Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study

Ellen Rieloff, Sandra C C Nunes, Alberto A. C. C. Pais, Marie Skepö

Research output: Contribution to journalArticlepeer-review

Abstract

Bubbles in DNA are involved in many important biological processes. In this work, a coarse-grained model is used for characterizing bubbles formed in DNA melting. The model resorts only to electrostatic interactions at the Debye-Hückel level, in combination with a short-ranged attractive interaction within a base pair. In spite of also omitting atomistic details, the model is able to capture experimentally established trends in persistence length and radius of gyration. By applying it on different systems, it is possible to conclude that there is a minimum size for stable bubbles, in the interval between 12 and 20 bp, which agrees well with previously published experimental findings. Simulated scattering data distinguishes between different bubbles and detects conformational changes in the melting process. Therefore, SAXS is regarded as useful for bubble formation studies, while simulations provide a molecular understanding.

Original languageEnglish
Pages (from-to)1915-1921
Number of pages7
JournalACS Omega
Volume2
Issue number5
DOIs
Publication statusPublished - 2017 May 31

Subject classification (UKÄ)

  • Biological Sciences

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