ArticleChemical science2021
Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex.
Article in Chemical science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Local Energy Decomposition of Intramolecular Interactions: The CovaLED Approach and Its Application to Molecular Recognition in Biomolecular Assemblies.ACS central science · 2026Article
- LEDAW: An Integrated Software Suite with GUI for Automating Local Energy Decomposition Analysis of Molecular Interactions.Journal of chemical information and modeling · 2025Article
- Discovery and optimization of a guanylhydrazone-based small molecule to replace bFGF for cell culture applications.Biochemistry and biophysics reports · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- A Generally Applicable Method for Disentangling the Effect of Individual Noncovalent Interactions on the Binding Energy.Angewandte Chemie (International ed. in English) · 2025Article
- Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China.Plants (Basel, Switzerland) · 2025Article
- Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A.ACS central science · 2024Article
- Binding energies and hydrogen bonds effects on DNA-cisplatin interactions: a DFT-xTB study.Journal of molecular modeling · 2024Article
- Local Energy Decomposition Analysis of London Dispersion Effects: From Simple Model Dimers to Complex Biomolecular Assemblies.Accounts of chemical research · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- Article
- Open-Shell Variant of the London Dispersion-Corrected Hartree-Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies.Journal of chemical theory and computation · 2022Article
- Ionization Energies and Redox Potentials of Hydrated Transition Metal Ions: Evaluation of Domain-Based Local Pair Natural Orbital Coupled Cluster Approaches.Journal of chemical theory and computation · 2022Article
- B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.ChemistryOpen · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
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