ArticleNucleic acids research2011
Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- Modulating G-quadruplexes for therapeutic intervention: Structural diversity, stability, and emerging nucleic-acid-based strategies.Molecular therapy. Nucleic acids · 2026Review
- Topological rules and anomalies in intramolecular G-quadruplex folding: a comprehensive study.Nucleic acids research · 2026Article
- Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNA.Nucleic acids research · 2026Article
- Unravelling the noncanonical extracellular DNA structures in biofilm and NETosis.Nucleic acids research · 2026Review
- Beyond Structure: Methylation Fine-Tunes Stability and Folding Kinetics of bcl2Mid G-Quadruplex.Angewandte Chemie (International ed. in English) · 2025Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- Affinity Chromatography-Based Assays for the Screening of Potential Ligands Selective for G-Quadruplex Structures.ChemistryOpen · 2022Article
- ONQUADRO: a database of experimentally determined quadruplex structures.Nucleic acids research · 2022Article
- Mechanistic insights into multiple-step transport of mitochondrial ADP/ATP carrier.Computational and structural biotechnology journal · 2022Article
- Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery.Journal of medicinal chemistry · 2021Article
- The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology.Nucleic acids research · 2021Article
- Expanding the Topological Landscape by a G-Column Flip of a Parallel G-Quadruplex.Chemistry (Weinheim an der Bergstrasse, Germany) · 2021Article
- Structural motifs and intramolecular interactions in non-canonical G-quadruplexes.RSC chemical biology · 2021Review
- Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter.Nucleic acids research · 2021Article
- NMR structural study on the self-trimerization of d(GTTAGG) into a dynamic trimolecular G-quadruplex assembly preferentially in Na+ solution with a moderate K+ tolerance.Nucleic acids research · 2021Article
- Targeting Telomeres: Molecular Dynamics and Free Energy Simulation of Gold-Carbene Binding to DNA.Biophysical journal · 2021Article
- Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.Nucleic acids research · 2020Article
- Structure of two G-quadruplexes in equilibrium in the KRAS promoter.Nucleic acids research · 2020Article
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3 authors.
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Abstract
Guanine-rich DNA sequences tend to form four-stranded G-quadruplex structures. Characteristic glycosidic conformational patterns along the G-strands, such as the 5'-syn-anti-syn-anti pattern observed with the Oxytricha nova telomeric G-quadruplexes, have been well documented. However, an explanation for these featured glycosidic patterns has not emerged. This work presents MD simulation and free energetic analyses for simplified two-quartet [d(GG)](4) models and suggests that the four base pair step patterns show quite different relative stabilities: syn-anti > anti-anti > anti-syn > syn-syn. This suggests the following rule: when folding, anti-parallel G-quadruplexes tend to maximize the number of syn-anti steps and avoid the unfavorable anti-syn and syn-syn steps. This rule is consistent with most of the anti-parallel G-quadruplex structures in the Protein Databank (PDB). Structural polymorphisms of G-quadruplexes relate to these glycosidic conformational patterns and the lengths of the G-tracts. The folding topologies of G2- and G4-tracts are not very polymorphic because each strand tends to populate the stable syn-anti repeat. G3-tracts, on the other hand, cannot present this repeating pattern on each G-tract. This leads to smaller energy differences between different geometries and helps explain the extreme structural polymorphism of the human telomeric G-quadruplexes.
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