Probability distribution of bubble lengths in DNA

Details Probability distribution of bubble lengths in DNA Probability distribution of bubble lengths in DNA

2006-07-05

arxiv.org/abs/q-bio/0607009v2

Nano Lett., 7 (2), 307 -311, 2007

Biology

Quantitative Biology

Biomolecules

5 pages, 4 figures, accepted version. The distribution obtained from the Peyrard-Bishop-Dauxois model is now fitted and discus

Scientific paper

10.1021/nl062304a

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.

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