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The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology.
- Source :
-
Nucleic acids research [Nucleic Acids Res] 2021 Sep 20; Vol. 49 (16), pp. 9548-9559. - Publication Year :
- 2021
-
Abstract
- 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.<br /> (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Subjects :
- Circular Dichroism
DNA genetics
DNA ultrastructure
Hydrogen Bonding
Molecular Dynamics Simulation
Nucleic Acid Conformation
Nucleotides chemistry
Oligonucleotides chemistry
RNA genetics
RNA ultrastructure
G-Quadruplexes
Nucleotides genetics
Oligonucleotides genetics
Polymorphism, Genetic genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1362-4962
- Volume :
- 49
- Issue :
- 16
- Database :
- MEDLINE
- Journal :
- Nucleic acids research
- Publication Type :
- Academic Journal
- Accession number :
- 34379785
- Full Text :
- https://doi.org/10.1093/nar/gkab681