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Insight into formation propensity of pseudocircular DNA G-hairpins
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SYSNO ASEP 0542802 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Insight into formation propensity of pseudocircular DNA G-hairpins Author(s) Zivkovic, M.L. (SI)
Gajarský, M. (CZ)
Bekova, K. (CZ)
Stadlbauer, Petr (BFU-R) ORCID
Vicherek, L. (CZ)
Petrová, Magdalena (UOCHB-X) RID
Fiala, R. (CZ)
Rosenberg, Ivan (UOCHB-X) RID, ORCID
Šponer, Jiří (BFU-R) RID, ORCID
Plavec, J. (SI)
Trantírek, L. (CZ)Number of authors 11 Source Title Nucleic Acids Research. - : Oxford University Press - ISSN 0305-1048
Roč. 49, č. 4 (2021), s. 2317-2332Number of pages 16 s. Publication form Online - E Language eng - English Country GB - United Kingdom Keywords molecular-dynamics simulations ; g-quadruplex structure ; amber force-field ; g-triplex ; folding pathways Subject RIV CE - Biochemistry OECD category Biochemistry and molecular biology Subject RIV - cooperation Institute of Organic Chemistry and Biochemistry - Biochemistry R&D Projects GA17-12703S GA ČR - Czech Science Foundation (CSF) EF15_003/0000477 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Open access Institutional support BFU-R - RVO:68081707 ; UOCHB-X - RVO:61388963 UT WOS 000637321900039 EID SCOPUS 85102407851 DOI 10.1093/nar/gkab029 Annotation 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). Workplace Institute of Biophysics Contact Jana Poláková, polakova@ibp.cz, Tel.: 541 517 244 Year of Publishing 2022 Electronic address https://academic.oup.com/nar/article/49/4/2317/6125665
Number of the records: 1