Erratum: “The probability analysis of opening of DNA” [J. Chem. Phys. 134, 115102 (2011)]

Srivastava, Shikha; Singh, Navin

doi:10.1063/1.3593196

Cited by 20 publications

(22 citation statements)

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“…Adenine-Thymine bps can be broken more easily and undergo larger stretching vibrations than Guanine-Cytosine bps [33,34]. Thus we set: D AT < D GC and b AT < b GC noticing that, with regard to their effective values, substantial variations have been reported depending both on the model and on the sequence properties [35,36,42].…”

Section: Hamiltonian Modelmentioning

confidence: 99%

J-factors of short DNA molecules

Zoli

2016

The Journal of Chemical Physics

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The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain end boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length (N) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.

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Section: Hamiltonian Modelmentioning

confidence: 99%

J-factors of short DNA molecules

Zoli

2016

The Journal of Chemical Physics

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“…Somewhat different sets of parameters have be used in other studies to test the (homogeneous) anharmonic PB model albeit without rotational degrees of freedom [27][28][29][30]. Morse parameters and harmonic force constants have been recently obtained also for RNA, fitting the PB model to the experimental melting temperatures [31].…”

Section: Model For Circular Dnamentioning

confidence: 99%

Helix untwisting and bubble formation in circular DNA

Zoli

2013

The Journal of Chemical Physics

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A recent experiment using fluorescence microscopy showed that double-stranded DNA fragments shorter than 100 base pairs loop with the probabilities higher by the factor of 10 2-10 6 than predicted by the worm-like chain (WLC) model [R. Vafabakhsh and T. Ha, Science 337, 1101(2012)]. Furthermore, the looping probabilities were found to be nearly independent of the loop size. The results signify a breakdown of the WLC model for DNA mechanics which works well on long length scales and calls for fundamental understanding for stressed DNA on shorter length scales. We develop an analytical, statistical mechanical model to investigate what emerges to the short DNA under a tight bending. A bending above a critical level initiates nucleation of a thermally induced bubble, which could be trapped for a long time, in contrast to the bubbles in both free and uniformly bent DNAs, which are either transient or unstable. The trapped bubble is none other than the previously hypothesized kink, which releases the bending energy more easily as the contour length decreases. It leads to tremendous enhancement of the cyclization probabilities, in a reasonable agreement with experiment. C 2015 AIP Publishing LLC. [http://dx.

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“…The trend of the results displayed for the homogeneous chains would not change by assuming different sets of parameter values also used in DNA models [24][25][26]. mark the free energy minima yielding the equilibrium < h > j * 's for the respective chains.…”

Section: Resultsmentioning

confidence: 99%

Short DNA persistence length in a mesoscopic helical model

Zoli¹

2018

EPL

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The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available to base pair fluctuations and derive the partition function. The apparent persistence lengths of a set of short chains have been computed as a function of the twist conformation both in the over-twisted and the untwisted regimes, whereby the equilibrium twist is selected by free energy minimization. The obtained values are significantly lower than those generally attributed to kilo-base long DNA. This points to an intrinsic helix flexibility at short length scales, arising from large fluctuational effects and local bending, in line with recent experimental indications. The interplay between helical untwisting and persistence length has been discussed for a heterogeneous fragment by weighing the effects of the sequence specificities through the non-linear stacking potential. 1The DNA double helical structure is stable enough to preserve genetic information encoded in the Watson-Crick paired bases and also loose enough to allow for those transient base pair (bp) openings [1] which make the code accessible to enzymes during the processes of replication, transcription and repair. At physiological temperatures DNA molecules fluctuate between a variety of random coil conformations in which even distant segments along the helical axis can be brought in close proximity [2]. This points to an inherent flexibility of the DNA chain which has been widely probed over the last twenty five years [3]. While these experiments demonstrate that stretch and twist elasticity are intertwined [4], they also call for models in which bp fluctuations and stacking interactions are considered as dependent on the specific twist conformation of the molecule. Modeling of the helix and its conformational states can be carried out at different levels of resolution ranging from all-atom simulations to continuous worm-like chain (WLC) models which simply treat DNA as a homogeneous and inextensible rod [5], not accounting for the interplay between twist and bp fluctuations. This may explain the shortcomings of the WLC model emerged in the analysis of the cyclization properties [6,7] at those short length scales in which the details of the bp interactions matter. In this regard, mechanical models such as the Dauxois-Peyrard-Bishop (DPB) model

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Erratum: “The probability analysis of opening of DNA” [J. Chem. Phys. 134, 115102 (2011)]

Cited by 20 publications

References 0 publications

J-factors of short DNA molecules

J-factors of short DNA molecules

Helix untwisting and bubble formation in circular DNA

Short DNA persistence length in a mesoscopic helical model

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