Structural Characterization of Bubbles Formed in DNA Melting : A Monte Carlo Simulation Study
(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
- Rieloff, Ellen LU ; Nunes, Sandra C C ; Pais, Alberto A. C. C. and Skepö, Marie LU
- organization
- publishing date
- 2017-05-31
- type
- Contribution to journal
- publication status
- published
- subject
- in
- ACS Omega
- volume
- 2
- issue
- 5
- pages
- 7 pages
- publisher
- The American Chemical Society (ACS)
- external identifiers
-
- scopus:85028998957
- wos:000404727800020
- pmid:30023650
- 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
- 2024-09-16 09:06:53
@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 = {{The 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}}, doi = {{10.1021/acsomega.7b00323}}, volume = {{2}}, year = {{2017}}, }