Showing papers on "Molecular models of DNA published in 2001"
TL;DR: A model in which topoisomerases introduce a sharp bend in DNA is designed and quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data.
Abstract: Type II DNA topoisomerases actively reduce the fractions of knotted and catenated circular DNA below thermodynamic equilibrium values. To explain this surprising finding, we designed a model in which topoisomerases introduce a sharp bend in DNA. Because the enzymes have a specific orientation relative to the bend, they act like Maxwell's demon, providing unidirectional strand passage. Quantitative analysis of the model by computer simulations proved that it can explain much of the experimental data. The required sharp DNA bend was demonstrated by a greatly increased cyclization of short DNA fragments from topoisomerase binding and by direct visualization with electron microscopy.
151 citations
01 Jan 2001
TL;DR: In this paper, the energy stored in a distorted Watson-Crick DNA model subjected to viscous low speed organic fluid loading is fonnulated and a proposal for matching of DNA sequential characteristics with respect to the nonlinear dynamical responses is outlined in order to reveal infonnation regarding DNA sequencing by means of a fluid-structure dynamical approach.
Abstract: The paper aims at extending, utilising and general ising 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 fonnulated. Numerical solutions based on the variational principle are presented for a linearized flow field as examples. Significant dynamical responses such as defonnation components and resultants are discussed. A proposal for matching of DNA sequential characteristics with respect to the nonlinear dynamical responses is outlined in order to reveal infonnation regarding DNA sequencing by means of a fluid-structure dynamical approach.
2 citations