Sequence dependency of canonical base pair opening in the DNA double helix

Sequence dependency of canonical base pair opening in the DNA double helix. Lindahl, V., Villa, A., & Hess, B. PLOS Computational Biology, 13(4):e1005463, April, 2017. tex.ids= lindahlSequenceDependencyCanonical2017 ISBN: 1111111111

Paper doi abstract bibtex

Author summary The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.

@article{Lindahl2017,
	title = {Sequence dependency of canonical base pair opening in the {DNA} double helix},
	volume = {13},
	issn = {1553-7358},
	url = {http://dx.plos.org/10.1371/journal.pcbi.1005463},
	doi = {10.1371/journal.pcbi.1005463},
	abstract = {Author summary The DNA double helix, a molecule that stores biological information, has become an iconic image of biomedical research. In order to use or repair the information it carries, the bases that are stacked in the helix need to be chemically exposed. This can happen either by separating the two strands in the helix or by flipping out individual bases. Here, we focus on the latter process. Usually proteins are involved in interactions with bases, but it is still unclear if bases are pulled out actively by proteins or if they act on spontaneously flipped bases. Although experiments can detect base pair opening, it is difficult to detect which base moves in which direction. Here, we present results from molecular dynamics simulations using a recently developed sampling method which improves the statistics in the simulations by enhancing the probability of the base pair opening event. We observe differences in probability, modes and mechanism of opening that depend not only on the types of the bases in the pair, but also strongly on their neighbors. This provides essential information for understanding how DNA functions.},
	number = {4},
	journal = {PLOS Computational Biology},
	author = {Lindahl, Viveca and Villa, Alessandra and Hess, Berk},
	editor = {MacKerell, Alexander},
	month = apr,
	year = {2017},
	pmid = {28369121},
	note = {tex.ids= lindahlSequenceDependencyCanonical2017
ISBN: 1111111111},
	pages = {e1005463},
}

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