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

J 2019

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

STADLBAUER, P., P. KUHROVA, Lukáš VICHEREK, P. BANAS, M. OTYEPKA et. al.

Základní údaje

Originální název

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

Autoři

STADLBAUER, P. (203 Česká republika), P. KUHROVA (203 Česká republika), Lukáš VICHEREK (203 Česká republika, domácí), P. BANAS (203 Česká republika), M. OTYEPKA (203 Česká republika), Lukáš TRANTÍREK (203 Česká republika, domácí) a Jiří ŠPONER (203 Česká republika, garant, domácí)

Vydání

Nucleic acids research, Oxford, Oxford University Press, 2019, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 11.502

Kód RIV

RIV/00216224:14740/19:00108142

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/nar/gkz610

UT WoS

000483815100016

Klíčová slova anglicky

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

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 3. 2020 20:10, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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.

Návaznosti

GA17-12075S, projekt VaV

Název: Polymorfní G-quadruplexy v promotorových oblastech genů

Investor: Grantová agentura ČR, Polymorfní G-quadruplexy v promotorových oblastech genů

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

STADLBAUER, P., P. KUHROVA, Lukáš VICHEREK, P. BANAS, M. OTYEPKA, Lukáš TRANTÍREK a Jiří ŠPONER. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic acids research. Oxford: Oxford University Press, 2019, roč. 47, č. 14, s. 7276-7293. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkz610.

@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 a 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, roč.~47, č.~14, s.~7276-7293. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkz610.

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