Bubble Nucleation and Cooperativity in DNA Melting

Ares, Saúl; Voulgarakis, Nikolaos K.; Rasmussen, Kim Ø.; Bishop, A. R.

doi:10.1103/physrevlett.94.035504

Cited by 122 publications

(186 citation statements)

References 19 publications

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“…One could of course introduce base pair dependent parameters in the zipper model, but a fixed set of such parameters does not represent different melting curves well (and the same applies to the nearest-neighbor model) [25]. Other models such as the Peyrard-BishopDauxois model do better in this respect [25,26], but it is not obvious how to couple the elastic energy to them. In the interest of keeping the number of fitting parameters to a minimum, we therefore choose average and in the zipper model.…”

Section: B Modelmentioning

confidence: 99%

Critical Torque for Kink Formation in Double-Stranded DNA

Wang

Tseng

et al. 2011

Phys. Rev. X

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We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque c at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find c ¼ 31 pN Â nm. This critical torque corresponds to a characteristic energy scale ð =2Þ c ¼ 12 kT room relevant for molecular biology processes associated with DNA bending.

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Section: B Modelmentioning

confidence: 99%

Critical Torque for Kink Formation in Double-Stranded DNA

Wang

Tseng

et al. 2011

Phys. Rev. X

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“…[12] for a number of review papers on the topic. In this case, the applications refer to nonlinear waveguide arrays [13] and photorefractive crystals [14], to Bose-Einstein condensates in deep optical lattices [15], to the local denaturation of the DNA double strand [16], and to micro-mechanical cantilever arrays [17] among many others.…”

Section: Introductionmentioning

confidence: 99%

Asymptotic calculation of discrete non-linear wave interactions

Kevrekidis¹,

Khare²,

Saxena³

et al. 2007

Mathematics and Computers in Simulation

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Abstract. We illustrate how to compute asymptotic interactions between discrete solitary waves of dispersive equations, using the approach proposed by Manton [Nucl. Phys. B 150, 397 (1979)]. We also discuss the complications arising due to discreteness and showcase the application of the method in nonlinear Schrödinger, as well as in Klein-Gordon lattices, finding excellent agreement with direct numerical computations.

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“…However, subsequent studies using more efficient methods for the calculation of bubble statistics in the Peyrard-Bishop-Dauxois (PBD) model [12,13] did not confirm the above non-local scenario, and pointed to more localized effects. See [14,15] for recent developments on this interesting problem.Many of these and other relevant issues have been investigated by employing the PBD model [4] (see below). The model phenomenology has been profusely analyzed by means of various analytical and numerical techniques: transfer integral calculations, Monte Carlo simulations, molecular dynamics, and Langevin dynamics, and the results have been found to properly describe experiments on the melting transition [16], pre-melting bubbles [15], etc.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

“…The model phenomenology has been profusely analyzed by means of various analytical and numerical techniques: transfer integral calculations, Monte Carlo simulations, molecular dynamics, and Langevin dynamics, and the results have been found to properly describe experiments on the melting transition [16], pre-melting bubbles [15], etc. Let us caution that under certain circumstances, torsional effects (absent in the PBD model) should be included to properly account for some of the described phenomenology [7,10,17].…”

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Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA

2008

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A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous samples, for which some implications, so far overlooked, of an analogy with equilibrium wetting transitions are highlighted. This analogy implies that the order-parameter, asymptotically, exhibits a second order transition even if it may be very abrupt for non-zero values of the stiffness parameter. Not surprisingly, we also find that for heterogeneous DNA, within this model the largest bubbles in the pre-melting stage appear in adenine-thymine rich regions, while we suggest the possibility of some sort of not strictly local effects owing to the merging of bubbles.PACS numbers: 02.50.-r,64.60.Ht 87.14.GgThe DNA thermal melting transition (also called denaturation, coiling, or un-zipping) occurs when, above a certain critical temperature, the double-stranded DNA molecule unravels into two separate coils, while for smaller temperatures (pre-melting stage) only localized openings or bubbles exist [1]. This phase transition is of importance for DNA duplication and transcription, and many studies have scrutinized its nature (whether first or second order), trying to pin down the relevant traits of the rich phenomenology experimentally observed (a nonexhaustive list of references is [2,3,4,5,6,7]). Moreover, it has been suggested that the dynamics of a DNA molecule in its pre-melting stage may play a role in its own transcription initiation. Indeed, bubbles are determined by sequence specificity and they have been reported to occur with high probability in the neighborhood of the, functionally relevant, transcription start site (TSS) and near other regulatory sites, facilitating further microbiological activity [7,8,9].This relation between thermal dynamics and biological functionality has been claimed to be borne out by experimental data from real promoter DNA sequences and is supported by results from a theoretical model (see below) [8,9]. Even if this might differ from biological, protein mediated processes, studies of thermal properties of the DNA by itself are a first step forward in understanding more complex situations [1] (see [10] for a different view).Let us mention some observations in this context, which have been the object of recent analyses. Even though one would expect that adenine-thymine (AT-)rich regions should be more prone to sustain bubbles than guanine-cytosine-(GC-)rich ones (as AT pairs bind the two strands more weakly than GC ones [1]), counterintuitive situations in which this is not the case have been reported [7,11]. In the same vein, the dependence of bubble formation on the specific base-pair sequence was reported to be highly nonlocal: Upon mutation of two AT base-pairs into two (stronger) GC base-pairs near the TSS, rendering a specific promoter sequence completely inactive for transcription, the opening profiles of the original sequence and its mutant var...

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Bubble Nucleation and Cooperativity in DNA Melting

Cited by 122 publications

References 19 publications

Critical Torque for Kink Formation in Double-Stranded DNA

Critical Torque for Kink Formation in Double-Stranded DNA

Asymptotic calculation of discrete non-linear wave interactions

Simplified Langevin approach to the Peyrard-Bishop-Dauxois model of DNA

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