Computer simulations of DNA stretching
Abstract In this chapter we will give short review of computer modelling/simulations of DNA manipulation as a complementary tool to current single molecule manipulation experiments in order to follow the impact on molecular structure during the manipulation experiments. As an example we report molecular dynamics simulations of a 22 base-pair DNA fragment in an explicit water solution with counter-ions to mimic a torsionally unconstrained single-molecule stretching experiment. Positions of the O5′ and O3′ atoms at one end of the 22-mer were fixed while an external linearly increasing tensile force was applied on the corresponding atoms at the other end. Changes in the intramolecular potentia…
Simple models for nonlinear states of double-helix DNA
Review type introduction is given to the simple modeling of DNA. Intrinsically simple modeling aims at understanding or explaining of some “core” phenomena, not giving any all-embracing model of the underlying system. As a consequence the amount of this type of models and their versions is large. Here we have restricted our contemplation to the most important lines in the path of theoretical understanding of DNA melting or denaturation which is one of the important phases occurring during DNAs replication and transcription processes. The model “line” initiated by Peyrard and Bishop shows the richness these simple models can have.
Solvating, manipulating, damaging, and repairing DNA in a computer
This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Internal Structure and Dynamics of the Decamer D(ATGCAGTCAG) 2 In Li + -H 2 O Solution: A molecular Dynamics Simulation Study
Molecular dynamics simulation of the decamer d(ATGCAGTCAG) 2 in aqueous solution, electroneutralized by Li + ions has been carried out. Emphasis is on the verification of the equilibrium conditions and the related structural and dynamical properties. Applicability of the kinetic part of Boltzmann's H function as a measure of thermodynamic equilibrium is tested. Overall structural stability has been confirmed by different RMSDs. Conformational and helicoidal parameters have been analyzed statistically and dynamically. Dynamical analysis reveals the existence of dynamical sub-states, which typically appear as abrupt changes from a mean level to another in the value of parameter. In statistica…
Molecular dynamics simulation of single DNA stretching reveals a novel structure
Abstract MD simulation, to closely mimic a torsionally unconstrained single-molecule stretching experiment of dsDNA, uncovers three distinct force regimes, characterized by fast and slow elongation regions with a transition regime in between, where the α and γ backbone torsion angles of the elongated double-stranded DNA find rapidly new stationary values. In the slow elongation regime DNA gradually looses its twist, collectively breaks all base-pair H-bonds and develops a remarkable base-stacked structure with the bases strongly tilted, forming a zipper-like stack on the major groove side, stabilized by the narrowing distance between the elongated strands, and by specific water interactions.