Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session H22: Nucleic Acids |
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Sponsoring Units: DBP Chair: Robert Austin, Princeton University Room: LACC 409B |
Tuesday, March 22, 2005 8:00AM - 8:12AM |
H22.00001: RNA Interference Induced by the Cationic Lipid Delivery of siRNA Nathan Bouxsein, Christopher McAllister, Kai Ewert, Charles Samuel, Cyrus Safinya Recent discoveries demonstrate that the introduction of synthetically prepared duplexes of 19-21 bp short interfering RNAs (siRNA) into mammalian cells results in the cleavage of target mRNA leading to post transcriptional gene silencing [1]. Our work focuses on the cationic-lipid (CL) mediated delivery of siRNA into mammalian cell lines in an approach similar to CL based gene delivery [2]. Co-transfection of a target and a non-target reporter plasmid followed by the CL delivery of a sequence specific siRNA allows us to probe the silencing efficiency (SE) of the target plasmid relative to non-specific silencing of both plasmids. We have created a phase diagram for SE as a function of the complex membrane charge density and as a function of the CL:siRNA charge ratio. X-ray diffraction was performed to probe the structure of the complexes at points along the phase diagram. Funding provided by NIH AI-12520, AI-20611 and GM-59288. [1] Elbashir et. al., Nature, 411 494-498 (2001) [2] Ewert et. al., Curr. Med. Chem. 11 133-149 (2004) [Preview Abstract] |
Tuesday, March 22, 2005 8:12AM - 8:24AM |
H22.00002: Theory of Bubble Nucleation and Cooperativity in DNA melting Nikos Voulgarkis, Saul Ares, Kim Rasmussen, Alan Bishop The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles and the possibility of a two states transition are studied. Excellent agreement with the experimental data is obtained. [Preview Abstract] |
Tuesday, March 22, 2005 8:24AM - 8:36AM |
H22.00003: Effects of sequence disorder on DNA looping and cyclization Yuri Popov, Alexei Tkachenko We study the effects of random sequencing in a DNA molecule on the probability of formation of the closed circles (the J- factor). The effects of both the sequence-dependent curvature and the sequence-dependent bending rigidity along the chain are explored theoretically. We demonstrate that random curvature gives rise to the renormalization of the persistence length in the disorder-free results of Shimada and Yamakawa (1984) for the dependence of the J-factor on the length of the molecule. On the other hand, random bending rigidity leads to an increase in the J-factor for short molecule lengths, possibly explaining the discrepancy between the earlier theoretical and the recent experimental results. [Preview Abstract] |
Tuesday, March 22, 2005 8:36AM - 8:48AM |
H22.00004: Large N transfer matrix models of DNA melting Vassili Ivanov, Giovanni Zocchi We introduce a new parameterization of the Yeramian [1] transfer matrix in the Poland - Scheraga model of DNA melting. The transfer matrixes of our model correspond to the overlapping nearest neighbor dimers along the DNA. As a result base pairing and stacking can be explicitly treated as separate degrees of freedom, and the interplay between pairing and stacking mimics the geometrical constraints in the real molecule, which is different from the Zimm - Bragg parameterization used in the other papers. The model is exactly solvable in the homogeneous thermodynamic limit, and we calculate critical exponent and all observables without use of the grand partition function. As is well known, models of this class have a first order or continuous phase transition at the temperature of complete strand separation depending on the value of the exponent of the bubble entropy. [1] E. Yeramian, et al, Biopolymers \textbf{30}, 481 (1991). [Preview Abstract] |
Tuesday, March 22, 2005 8:48AM - 9:00AM |
