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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Základní údaje
Originální název Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
Autoři STADLBAUER, Petr (203 Česká republika), Miroslav KREPL (203 Česká republika), Thomas E. CHEATHAM (840 Spojené státy), Jaroslav KOČA (203 Česká republika, domácí) a Jiří ŠPONER (203 Česká republika, garant, domácí).
Vydání Nucleic Acids Research, Oxford, UK, Oxford Press, 2013, 0305-1048.
Další údaje
Originální jazyk angličtina
Typ výsledku Článek v odborném periodiku
Obor 10403 Physical chemistry
Stát vydavatele Velká Británie
Utajení není předmětem státního či obchodního tajemství
WWW URL
Impakt faktor Impact factor: 8.808
Kód RIV RIV/00216224:14740/13:00069533
Organizační jednotka Středoevropský technologický institut
Doi http://dx.doi.org/10.1093/nar/gkt412
UT WoS 000323050700037
Klíčová slova anglicky HUMAN TELOMERIC DNA; TETRAMOLECULAR G-QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; NUCLEIC-ACIDS; CRYSTAL-STRUCTURE; BIOMOLECULAR SIMULATIONS; INTERACTION POTENTIALS; FORMATION PATHWAYS; SOLUTION INSIGHTS
Štítky ok, rivok
Příznaky Mezinárodní význam, Recenzováno
Změnil Změnila: Olga Křížová, učo 56639. Změněno: 1. 10. 2013 09:55.
Anotace
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.
Návaznosti
ED1.1.00/02.0068, projekt VaVNázev: CEITEC - central european institute of technology
VytisknoutZobrazeno: 16. 8. 2022 06:33