Topic
Molecular models of DNA
About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.
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11 Jul 2018
TL;DR: In this article, a non-linear model for DNA denaturation is presented, where the double-strands DNA interact via a realistic generalized Morse potential that reproduces well the features of the real interaction, as well as the used DNA model and that of Peyrard and Bishop.
Abstract: In this paper, we present a non-linear model for DNA denaturation. We assume that the double-strands DNA interact via a realistic generalized Morse potential that reproduces well the features of the real interaction, as well as the used DNA model and that of Peyrard and Bishop. Using the Transfer Matrix Method , based on the resolution of a Schrodinger equation, we first determine exactly their solution, which are found to be bound states . Second, from an exact expression of the ground state, we compute the denaturation temperature and the free energy density, in terms of the potential parameters. Then, we calculate the contact probability, which is the probability to find the double-strands at a (finite) distance apart. The main conclusion is that, the present analytical study reveals that the generalized Morse potential is a good candidate for the study of DNA denaturation.
TL;DR: In this paper, a method of process DNA-based process management for significant model project is proposed to solve the problem of "two command line" existing in the major model project management at present, and the two-level structure of the process DNA double-strand is analyzed.
Abstract: To solve the problem of “two command line” existing in the significant model project management at present, this paper proposes a method of process DNA-based process management for significant model project. First, the technology process and management process of significant model project are analyzed. Second, the process DNA double-strand of significant model project is constructed employing the elements of technology and management as building blocks; and also, the two-level structure of the process DNA double-strand is analyzed. Third, the process DNA model of significant model project is established and the related formal definitions are given.
02 Aug 2016
TL;DR: In this opinion article, specificity and accuracy of these molecular techniques can be enhanced by considering both parallel and anti-parallel hybridization of DNA.
Abstract: Many fundamental molecular techniques (PCR, Microarray, Southern and northern hybridization, siRNA, CRISPR/Cas9 etc,) developed so far shows errors. I wish to highlight these molecular techniques are developed on basis of Watson-Crick DNA model, ignoring the concept of parallel stranded DNA. Through this opinion article I wish to highlight specificity and accuracy of these molecular techniques can be enhanced by considering both parallel and anti-parallel hybridization of DNA. Hopefully my views will also solve issue of irreproducibility in life science research.
01 Jan 1998
TL;DR: In this article, the authors studied the site juxtaposition process in supercoiled DNA and showed that the site alignment is a slow process, and that the times of juxtaposition are in the range of ms even for highly supercoiling DNA, about two orders of magnitude higher than the relaxation times of writhe and radius of gyration for the same molecules.
Abstract: Thermal motions in supercoiled DNA are studied by Brownian dynamics (BD) simulations with a focus on the site juxtaposition process. It had been shown in the last decade that the BD approach is capable of describing actual times of large-scale DNA motion. The bead model of DNA used here accounts for bending and torsional elasticity as well as the electrostatic repulsion among DNA segments. The hydrodynamic interaction among the beads of the model chain and the aqueous solution is incorporated through the Rotne-Prager tensor. All simulations were performed for the sodium ion concentration of 0.01 M. We first showed, to test our BD procedure, that the same distributions of equilibrium conformational properties are obtained as by Monte Carlo simulations for the corresponding DNA model. The BD simulations also predict with accuracy published experimental values of the diffusion coefficients of supercoiled DNA. To describe the rate of conformational changes, we also calculated the autocorrelation functions for the writhe and radius of gyration for the supercoiled molecules. The rate of site juxtaposition was then studied for DNA molecules up to 3000 bp in length. We find that site juxtaposition is a very slow process: although accelerated by a factor of more than 100 by DNA supercoiling, the times of juxtaposition are in the range of ms even for highly supercoiled DNA, about two orders of magnitude higher than the relaxation times of writhe and the radius of gyration for the same molecules. By inspecting successive simulated conformations of supercoiled DNA, we conclude that slithering of opposing segments of the interwound superhelix is not an efficient mechanism to accomplish site juxtaposition, at least for conditions of low salt concentration. Instead, transient distortions of the interwound superhelix, followed by continuous reshaping of the molecule, contribute more significantly to site juxtaposition kinetics. # 1998 Academic Press
TL;DR: Collective coordinate method is used to explain a previously observed numerical evidence that breathers placed far from defects are difficult to trap, and the motional effect of RNA-polymerase is investigated.
Abstract: Previous numerical investigations of a one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with realistic parameters obtained from experiments. Furthermore, collective coordinate method is used to explain a previously observed numerical evidence that breathers placed far from defects are difficult to trap, and the motional effect of RNA-polymerase is investigated.