ArticleNucleic acids research2021
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 51 citations in OpenAlex.
- KRSC advances · 2026Article
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- How loop lengths shape topological preferences of two-tetrad G-quadruplexes.Nucleic acids research · 2026Article
- Topological rules and anomalies in intramolecular G-quadruplex folding: a comprehensive study.Nucleic acids research · 2026Article
- Revealing G4 Structures as Drug Targets: Exploring the Potential of Novel Therapeutic Agents.Research (Washington, D.C.) · 2026Review
- Sequence Determinants of G-Quadruplex Thermostability: Aligning Evidence from High-Precision Biophysics and High-Throughput Genomics.Biomolecules · 2025Review
- Quadruplexes with a grain of salt: influence of cation type and concentration on DNA G4 stability.European biophysics journal : EBJ · 2025Article
- Crystal structures of distinct parallel and antiparallel DNA G-quadruplexes reveal structural polymorphism in C9orf72 G4C2 repeats.Nucleic acids research · 2025Article
- Mammalian conservation of endogenous G-quadruplex reveals their associations with complex traits.Genome biology · 2025Article
- Effects of flanking regions on DNA i-motif folding and stability.Nucleic acids research · 2025Article
- Putative G‑Quadruplex Structures in Dysregulated Long Non-coding RNA of Ovarian Cancer and Their Binding Interactions with Human Serum Albumin.ACS omega · 2025Article
- Analysis of quadruplex propensity of aptamer sequences.Nucleic acids research · 2025Article
- Imperfect G-quadruplex as an emerging candidate for transcriptional regulation.Nucleic acids research · 2025Article
- RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?Nucleic acids research · 2024Article
- Overcoming Cancer Persister Cells by Stabilizing the ATF4 Promoter G-quadruplex.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Real-time observation of sub-100-fs charge and energy transfer processes in DNA dinucleotides.Chemical science · 2024Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling.Chemical science · 2023Article
- Target response controlled enzyme activity switch for multimodal biosensing detection.Journal of nanobiotechnology · 2023Article
- Inhibited complete folding of consecutive human telomeric G-quadruplexes.Nucleic acids research · 2023Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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