ArticleJournal of the American Chemical Society2013
Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.
Article in Journal of the American Chemical Society, 2013. 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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30 citing papers in PubMed, 113 citations in OpenAlex.
- Topological rules and anomalies in intramolecular G-quadruplex folding: a comprehensive study.Nucleic acids research · 2026Article
- Large-Scale Conformational Analysis Explains G-Quadruplex Topological Landscape.The journal of physical chemistry. B · 2025Article
- Eps2Fold: a rapid method to characterize G-quadruplex DNA structures using single absorbance spectra.Nucleic acids research · 2025Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- 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
- Why Are Left-Handed G-Quadruplexes Scarce?The journal of physical chemistry letters · 2024Article
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- Small Heterocyclic Ligands as Anticancer Agents: QSAR with a Model G-Quadruplex.Molecules (Basel, Switzerland) · 2022Article
- Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding.International journal of molecular sciences · 2022Article
- Article
- B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.ChemistryOpen · 2022Article
- 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
- 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
- Understanding alkali metal cation affinities of multi-layer guanine quadruplex DNA.Physical chemistry chemical physics : PCCP · 2020Article
- Exploring potentially alternative non-canonical DNA duplex structures through simulation.Journal of biomolecular structure & dynamics · 2019Article
- Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
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Authors and funding
6 authors at 6 institutions in 4 countries.
Funding
Abstract
We provide theoretical predictions of the intrinsic stability of different arrangements of guanine quadruplex (G-DNA) stems. Most computational studies of nucleic acids have applied Molecular Mechanics (MM) approaches using simple pairwise-additive force fields. The principle limitation of such calculations is the highly approximate nature of the force fields. In this study, we for the first time apply accurate QM computations (DFT-D3 with large atomic orbital basis sets) to essentially complete DNA building blocks, seven different folds of the cation-stabilized two-quartet G-DNA stem, each having more than 250 atoms. The solvent effects are approximated by COSMO continuum solvent. We reveal sizable differences between MM and QM descriptions of relative energies of different G-DNA stems, which apparently reflect approximations of the DNA force field. Using the QM energy data, we propose correction to earlier free energy estimates of relative stabilities of different parallel, hybrid, and antiparallel G-stem folds based on classical simulations. The new energy ranking visibly improves the agreement between theory and experiment. We predict the 5'-anti-anti-3' GpG dinucleotide step to be the most stable one, closely followed by the 5'-syn-anti-3' step. The results are in good agreement with known experimental structures of 2-, 3-, and 4-quartet G-DNA stems. Besides providing specific results for G-DNA, our study highlights basic limitations of force field modeling of nucleic acids. Although QM computations have their own limitations, mainly the lack of conformational sampling and the approximate description of the solvent, they can substantially improve the quality of calculations currently relying exclusively on force fields.
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