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The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
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SYSNO ASEP 0554476 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology Author(s) Chen, J. (CN)
Cheng, M. (CN)
Salgado, G.F. (FR)
Stadlbauer, Petr (BFU-R) ORCID
Zhang, X. (CN)
Amrane, S. (FR)
Guédin, A. (FR)
He, F. (CN)
Šponer, Judit E. (BFU-R) RID, ORCID
Ju, H. (CN)
Mergny, Jean-Louis (BFU-R) ORCID, RID
Zhou, J. (CN)Number of authors 12 Source Title Nucleic Acids Research. - : Oxford University Press - ISSN 0305-1048
Roč. 49, č. 16 (2021), s. 9548-9559Number of pages 12 s. Publication form Print - P Language eng - English Country GB - United Kingdom Keywords loop-length ; k+ solution ; dna ; stability ; sequence Subject RIV CE - Biochemistry OECD category Biochemistry and molecular biology R&D Projects GA21-23718S 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 UT WOS 000701664900040 EID SCOPUS 85116221722 DOI 10.1093/nar/gkab681 Annotation Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the 'flanking effect' in this work. This 'flanking effect' was more pronounced when nucleotides were added at the 5'end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5'-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context. 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/49/16/9548/6348194
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