ArticleNucleic acids research2013
Guanine base stacking in G-quadruplex nucleic acids.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 144 citations in OpenAlex.
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
- Promoter G-quadruplex structures regulate tissue-specific gene expression and functional differentiation in Bombyx mori.BMC biology · 2026Article
- Recognition of multimolecular G-quadruplex regulates phase separation of cockayne syndrome B.Nucleic acids research · 2026Article
- Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra.Nucleic acids research · 2025Article
- Conformational Change in a Four-Tetrad DNA G-Quadruplex upon Intercalation of a Small-Molecule Ligand PyDH2.Angewandte Chemie (International ed. in English) · 2025Article
- Primary Sequence-Intrinsic Immune Evasion by Viral Proteins Guides CTL-Based Vaccine Strategies.Viruses · 2025Review
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
- RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?Nucleic acids research · 2024Article
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs.Molecules (Basel, Switzerland) · 2024Review
- Crystal structure of a tetrameric RNA G-quadruplex formed by hexanucleotide repeat expansions of C9orf72 in ALS/FTD.Nucleic acids research · 2024Article
- DNA as a perfect quantum computer based on the quantum physics principles.Scientific reports · 2024Article
- Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry.International journal of mass spectrometry · 2024Article
- Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism.Nucleic acids research · 2024Article
- G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection.Pathogens (Basel, Switzerland) · 2024Review
- G-quadruplex formation in RNA aptamers selected for binding to HIV-1 capsid.Frontiers in chemistry · 2024Article
- Insect multimeric G-quadruplexes fold into antiparallel structures of different compactness and stability in KRSC advances · 2023Article
- Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States.Genes · 2023Article
- Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.International journal of molecular sciences · 2023Article
- Highly Selective Fluorescent Sensors: Polyethylenimine Derivatives of Triphenylamine and Coumarin for GTP and ATP Interaction via Fluorescence Lifetime Imaging Microscopy.ACS applied polymer materials · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another within the G-tetrad core. Individual G-quadruplexes can also stack with one another at their G-tetrad interface leading to higher-order structures as observed in telomeric repeat-containing DNA and RNA. In this study, we investigate how guanine base stacking influences the stability of G-quadruplexes and their stacked higher-order structures. A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. We couple this survey with a systematic computational examination of stacked G-tetrad energy landscapes using quantum mechanical computations. Energy calculations of stacked G-tetrads reveal large energy differences of up to 12 kcal/mol between experimentally observed geometries at the interface of stacked G-quadruplexes. Energy landscapes are also computed using an AMBER molecular mechanics description of stacking energy and are shown to agree quite well with quantum mechanical calculated landscapes. Molecular dynamics simulations provide a structural explanation for the experimentally observed preference of parallel G-quadruplexes to stack in a 5'-5' manner based on different accessible tetrad stacking modes at the stacking interfaces of 5'-5' and 3'-3' stacked G-quadruplexes.
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