STADLBAUER, Petr, Miroslav KREPL, Thomas E. CHEATHAM, Jaroslav KOČA and 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, vol. 41, No 14, p. 7128-7143. ISSN 0305-1048. doi:10.1093/nar/gkt412.
Other formats:   BibTeX LaTeX RIS
Basic information
Original name Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations
Authors STADLBAUER, Petr (203 Czech Republic), Miroslav KREPL (203 Czech Republic), Thomas E. CHEATHAM (840 United States of America), Jaroslav KOČA (203 Czech Republic, belonging to the institution) and Jiří ŠPONER (203 Czech Republic, guarantor, belonging to the institution).
Edition Nucleic Acids Research, Oxford, UK, Oxford Press, 2013, 0305-1048.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 10403 Physical chemistry
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 8.808
RIV identification code RIV/00216224:14740/13:00069533
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1093/nar/gkt412
UT WoS 000323050700037
Keywords in English HUMAN TELOMERIC DNA; TETRAMOLECULAR G-QUADRUPLEXES; PARTICLE MESH EWALD; AMBER FORCE-FIELD; NUCLEIC-ACIDS; CRYSTAL-STRUCTURE; BIOMOLECULAR SIMULATIONS; INTERACTION POTENTIALS; FORMATION PATHWAYS; SOLUTION INSIGHTS
Tags ok, rivok
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 1. 10. 2013 09:55.
Abstract
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.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
PrintDisplayed: 4. 10. 2022 16:07