Twist-writhe partitioning in a coarse-grained DNA minicircle model

Sayar, Mehmet; Avşaroğlu, Barış; Kabakçıoğlu, Alkan

doi:10.1103/physreve.81.041916

Cited by 35 publications

(50 citation statements)

References 39 publications

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“…Bottom-up approaches have been used to study RNA nanostructures, 48 the response of DNA minicircles to supercoiling, 49,50 the behavior of B-DNA over a range of conditions, 51 binding of DNA to the nucleosome 52 and the properties of the resultant model as a function of parameterization. 53 Although systematically coarse-graining removes some of the arbitrary choices in designing a minimal model, there are drawbacks.…”

Section: Ab] [A][b]mentioning

confidence: 99%

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Ouldridge¹,

Louis²,

Doye³

2011

The Journal of Chemical Physics

450

697

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We explore in detail the structural, mechanical, and thermodynamic properties of a coarse-grained model of DNA similar to that recently introduced in a study of DNA nanotweezers [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Phys. Rev. Lett. 134, 178101 (2010)]. Effective interactions are used to represent chain connectivity, excluded volume, base stacking, and hydrogen bonding, naturally reproducing a range of DNA behavior. The model incorporates the specificity of Watson-Crick base pairing, but otherwise neglects sequence dependence of interaction strengths, resulting in an "average base" description of DNA. We quantify the relation to experiment of the thermodynamics of single-stranded stacking, duplex hybridization, and hairpin formation, as well as structural properties such as the persistence length of single strands and duplexes, and the elastic torsional and stretching moduli of double helices. We also explore the model's representation of more complex motifs involving dangling ends, bulged bases and internal loops, and the effect of stacking and fraying on the thermodynamics of the duplex formation transition.

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Section: Ab] [A][b]mentioning

confidence: 99%

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Ouldridge¹,

Louis²,

Doye³

2011

The Journal of Chemical Physics

450

697

View full text Add to dashboard Cite

show abstract

“…All these models involve classical effective potentials between beads, such as harmonic potentials for covalent bonds, and quadratic angle and dihedral potentials for bending and torsion. The effective non-linear potential chosen for mimicking hydrogen-bonding is either a Lennard-Jones [84,92,93,99] or a Morse one [89,90,94] (see Ref. [39] for an overview of these various coarse-grained models).…”

Section: Numerical Coarse-grained Models With Several Beads Per Nuclementioning

confidence: 99%

Physics of base-pairing dynamics in DNA

Manghi

Destainville

2016

Physics Reports

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As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque- driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain degrees of freedom can be integrated out, and the quasi- static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.Comment: Review Article, revised versio

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“…Other numerical works focus on the chain and internal dynamics with various levels of coarse-graining, using molecular dynamics [23][24][25][26] or Langevin dynamics simulations [27][28][29][30]. However, they failed to capture the μs time scale time due to their high level of precision, or they are limited to short 30-bp-long DNA [31].…”

Section: Introductionmentioning

confidence: 99%

Slow closure of denaturation bubbles in DNA: Twist matters

et al. 2013

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The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double helix is made of two interacting bead-spring freely rotating strands, with a nonzero torsional modulus in the duplex state, κ(φ)=200 to 300k(B)T. For DNAs of lengths N=40 to 100 base pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100μs are found. The bubble starts winding from both ends until it reaches a ≈10 bp metastable state due to the large elastic energy stored in the bubble. The final closure is limited by three competing mechanisms depending on κ(φ) and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this last temperature-activated mechanism, yielding a good quantitative agreement with the experiments.

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Twist-writhe partitioning in a coarse-grained DNA minicircle model

Cited by 35 publications

References 39 publications

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Physics of base-pairing dynamics in DNA

Slow closure of denaturation bubbles in DNA: Twist matters

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