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.

Basic information

Original name

Insight into formation propensity of pseudocircular DNA G-hairpins

Authors

LENARČIČ ŽIVKOVIĆ, Martina (705 Slovenia, belonging to the institution), Martin GAJARSKÝ (703 Slovakia, belonging to the institution), Kateřina BEKOVÁ (203 Czech Republic, belonging to the institution), P. STADLBAUER, Lukáš VICHEREK (203 Czech Republic, belonging to the institution), M. PETROVA, Radovan FIALA (203 Czech Republic, belonging to the institution), I. ROSENBERG, Jiří ŠPONER (203 Czech Republic, belonging to the institution), J. PLAVEC and Lukáš TRANTÍREK (203 Czech Republic, guarantor, belonging to the institution)

Edition

Nucleic acids research, Oxford, Oxford University Press, 2021, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 19.160

RIV identification code

RIV/00216224:14740/21:00119635

Organization unit

Central European Institute of Technology

DOI

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

UT WoS

000637321900039

Keywords in English

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

Abstract

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).

Links

EF18_070/0009846, research and development project

Name: MSCAfellow2@MUNI

GX19-26041X, research and development project

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

Investor: Czech Science Foundation

LM2018127, research and development project

Name: Česká infrastruktura pro integrativní strukturní biologii (Acronym: CIISB)

Investor: Ministry of Education, Youth and Sports of the CR

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

90127, large research infrastructures

Name: CIISB II

Citovat

LENARČIČ ŽIVKOVIĆ, Martina, Martin GAJARSKÝ, Kateřina BEKOVÁ, P. STADLBAUER, Lukáš VICHEREK, M. PETROVA, Radovan FIALA, I. ROSENBERG, Jiří ŠPONER, J. PLAVEC and Lukáš TRANTÍREK. Insight into formation propensity of pseudocircular DNA G-hairpins. Nucleic acids research. Oxford: Oxford University Press, 2021, vol. 49, No 4, p. 2317-2332. ISSN 0305-1048. Available from: 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 and Lukáš TRANTÍREK. Insight into formation propensity of pseudocircular DNA G-hairpins. \textit{Nucleic acids research}. Oxford: Oxford University Press, 2021, vol.~49, No~4, p.~2317-2332. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkab029.

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