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Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
P. Stadlbauer, P. Kührová, L. Vicherek, P. Banáš, M. Otyepka, L. Trantírek, J. Šponer,
Jazyk angličtina Země Velká Británie
Typ dokumentu časopisecké články, práce podpořená grantem
NLK
Directory of Open Access Journals
od 2005
Free Medical Journals
od 1996
PubMed Central
od 1974
Europe PubMed Central
od 1974
Open Access Digital Library
od 1996-01-01 do 2030-12-31
Open Access Digital Library
od 1974-01-01
Open Access Digital Library
od 1996-01-01
Open Access Digital Library
od 1996-01-01
Medline Complete (EBSCOhost)
od 1996-01-01
Oxford Journals Open Access Collection
od 1996-01-01
ROAD: Directory of Open Access Scholarly Resources
od 1974
PubMed
31318975
DOI
10.1093/nar/gkz610
Knihovny.cz E-zdroje
- MeSH
- DNA chemie genetika metabolismus MeSH
- G-kvadruplexy * MeSH
- guanin chemie metabolismus MeSH
- jednovláknová DNA chemie genetika metabolismus MeSH
- kinetika MeSH
- konformace nukleové kyseliny * MeSH
- lidé MeSH
- sekvence nukleotidů MeSH
- simulace molekulární dynamiky * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
Citace poskytuje Crossref.org
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