Showing papers on "Molecular models of DNA published in 2002"
TL;DR: General methods are presented for modeling and simulating DNA molecules with bound proteins on the macromolecular level, based on the wormlike chain model of long DNA molecules, which account for basic elements of protein binding effects on DNA local structure but remain computational tractable.
Abstract: General methods are presented for modeling and simulating DNA molecules with bound proteins on the macromolecular level. These new approaches are motivated by the need for accurate and affordable methods to simulate slow processes (on the millisecond time scale) in DNA/protein systems, such as the large-scale motions involved in the Hin-mediated inversion process. Our approaches, based on the wormlike chain model of long DNA molecules, introduce inhomogeneous potentials for DNA/protein complexes based on available atomic-level structures. Electrostatically, treat those DNA/protein complexes as sets of effective charges, optimized by our discrete surface charge optimization package, in which the charges are distributed on an excluded-volume surface that represents the macromolecular complex. We also introduce directional bending potentials as well as non-identical bead hydrodynamics algorithm to further mimic the inhomogeneous effects caused by protein binding. These models thus account for basic elements of protein binding effects on DNA local structure but remain computational tractable. To validate these models and methods, we reproduce various properties measured by both Monte Carlo methods and experiments. We then apply the developed models to study the Hin-mediated inversion system in long DNA. By simulating supercoiled, circular DNA with or without bound proteins, we observe significant effects of protein binding on global conformations and long-time dynamics of the DNA on the kilo basepair length.
40 citations
21 Oct 2002
TL;DR: In this paper, the authors investigated the assembly of G-wires by SFM, using different sequences described in the literature, and the assembled structures were adsorbed on mica and imaged by the SFM.
Abstract: G‐wires are DNA superstructures based on the intermolecular interactions of four Guanine bases. They allow the fabrication of structures reaching the micrometer scale using only short DNA oligonucleotides, what makes them potentially interesting for molecular nanotechnology. We investigated the assembly of G‐wires by SFM, using different sequences described in the literature. The assembled structures were adsorbed on mica and imaged by SFM. The influence of time and temperature of the growth was investigated, and the topology of the assemblies was studied.
9 citations
TL;DR: The techniques of optical and magnetic tweezers whereby external force can be applied to individual DNA molecules were used to assess the structural transitions of the DNA double helix under such conditions.
Abstract: Briefly discussed are experiments with single molecules, representing a novel trend in the biophysical study of DNA. The techniques of optical and magnetic tweezers whereby external force can be applied to individual DNA molecules were used to assess the structural transitions of the DNA double helix under such conditions. Discussed are the latest data on the dependence of the rate of complementary chain synthesis by DNA polymerase on the stretching of the template.
4 citations
22 Apr 2002
TL;DR: In this paper, the energy stored in a distorted Watson-Crick DNA model subjected to viscous, low-speed organic fluid loading is examined, and significant dynamical responses such as energy distribution, bending and twisting of DNA model under organic fluid excitations are discussed.
Abstract: The paper aims at extending, utilising and generalising research in nonlinear dynamics of (i) spiral/helicoidal structures, and (ii) viscous, low speed fluid to biomechanical DNA fluid-structure interaction. Employing a nonlinear helicoidal model, the energy stored in a distorted Watson-Crick DNA model subjected to viscous, low speed organic fluid loading is examined. An efficient recursive numerical scheme based on the variational principle is presented. Significant dynamical responses such as energy distribution, bending and twisting of DNA model under organic fluid excitations are discussed. Matching of DNA sequential characteristics with respect to the nonlinear dynamical responses is outlined in order to reveal information regarding DNA sequencing by means of a fluid-structure dynamical approach.
1 citations