H22.00005: Mechanical unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF Douglas E. Smith, Gregory J. Gemmen, Ronald Sim, Karl A. Haushalter, Pu-Chun Ke, James T. Kadonaga Nucleosomes were assembled on lambda DNA using core histones, the histone chaperone NAP-1, and ATP-dependent chromatin assembly and remodeling factor (ACF). The mechanical properties of these complexes were interrogated with optical tweezers. Abrupt events releasing 55 to 95 base pairs of DNA, attributable to the unraveling of individual nucleosomes, were frequently observed. This finding is comparable to previous results on nucleosomes assembled by salt dialysis on repeating positioning elements but differs from findings on complexes formed by exposing single DNA molecules to Xenopus extracts. Unraveling events occurred over a wide range of forces, which we attribute to variation in nucleosome stability with DNA sequence. The mean unraveling force decreased from 31 to 24 pN with NaCl increasing from 5 to 100 mM. Elasticity fits yielded an average persistence length of 18 nm and stretch modulus of 770 pN in 100 mM NaCl. Spontaneous DNA re-wrapping events were occasionally observed during force relaxation. [Preview Abstract] |
Tuesday, March 22, 2005 9:00AM - 9:12AM |
H22.00006: Brownian dynamics simulation of the nucleosome chirality - the wrapping direction of DNA on the histone octamer Peng-Ye Wang, Wei Li, Shuo-Xing Dou In eukaryote nucleosome, DNA wraps around a histone octamer in a left-handed way. We study the process of chirality formation of nucleosome with Brownian dynamics simulation. We model the histone octamer with a quantitatively adjustable chirality: left-handed, right-handed or non-chiral, and simulate the dynamical wrapping process of a DNA molecule on it. We find that the chirality of a nucleosome formed is strongly dependent on that of the histone octamer, and different chiralities of the histone octamer induce its different rotation directions in the wrapping process of DNA. In addition, a very weak chirality of the histone octamer is quite enough for sustaining the correct chirality of the nucleosome formed. We also show that the chirality of a nucleosome may be broken at elevated temperature. [Preview Abstract] |
Tuesday, March 22, 2005 9:12AM - 9:24AM |
H22.00007: Force dependence of the opening rate of a single DNA hairpin-loop Jeungphill Hanne, Mukta Singh-Zocchi, Giovanni Zocchi We directly measure the opening rate of a single DNA hairpin- loop (beacon) for different mechanical forces by optically monitoring the displacement of a $\mu $m sized bead tethered to a surface by a single DNA beacon (20 base pairs loop). We thus obtain a spectrum of rates, depending on mechanical forces (the range of 0-10pN), in contrast to FRET measurements which obtain only the zero force rate. In addition, our method gives access to long time scales. [Preview Abstract] |
Tuesday, March 22, 2005 9:24AM - 9:36AM |
H22.00008: Applied stress and the thermal denaturation of DNA Tatiana Kuriabova, Joseph Rudnick Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We discuss the effects on this transition of a stretching force applied to opposite ends of one of the DNA strands, including full consideration of the consequences of excluded volume, the analysis of which is greatly simplified in this case. We also discuss the interplay of thermal denaturation and force-generated separation when the tension is generated by a force at the end of one of the duplexed strands and an equal and opposite force applied to the other end of the second strand. [Preview Abstract] |
Tuesday, March 22, 2005 9:36AM - 9:48AM |
H22.00009: Molecular mechanical studies of hydrated B-DNAs: conformation and counterions Charles Cleveland, Uzi Landman We examine through molecular mechanics the fully hydrated DNA duplex 5'{\-}d(AAACCTAAACCTAATAT){\-}3' and a similar structure where four sugars near the G-C base pairs are modified by adding isopropyl groups which intrude into the minor groove. Attention is paid to the distributions of water molecules and sodium counterions and the conformation of the duplexes. Apart from the effects of the chemical modification we are interested in the degree and kinds of correspondence between temporal variations of counterion positions and variations in the duplex conformation as expressed through structural parameters such as the width of the major and minor grooves, base-pair parameters such as roll, twist, and buckle, and such. [Preview Abstract] |
Tuesday, March 22, 2005 9:48AM - 10:00AM |
