Insight into formation propensity of pseudocircular DNA
G-hairpins

J 2021

Insight into formation propensity of pseudocircular DNA G-hairpins

LENARČIČ ŽIVKOVIĆ, Martina, Martin GAJARSKÝ, Kateřina BEKOVÁ, P. STADLBAUER, Lukáš VICHEREK et. al.

Základní údaje

Originální název

Insight into formation propensity of pseudocircular DNA G-hairpins

Autoři

LENARČIČ ŽIVKOVIĆ, Martina (705 Slovinsko, domácí), Martin GAJARSKÝ (703 Slovensko, domácí), Kateřina BEKOVÁ (203 Česká republika, domácí), P. STADLBAUER, Lukáš VICHEREK (203 Česká republika, domácí), M. PETROVA, Radovan FIALA (203 Česká republika, domácí), I. ROSENBERG, Jiří ŠPONER (203 Česká republika, domácí), J. PLAVEC a Lukáš TRANTÍREK (203 Česká republika, garant, domácí)

Vydání

Nucleic acids research, Oxford, Oxford University Press, 2021, 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: 19.160

Kód RIV

RIV/00216224:14740/21:00119635

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1093/nar/gkab029

UT WoS

000637321900039

Klíčová slova anglicky

MOLECULAR-DYNAMICS SIMULATIONSG-QUADRUPLEX STRUCTUREAMBER FORCE-FIELDG-TRIPLEXFOLDING PATHWAYSNUCLEIC-ACIDSRNAIDENTIFICATIONVISUALIZATIONINVOLVEMENT

Štítky

CF NMR, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 30. 10. 2024 14:16, Ing. Martina Blahová

Anotace

V originále

We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its 'circular' nature, PGHs tolerate single-stranded (ss) protrusions. High-resolution NMR structure of a novel member of PGH family reveals the atomistic details on a junction between ssDNA and PGH unit. Identification of new sequences capable of folding into one of the two forms of PGH helped in defining minimal sequence requirements for their formation. Our time-resolved NMR data indicate a possibility that PGHs fold via a complex kinetic partitioning mechanism and suggests the existence of K+ ion-dependent PGH folding intermediates. The data not only provide an explanation of cation-type-dependent formation of PGHs, but also explain the unusually large hysteresis between PGH melting and annealing noted in our previous study. Our findings have important implications for DNA biology and nanotechnology. Overrepresentation of sequences able to form PGHs in the evolutionary-conserved regions of the human genome implies their functionally important biological role(s).

Návaznosti

EF18_070/0009846, projekt VaV

Název: MSCAfellow2@MUNI

GX19-26041X, projekt VaV

Název: Strukturní biologie nové generace: Od izolovaných molekul k buňkám, od buněk ke tkáním.

Investor: Grantová agentura ČR, STRUCTURAL BIOLOGY – NEXT GENERATION: from isolated molecules to cells, from cells to tissues.

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

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

90127, velká výzkumná infrastruktura

Název: CIISB II

Citovat

LENARČIČ ŽIVKOVIĆ, Martina, Martin GAJARSKÝ, Kateřina BEKOVÁ, P. STADLBAUER, Lukáš VICHEREK, M. PETROVA, Radovan FIALA, I. ROSENBERG, Jiří ŠPONER, J. PLAVEC a Lukáš TRANTÍREK. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic acids research. Oxford: Oxford University Press, 2021, roč. 49, č. 4, s. 2317-2332. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab029.

@article{1831038,
   author = {Lenarčič Živković, Martina and Gajarský, Martin and Beková, Kateřina and Stadlbauer, P. and Vicherek, Lukáš and Petrova, M. and Fiala, Radovan and Rosenberg, I. and Šponer, Jiří and Plavec, J. and Trantírek, Lukáš},
   article_location = {Oxford},
   article_number = {4},
   doi = {http://dx.doi.org/10.1093/nar/gkab029},
   keywords = {MOLECULAR-DYNAMICS SIMULATIONSG-QUADRUPLEX STRUCTUREAMBER FORCE-FIELDG-TRIPLEXFOLDING PATHWAYSNUCLEIC-ACIDSRNAIDENTIFICATIONVISUALIZATIONINVOLVEMENT},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic acids research},
   title = {Insight into formation propensity of pseudocircular DNA G-hairpins},
   url = {https://academic.oup.com/nar/article/49/4/2317/6125665},
   volume = {49},
   year = {2021}
}

TY  - JOUR
ID  - 1831038
AU  - Lenarčič Živković, Martina - Gajarský, Martin - Beková, Kateřina - Stadlbauer, P. - Vicherek, Lukáš - Petrova, M. - Fiala, Radovan - Rosenberg, I. - Šponer, Jiří - Plavec, J. - Trantírek, Lukáš
PY  - 2021
TI  - Insight into formation propensity of pseudocircular DNA G-hairpins
JF  - Nucleic acids research
VL  - 49
IS  - 4
SP  - 2317-2332
EP  - 2317-2332
PB  - Oxford University Press
SN  - 03051048
KW  - MOLECULAR-DYNAMICS SIMULATIONSG-QUADRUPLEX STRUCTUREAMBER FORCE-FIELDG-TRIPLEXFOLDING PATHWAYSNUCLEIC-ACIDSRNAIDENTIFICATIONVISUALIZATIONINVOLVEMENT
UR  - https://academic.oup.com/nar/article/49/4/2317/6125665
N2  - We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their function in vivo and their applications in biotechnology, has not been elucidated. Here, we show that despite its 'circular' nature, PGHs tolerate single-stranded (ss) protrusions. High-resolution NMR structure of a novel member of PGH family reveals the atomistic details on a junction between ssDNA and PGH unit. Identification of new sequences capable of folding into one of the two forms of PGH helped in defining minimal sequence requirements for their formation. Our time-resolved NMR data indicate a possibility that PGHs fold via a complex kinetic partitioning mechanism and suggests the existence of K+ ion-dependent PGH folding intermediates. The data not only provide an explanation of cation-type-dependent formation of PGHs, but also explain the unusually large hysteresis between PGH melting and annealing noted in our previous study. Our findings have important implications for DNA biology and nanotechnology. Overrepresentation of sequences able to form PGHs in the evolutionary-conserved regions of the human genome implies their functionally important biological role(s).
ER  -

LENARČIČ ŽIVKOVI$\backslash$'C, Martina, Martin GAJARSKÝ, Kateřina BEKOVÁ, P. STADLBAUER, Lukáš VICHEREK, M. PETROVA, Radovan FIALA, I. ROSENBERG, Jiří ŠPONER, J. PLAVEC a Lukáš TRANTÍREK. Insight into formation propensity of pseudocircular DNA G-hairpins. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2021, roč.~49, č.~4, s.~2317-2332. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkab029.

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