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

Rieloff, Ellen LU ; Nunes, Sandra C C; Pais, Alberto A. C. C. and Skepö, Marie LU (2017) In ACS Omega 2(5). p.1915-1921
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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
ACS Omega
volume
2
issue
5
pages
7 pages
publisher
American Chemical Society (ACS)
external identifiers
  • scopus:85028998957
  • wos:000404727800020
ISSN
2470-1343
DOI
10.1021/acsomega.7b00323
language
English
LU publication?
yes
id
da522d3f-b668-4023-897b-2c8ec134d748
date added to LUP
2017-09-27 13:02:42
date last changed
2018-01-16 13:27:12
@article{da522d3f-b668-4023-897b-2c8ec134d748,
  abstract     = {<p>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.</p>},
  author       = {Rieloff, Ellen and Nunes, Sandra C C and Pais, Alberto A. C. C. and Skepö, Marie},
  issn         = {2470-1343},
  language     = {eng},
  month        = {05},
  number       = {5},
  pages        = {1915--1921},
  publisher    = {American Chemical Society (ACS)},
  series       = {ACS Omega},
  title        = {Structural Characterization of Bubbles Formed in DNA Melting : A Monte Carlo Simulation Study},
  url          = {http://dx.doi.org/10.1021/acsomega.7b00323},
  volume       = {2},
  year         = {2017},
}