H22.00010: Optical conductivity of wet DNA Arnd Hubsch, Robert G. Endres, Daniel L. Cox, Rajiv R.P. Singh DNA has attracted much attention in view of its possible application to nano-devices, both for device scaffolding and assembly as well as its potential as a molecular electronics component. Despite extensive efforts, however, the experimental and theoretical understandings of the conductivity of DNA are still rather controversial. Motivated by recent experiments [1] we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with order 200 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks. [1] E. Helgren, A. Omerzu, G. Gruner, D. Mihailovic, R. Podgornik, and H. Grimm, cond-mat/0111299. [Preview Abstract] |
Tuesday, March 22, 2005 10:00AM - 10:12AM |
H22.00011: Low Temperature Intrinsic Paramagnetism in B-DNA Sawako Nakamae, Maximilien Cazayous, Alain Sacuto, Philippe Monod, Dominique Durand, Helene Bouchiat The electrical conduction through DNA remains controversial spanning from insulator, semi-conductor, metal to proximity induced superconductor (1). Such variance illustrates the complexity of interactions between DNA and their environment, $i.e.$, buffer solutions, electrodes, as well as more internal factors such as molecular structures and base-pair sequences. Magnetization is an alternative, non-invasive mean to probe the intrinsic electronic properties of matter, as the measurements do not require any electrode attachments. We have explored the magnetization combined with simultaneous structural measurements via micro-Raman on $\lambda $-DNA molecules to study the interplay between the molecular structures (A- and B-DNA) and the magnetic property. Unexpectedly, in the B-DNA state, the magnetization of $\lambda $-DNA molecules exhibits paramagnetic behavior below 20 K that is non-linear in applied magnetic field whereas molecules in A-DNA state remain diamagnetic down to 2 K. We discuss the possible orbital origin of this magnetism and its relation to the existence of long-range coherent transport in B-DNA at low temperature. References: (1) See, for example, R. G. Endres, D. L. Cox and R. R. P. Singh, \textit{Reviews of Modern Physics} 76, 195-214 (2004). [Preview Abstract] |
Tuesday, March 22, 2005 10:12AM - 10:24AM |
H22.00012: Experimental investigation of the influence of DNA structure on its the charge transport properties V. Soghomonian, B. Hartzell, Hong Chen, J.J. Heremans We present experimental results demonstrating the influence of DNA structure on its electronic properties. Comparative current-voltage measurements for the random-sequence lambda-DNA and modified lambda-DNA molecules are studied. Modifications include the introduction of various numbers of nicks in the phosphate backbone of a strand, influence of intercalated metal ions, as well as comparative measurements between double and single stranded molecules. In fact, single stranded DNA, or double stranded DNA with a large number of nicks (greater than 3 per molecule), result in current values barely above that of an open device. Moreover, the resulting I-V curve shapes reflect the influence of, and hint at, an integral relationship between the native structure of DNA with its stacked base pairs and the molecule's ability to transport charge. Understanding the charge transport properties of this biomolecule is important if DNA is to be utilized as an electronic material for applications in nanotechnology (NSF DMR 0103034). [Preview Abstract] |
Tuesday, March 22, 2005 10:24AM - 10:36AM |
H22.00013: Single state tight binding model for transport through DNA H. Mehrez, M.P. Anantram We develop a new approach to derive the DNA tight binding parameters. Our model is based on {\it first principles} calculations and can be applied to various DNA configurations with different sequences. These parameters are used to model charge transport through finite length DNA. We investigate (i) the rigor of reducing the full DNA Hamiltonian to a single HOMO-LUMO state to represent charge transport in the vicinity of valence-conduction band (ii) DNA helix symmetry effects on the hopping parameters (iii) on-site energies and tight binding parameters dependence on the DNA sequence. We find that transport characteristics through PolyG-PolyC and PolyA-PolyT can be represented within HOMO-LUMO states. However transmission coefficient spectrum position shifts in energy and is substantially reduced for thymine. This effect can be corrected within $2^{nd}$ order time independent perturbation theory. Inter-strand charge transport has also been analyzed and it is found to be strongly asymmetric in PolyG-PolyC in the vicinity of the HOMO state. This is attributed to asymmetric hopping parameters between 5'G$\rightarrow$5'C and 3'G$\rightarrow$3'C. Finally, we have determined on-site energies and inter-bases couplings for DNA structures with different sequences. We find that these parameters have long range dependence as well as helix directional dependence. Hence tight binding model for such structures is not simple. Our derived representation depend strongly on the DNA sequence. [Preview Abstract] |
