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@article{1616857,
author = {Stadlbauer, P. and Kuhrova, P. and Vicherek, Lukáš and Banas, P. and Otyepka, M. and Trantírek, Lukáš and Šponer, Jiří},
article_location = {Oxford},
article_number = {14},
doi = {http://dx.doi.org/10.1093/nar/gkz610},
keywords = {TELOMERIC G-QUADRUPLEX; AMBER FORCE-FIELD; MONOVALENT ION PARAMETERS; SINGLE-MOLECULE FRET; PARTICLE MESH EWALD; NUCLEIC-ACIDS; REPLICA-EXCHANGE; K+ SOLUTION; CRYSTAL-STRUCTURE; ENERGY LANDSCAPE},
language = {eng},
issn = {0305-1048},
journal = {Nucleic acids research},
title = {Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes},
url = {https://academic.oup.com/nar/article/47/14/7276/5535705},
volume = {47},
year = {2019}
}
TY - JOUR
ID - 1616857
AU - Stadlbauer, P. - Kuhrova, P. - Vicherek, Lukáš - Banas, P. - Otyepka, M. - Trantírek, Lukáš - Šponer, Jiří
PY - 2019
TI - Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
JF - Nucleic acids research
VL - 47
IS - 14
SP - 7276-7293
EP - 7276-7293
PB - Oxford University Press
SN - 03051048
KW - TELOMERIC G-QUADRUPLEX
KW - AMBER FORCE-FIELD
KW - MONOVALENT ION PARAMETERS
KW - SINGLE-MOLECULE FRET
KW - PARTICLE MESH EWALD
KW - NUCLEIC-ACIDS
KW - REPLICA-EXCHANGE
KW - K+ SOLUTION
KW - CRYSTAL-STRUCTURE
KW - ENERGY LANDSCAPE
UR - https://academic.oup.com/nar/article/47/14/7276/5535705
L2 - https://academic.oup.com/nar/article/47/14/7276/5535705
N2 - 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.
ER -
STADLBAUER, P., P. KUHROVA, Lukáš VICHEREK, P. BANAS, M. OTYEPKA, Lukáš TRANTÍREK and Jiří ŠPONER. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2019, vol.~47, No~14, p.~7276-7293. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkz610.
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