The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F21%3A00554476" target="_blank" >RIV/68081707:_____/21:00554476 - isvavai.cz</a>
Alternative codes found
RIV/61989592:15640/21:73611207
Result on the web
<a href="https://academic.oup.com/nar/article/49/16/9548/6348194" target="_blank" >https://academic.oup.com/nar/article/49/16/9548/6348194</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkab681" target="_blank" >10.1093/nar/gkab681</a>

Result language
angličtina
Original language name
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
Original language description
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.
Czech name
—
Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
—
OECD FORD branch
10608 - Biochemistry and molecular biology

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2021
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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