Tuesday, March 22, 2005 10:36AM - 10:48AM |
H22.00014: First-principles Study of Muon and Muonium in A- and B-form DNA E. Torikai, R.H. Scheicher, T.P. Das, F.L. Pratt, K. Nagamine We have carried out a systematic first-principles study of muon ($\mu^+$) and muonium ($\mu^+ e^-$) adducts in A--form and B--form DNA. All potential trapping sites in the four bases ADE, CYT, GUA, and THY were considered. Our results indicate that the difference in structural geometry between A-- and B--form DNA can lead to substantial deviations in the hyperfine fields at the $\mu^+$ sites. This could have important implications for the interpretation of Muon Spin Relaxation measurements that have shown evidence for an enhanced electron mobility in A--form DNA, but implicitly assume a negligible difference in the magnitude of the hyperfine fields at the trapped $\mu^+$ site between A-- and B--form DNA. [Preview Abstract] |
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H22.00015: Disorder in DNA-Linked Gold Nanoparticle Assemblies Nolan Harris, Ching-Hwa Kiang We report experimental observations of the effects of disorder on the phase behavior of DNA-linked nanoparticle networks. Variation in DNA linker lengths results in different melting temperatures, and hence stabilities, of DNA-linked nanoparticle assemblies. We discovered an unusual trend in the melting temperatures, resulting from the introduction of linker DNA which produced unequal DNA duplex lengths between particles. Comparison with DNA thermodynamics proves that such an anomaly does not exist for free DNA duplex melting, and suggests the influence of disorder on the collective behavior of DNA-linked nanoparticle assemblies. This disorder, brought about by the presence of two duplexes of different length and energy between each particle pair lowers the overall stability of the network formed.\\~\\ 1. C.-H.\ Kiang, ``Phase Transition of DNA-Linked Gold Nanoparticles,'' {\em Physica A} {\bf 321} (2003) 164--169.\\ 2. N.\ C.\ Harris and C.\ H.\ Kiang, ``Disorder in DNA-Linked Gold Nanoparticle Assemblies,'' {\em submitted} (2004). [Preview Abstract] |
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H22.00016: A Systematic Study of Single-stranded DNA Electrophoresis in Photopolymerized Crosslinked Polyacrylamide Gels Roger Lo, Victor Ugaz In this paper, we present a systematic investigation of mobility, diffusion, and dispersion in crosslinked polyacrylamide gels through parallel use of an automated DNA sequencer and a microfabricated electrophoresis device with integrated on-chip electrodes, heaters, and temperature sensors. DNA separations are conducted using the same sample, gel formulations, and operating conditions in both platforms. The microfabricated electrophoresis chip make it possible to collect a complete set of diffusion and dispersion data within about one hour, while it takes several days to finish the same work using a traditional sequencer under the same experimental conditions. By comparing data collected from these two platforms, we can isolate key parameters governing separation performance in both systems. These experimental results are compared with reptation theory to extract information on the gel structure and also predict achievable separation resolution under various operating conditions. We also investigate the effects of gel composition and polymerization chemistry and find that these photopolymerized crosslinked polyacrylamide gels provide good separation resolution at relatively low electric field strengths (10-20 V/cm). This makes it possible to customize the microfabricated electrophoresis chip for microdevice-based applications according to desired separation performance. [Preview Abstract] |
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