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Equilibrium melting probabilities of a DNA molecule with a defect : An exact solution of the Poland-Scheraga model

Genthon, Arthur ; Dvirnas, Albertas LU and Ambjörnsson, Tobias LU (2023) In Journal of Chemical Physics 159(14).
Abstract

In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson-Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland-Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct... (More)

In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson-Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland-Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct importance, for instance, for studies where fluorophore-quencher pairs are used for studying single basepair fluctuations of designed DNA molecules.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
159
issue
14
article number
145102
pages
12 pages
publisher
American Institute of Physics (AIP)
external identifiers
  • pmid:37815110
  • scopus:85174848477
ISSN
0021-9606
DOI
10.1063/5.0168915
language
English
LU publication?
yes
id
6debfed5-2e3c-4869-8aab-008221a61577
date added to LUP
2024-01-12 08:37:26
date last changed
2024-04-27 04:04:44
@article{6debfed5-2e3c-4869-8aab-008221a61577,
  abstract     = {{<p>In this study we derive analytically the equilibrium melting probabilities for basepairs of a DNA molecule with a defect site. We assume that the defect is characterized by a change in the Watson-Crick basepair energy of the defect basepair, and in the associated two stacking energies for the defect, as compared to the remaining parts of the DNA. The defect site could, for instance, occur due to DNA basepair mismatching, cross-linking, or by the chemical modifications when attaching fluorescent labels, such as fluorescent-quencher pairs, to DNA. Our exact solution of the Poland-Scheraga model for DNA melting provides the probability that the labeled basepair, and its neighbors, are open at different temperatures. Our work is of direct importance, for instance, for studies where fluorophore-quencher pairs are used for studying single basepair fluctuations of designed DNA molecules.</p>}},
  author       = {{Genthon, Arthur and Dvirnas, Albertas and Ambjörnsson, Tobias}},
  issn         = {{0021-9606}},
  language     = {{eng}},
  month        = {{10}},
  number       = {{14}},
  publisher    = {{American Institute of Physics (AIP)}},
  series       = {{Journal of Chemical Physics}},
  title        = {{Equilibrium melting probabilities of a DNA molecule with a defect : An exact solution of the Poland-Scheraga model}},
  url          = {{http://dx.doi.org/10.1063/5.0168915}},
  doi          = {{10.1063/5.0168915}},
  volume       = {{159}},
  year         = {{2023}},
}