Distribution of Bubble Lengths in DNA

Distribution of Bubble Lengths in DNA

The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine−cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard−Bishop−Dauxois model at 310 K. An analytical description of the obtained distribution in the whole regime investigated...

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Veröffentlicht in:Nano letters 2007-02, Vol.7 (2), p.307-311
Hauptverfasser: Ares, S, Kalosakas, G
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Sprache:eng
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Base Pairing
DNA - chemistry
Models, Molecular
Monte Carlo Method
Nanotechnology - methods
Nucleic Acid Conformation
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Kalosakas, G
description The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine−cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard−Bishop−Dauxois model at 310 K. An analytical description of the obtained distribution in the whole regime investigated, i.e., up to bubble widths of the order of tens of nanometers, is available. We find that the decay lengths and characteristic exponents of this distribution show two distinct regimes as a function of GC content. The observed distribution is attributed to the anharmonic interactions within base pairs. The results are discussed in the framework of the Poland−Scheraga and the Peyrard−Bishop (with linear instead of nonlinear stacking interaction) models.
doi_str_mv 10.1021/nl062304a
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subjects Base Pairing
DNA - chemistry
Models, Molecular
Monte Carlo Method
Nanotechnology - methods
Nucleic Acid Conformation
title Distribution of Bubble Lengths in DNA
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