Dynamics of a bubble formed in double-stranded DNA

Srivastava, Shikha; Singh, Yashwant

doi:10.1209/0295-5075/85/38001

Cited by 15 publications

(10 citation statements)

References 38 publications

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“…Simple models, e.g, Poland Scheraga (PS) model [9] or Peyrard-Bishop-Dauxious (PBD) model [10][11][12] have described some of the essential macroscopic features of the meting profile of dsDNA quite effectively and predicted that the force-induced melting transition is a first order transition [14][15][16]. However, semimicroscopic information about the opening such as whether a dsDNA opens from the end or interior of the chain, distribution of partially opened regions in the form of bubbles in the chain [12,13,[17][18][19][20], are some of the intriguing issues in these studies. Moreover, in all SMFS experiments, the experimental setup puts an extra constraint on the ends of the chain, which makes force-induced melting different from the thermal melting.…”

Section: Introductionmentioning

confidence: 99%

The probability analysis of opening of DNA

Srivastava

Singh

2011

The Journal of Chemical Physics

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We have studied the separation of a double stranded DNA (dsDNA), which is driven by either the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force-induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends are free.

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Section: Introductionmentioning

confidence: 99%

The probability analysis of opening of DNA

Srivastava

Singh

2011

The Journal of Chemical Physics

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“…But strand dynamics is expected to be dominant at least for long DNAs and large bubbles, since for a flexible chain of length N the Rouse diffusion time scales like N 2 . (iii) Other models fit well the experimental autocorrelation function [9,16,17], but with the relaxation time as a fitting parameter, which does not shed light on the origin of such large times.…”

Section: Introductionmentioning

confidence: 87%

Strand diffusion-limited closure of denaturation bubbles in DNA

Dasanna¹,

Destainville²,

Palmeri³

et al. 2012

EPL

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The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semiflexible interacting single strands (ssDNA) and a bending modulus which depends on the base-pair state, with double-strand DNA (dsDNA) segments being 50 times stiffer than ssDNA ones. For DNA lengths from N = 20 to 100 base-pairs (bp) and initial bubble sizes of N − 6 bp, long closure times of 0.1 to 4 µs are found, following a scaling law in N 2.4 . The bubble starts to close by a fast zipping which stops when the bubble reaches a highly bent metastable state of length around 10 bp. The limiting final step to complete closure is controlled by the dsDNA "arms" rotational diffusion, with closure occurring once they are nearly aligned. The central role of chain bending, which cannot be accounted for in one-dimensional models, is thus illuminated.

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“…It has recently regained interest with the development of new experimental tools that allow for the direct observation of the dynamics of a single DNA molecule [7,8]. On the theoretical side, various methods have been used to study different aspects of the breathing process [9,10], and to investigate the interaction of the DNA with binding proteins: the master equation approach [11,12], a stochastic Gillespie scheme [13], the Fokker-Planck equation approach based on the Poland-Scheraga free energy function [5,[14][15][16], and stochastic dynamic simulations based on the Dauxios-Peyrard-Bishop model [17,18]. Specifically, the thermally-induced denaturation problem has been recently studied by mapping it onto a quantum Coulomb problem [19,20].…”

Section: Introductionmentioning

confidence: 99%

“…Using the BFP method, we derive and solve differential equations for the Laplace transforms of various Brownian functionals. This is in contrast to the standard Fokker-Planck treatment, which yields the distribution function to obtain a bubble of a given size at a given time [14][15][16]18]. Utilizing the PD approach, we can calculate the distribution functions of interest by splitting a representative path of the dynamics into parts, and then considering the weight of each part separately.…”

Section: Introductionmentioning

confidence: 99%

DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals

Bandyopadhyay¹,

Gupta²,

Segal³

2011

Phys. Rev. E

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We investigate DNA breathing dynamics by suggesting and examining several Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base pairs. The walk takes place on the Poland-Scheraga free-energy landscape. We suggest several probability distribution functions that characterize the breathing process, and adopt the recently studied backward Fokker-Planck method and the path decomposition method as elegant and flexible tools for deriving these distributions. In particular, for a bubble of an initial size x₀, we derive analytical expressions for (i) the distribution P(t{f}|x₀) of the first-passage time t{f}, characterizing the bubble lifetime, (ii) the distribution P(A|x₀) of the area A until the first-passage time, providing information about the effective reactivity of the bubble to processes within the DNA, (iii) the distribution P(M) of the maximum bubble size M attained before the first-passage time, and (iv) the joint probability distribution P(M,t{m}) of the maximum bubble size M and the time t{m} of its occurrence before the first-passage time. These distributions are analyzed in the limit of small and large bubble sizes. We supplement our analytical predictions with direct numericalsimulations of the related Langevin equation, and obtain a very good agreement in the appropriate limits. The nontrivial scaling behavior of the various quantities analyzed here can, in principle, be explored experimentally.

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Dynamics of a bubble formed in double-stranded DNA

Cited by 15 publications

References 38 publications

The probability analysis of opening of DNA

The probability analysis of opening of DNA

Strand diffusion-limited closure of denaturation bubbles in DNA

DNA breathing dynamics: Analytic results for distribution functions of relevant Brownian functionals

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