osmotic stress study provides a probe of the inter-protofilament bond strength and gives insight into the mechanisms by which microtubule associated proteins and the cancer chemotherapeutic drug Taxol stabilize MTs. We present further measurements of the mechanical properties of MT walls, MT-MT interactions, and the entry of polymers into the microtubule lumen. Supported by NSF DMR- 0203755, NIH GM-59288 and NS-13560, and CTS-0103516. SSRL is supported by the U.S. DOE. [Preview Abstract] |
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P31.00014: Higher Order Assembly of Microtubules by Counter-ions Daniel Needleman, Miguel Ojeda-Lopez, Uri Raviv, Herbert Miller, Leslie Wilson, Cyrus Safinya Cellular factors tightly regulate the architecture of bundles of filamentous cytoskeletal proteins, giving rise to assemblies with distinct morphologies and physical properties in vivo, but it is unclear how the microscopic interactions between filaments result in the observed structures. We study a model system consisting of microtubules (MTs) and multivalent cations, and demonstrate the formation of distinct bundle phases. We have characterized the structure of these self-assemblies of MTs from the nanoscale to the mesoscale using synchrotron x-ray scattering and diffraction, video enhanced DIC and fluorescence microscopy, and electron microscopy. Tightly packed hexagonal bundles with controllable diameters are observed for large tri-, tetra-, and pentavalent counterions. Unexpectedly, in the presence of small divalent cations, we have discovered a living necklace bundle phase, comprised of dynamical assemblies of MT nematic membranes with linear, branched, and loop topologies. Supported by NSF DMR- 0203755, NIH GM-59288 and NS-13560, and CTS-0103516. SSRL is supported by the U.S. DOE. [Preview Abstract] |
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