| STADLBAUER, Petr, Miroslav KREPL, Thomas E. CHEATHAM, Jaroslav KOČA a Jiří ŠPONER. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Research. Oxford, UK: Oxford Press, 2013, roč. 41, č. 14, s. 7128-7143. ISSN 0305-1048. doi:10.1093/nar/gkt412. |
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@article{1124236,
author = {Stadlbauer, Petr and Krepl, Miroslav and Cheatham, Thomas E. and Koča, Jaroslav and Šponer, Jiří},
article_location = {Oxford, UK},
article_number = {14},
doi = {http://dx.doi.org/10.1093/nar/gkt412},
keywords = {HUMAN TELOMERIC DNA; TETRAMOLECULAR G-QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; NUCLEIC-ACIDS; CRYSTAL-STRUCTURE; BIOMOLECULAR SIMULATIONS; INTERACTION POTENTIALS; FORMATION PATHWAYS; SOLUTION INSIGHTS},
language = {eng},
issn = {0305-1048},
journal = {Nucleic Acids Research},
title = {Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations},
url = {http://nar.oxfordjournals.org/content/41/14/7128},
volume = {41},
year = {2013}
}
TY - JOUR
ID - 1124236
AU - Stadlbauer, Petr - Krepl, Miroslav - Cheatham, Thomas E. - Koča, Jaroslav - Šponer, Jiří
PY - 2013
TI - Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
JF - Nucleic Acids Research
VL - 41
IS - 14
SP - 7128-7143
EP - 7128-7143
PB - Oxford Press
SN - 03051048
KW - HUMAN TELOMERIC DNA
KW - TETRAMOLECULAR G-QUADRUPLEXES
KW - PARTICLE MESH EWALD
KW - AMBER FORCE-FIELD
KW - NUCLEIC-ACIDS
KW - CRYSTAL-STRUCTURE
KW - BIOMOLECULAR SIMULATIONS
KW - INTERACTION POTENTIALS
KW - FORMATION PATHWAYS
KW - SOLUTION INSIGHTS
UR - http://nar.oxfordjournals.org/content/41/14/7128
L2 - http://nar.oxfordjournals.org/content/41/14/7128
N2 - Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
ER -
STADLBAUER, Petr, Miroslav KREPL, Thomas E. CHEATHAM, Jaroslav KOČA a Jiří ŠPONER. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. \textit{Nucleic Acids Research}. Oxford, UK: Oxford Press, 2013, roč.~41, č.~14, s.~7128-7143. ISSN~0305-1048. doi:10.1093/nar/gkt412.
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