Molecular dynamics study of DNA oligomers under angled pulling

Naserian-Nik, AM; Tahani, Masoud; Karttunen, Mikko

doi:10.1039/c3ra45604h

Cited by 5 publications

(3 citation statements)

References 61 publications

(69 reference statements)

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“…On the other hand, molecular dynamics (MD) simulations, both fully atomistic − and coarse-grained (mesoscopic), − have provided a number of valuable insights into the mechanical properties of nucleic acids, including, most notably, their sequence dependence. − The specific choice of the level of granularity of the model depends on the problem at hand. Several MD simulation studies of nucleic acids at this level of description have focused on the entire force–extension curve, including the plateau region. ,,,− Properties of the overstretching transition, including the plateau force, were found to be sequence dependent, in agreement with the experiments. , In general, these models rely on empirical potential functions (force fields) that describe interactions between atoms or beads through a combination of bond stretching and bending and torsional and electrostatic potentials, to name a few, where each potential has multiple fitted parameters, making the total number of parameters as many as a hundred for some general-purpose biomolecular force fields. , An advantage of these models, compared to fully phenomenological models such as the variants of the WLC, is that they can provide a microscopic, including atomic level, interpretation of the experiment.…”

Section: Introductionmentioning

confidence: 99%

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

Afanasyev

Onufriev

2022

J. Chem. Theory Comput.

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We propose an approach to help interpret polymer force–extension curves that exhibit plateau regimes. When coupled to a bead–spring dynamic model, the approach accurately reproduces a variety of experimental force–extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force–extension curves. The applicability of the approach to the force–extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force–extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.

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Section: Introductionmentioning

confidence: 99%

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

Afanasyev

Onufriev

2022

J. Chem. Theory Comput.

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“…On the other hand, molecular dynamics models, fully atomistic [28][29][30][31][32][33][34][35][36][37][38][39][40] or coarse-grained (mesoscopic), [41][42][43][44][45][46] provide different insight into the mechanics of the nucleic acids. The specific choice of the level of granularity of the models depends on the problem at hand.…”

Section: Introductionmentioning

confidence: 99%

Stretching of long double-stranded DNA and RNA described by the same model

Afanasyev

Onufriev

2022

Preprint

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We propose a bead-spring model that accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA, and negatively supercoiled DNA. A key feature of the model is a specific non-convex energy function of the spring. We provide an algorithm for obtaining five required parameters of the model from experimental force-extension curves. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases.

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“…Molecular Dynamics (MD) is a useful method to simultaneously analyze the mechanical and thermal behaviors of material at an atomic level by numerically solving the Newton's equations of motion and has been successfully applied in medical research, 12 material research, 13 physical and chemical research, 14 and even in material machining. 15 In recent years, thanks to the technical progresses in EDM, especially that the machining dimension range of EDM can be in the nanometer scale, MD simulations on nano EDM have been made possible in theory and practice.…”

Section: Introductionmentioning

confidence: 99%