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

Jielin Chen,Aurore Guédin,Jun Zhou,Jean-Louis Mergny,Mingpan Cheng,Jiří Šponer,Petr Stadlbauer,Xiaobo Zhang,Huangxian Ju,Gilmar F Salgado,Samir Amrane,Fangni He

doi:10.1093/nar/gkab681

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.

Highlights

G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine-rich sequences [1,2], which are distributed in key regions of the genomes, such as telomeres and oncogene promoters (e.g. c-kit, KRAS, c-myc, VEGF)
These sequences are represented as 5 GGGTaGGGTbGGGTcGGG-3, where a, b and c are three integers corresponding to the number of nucleotides in the first (5 ), second, and third (3 ) loops, respectively, with a total loop length (a + b + c) of 7–13 nucleotides
A group of sequences is defined as all sequences formed by loop swapping; for instance, the 136 group is composed of six oligonucleotides with any combination of loops with one, three, and six thymines, which gives sequences with a, b, c values of 136, 163, 316, 361, 613 and 631; the group names are written in bold, italicized font

Summary

Introduction

G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine-rich sequences [1,2], which are distributed in key regions of the genomes, such as telomeres and oncogene promoters (e.g. c-kit, KRAS, c-myc, VEGF). They contribute to essential cellular processes such as initiation of DNA replication, telomere maintenance and control of gene expression [3,4,5]. To simplify experimental design, studies have generally focused on short DNA (or RNA) oligonucleotides that match the core of the G-rich motif without considering its natural sequence context. Efforts have been dedicated to the study of loop effects [6,7,8], but the role of flanking sequences has

Methods

Results

Discussion

Conclusion