Impact of Loop Statistics on the Thermodynamics of RNA Folding

Einert, Thomas R.; Näger, Paul M.; Orland, Henri; Netz, Roland R.

doi:10.1103/physrevlett.101.048103

Cited by 22 publications

(38 citation statements)

References 18 publications

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“…[16] we explicitly introduced, as a partial cure for this difficulty, the multibranched configurations shown in Table I. However, since loop statistics turn out to have a deep impact on the thermodynamics of RNA folding (as has been clearly pointed out in a nice paper by Einert and coworkers [30]), we can conclude that special cautions are in order for the interpretation of our results in terms of real RNA properties.…”

Section: The Bethe Approximationmentioning

confidence: 83%

Chemically controlled unfolding of a RNA-like polymer model

Buzano

Pretti

2012

Phys. Rev. E

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We consider a lattice polymer model of the two-tolerant type (i.e., a random walk allowed to visit lattice bonds at most twice), in which doubly visited bonds yield an attractive energy term (pairing energy). Such a model has been previously proposed as a rough, nonspecific description of the RNA folding mechanism. Indeed, the model predicts, besides the usual theta collapse, an extra transition to a low-temperature fully paired state. In the current work, we propose an extension of the model, in which a "micromolecular" chemical species can bind the polymer and locally forbid segment pairing. We investigate equilibrium thermodynamics in the grand-canonical picture, at the level of a Bethe approximation, which is, a refined mean-field technique, equivalent to the exact solution on a random-regular graph. The general trend we observe is that expected from the mechanism implemented in the model (increasing micromolecule concentration favors unfolding and lowers the transition temperature), but the resulting phase diagram turns out to be remarkably interesting and rich.

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Section: The Bethe Approximationmentioning

confidence: 83%

Chemically controlled unfolding of a RNA-like polymer model

Buzano

Pretti

2012

Phys. Rev. E

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“…The energy landscape is flat because pairing energies are sequence averaged. The Fokker-Planck equation for the centre position reads [20], renormalised value in the presence of an external stretching force (c = 1.85) [38,39], self-avoiding and mutually avoiding loops (c = 2.12) [21], and the maximal allowed value for RNA with pseudoknots and hairpins (c = 2.49) [40]. 12 and x 0 = 1.…”

Section: Meeting Position Pdfmentioning

confidence: 99%

Loop exponent in DNA bubble dynamics

Kaiser¹,

Novotný²

2014

J. Phys. A: Math. Theor.

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Abstract. Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting time and meeting position probability distributions are derived from the solutions. Probability distribution functions reflect the value of the loop exponent of the entropic interaction. Our results extend previous results which concentrated mainly on the tails of the probability distribution functions and open a way to determining the strength of the entropic interaction experimentally which has been a matter of recent discussions. Using numerical integration, we also discuss the influence of the finite size of a DNA chain on the bubble dynamics. Analogous results are obtained also for the case of subdiffusive dynamics of a DNA bubble in a heteropolymer, revealing highly universal asymptotics of meeting time and position probability functions.

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“…These recursions have been derived in several different contexts, e.g. force induced RNA denaturations [10], the investigate of loop entropy dependence [7], the analysis of FRET signals in the presence of single-stranded binding proteins [9], as well as in mathematical studies of RNA panhandle-like structures [2,13].…”

Section: Recursions Of Z Vw [D]: V and W Are Externalmentioning

confidence: 99%

“…in atom force microscopy or export through a small pore) [10,23,11]. It also plays a role for the effect of loop energy parameters [7].…”

Section: Introductionmentioning

confidence: 99%

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

Backofen

Fricke

Marz

et al. 2013

Lecture Notes in Computer Science

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Abstract. Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium therefore provides useful information on the overall shape of the molecule can provide insights into the interplay of its functional domains. Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between arbitrary nucleotides can be computed in polynomial time by means of dynamic programming. A naive implementation would yield recursions with a very high time complexity of O(n 11 ). Although we were able to reduce this to O(n 6 ) for many practical applications a further reduction seems difficult. We conclude, therefore, that sampling approaches, which are much easier to implement, are also theoretically favorable for most real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules.

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Impact of Loop Statistics on the Thermodynamics of RNA Folding

Cited by 22 publications

References 18 publications

Chemically controlled unfolding of a RNA-like polymer model

Chemically controlled unfolding of a RNA-like polymer model

Loop exponent in DNA bubble dynamics

Distribution of Graph-Distances in Boltzmann Ensembles of RNA Secondary Structures

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