Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

0518355 - BFÚ 2020 RIV GB eng J - Journal Article
Stadlbauer, Petr - Kührová, P. - Vicherek, L. - Banáš, Pavel - Otyepka, Michal - Trantírek, Lukáš - Šponer, Jiří
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes.
Nucleic Acids Research. Roč. 47, č. 14 (2019), s. 7276-7293. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA ČR(CZ) GA16-13721S; GA ČR GA17-12075S; GA MŠMT EF15_003/0000477
Institutional support: RVO:68081707
Keywords : telomeric g-quadruplex * amber force-field * monovalent ion parameters * single-molecule fret * particle mesh ewald * nucleic-acids
OECD category: Biochemistry and molecular biology
Impact factor: 11.502, year: 2019
Method of publishing: Open access
https://academic.oup.com/nar/article-pdf/47/14/7276/29185953/gkz610.pdf

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 similar to 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, GGGAGGGand 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.
Permanent Link: http://hdl.handle.net/11104/0303512