ArticleChemistryOpen2013
B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands.
Article in ChemistryOpen, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Simplified PCR-Based Quantification of Proteins with DNA Aptamers and Methylcellulose as a Blocking Agent.International journal of molecular sciences · 2023Article
- Article
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.ChemistryOpen · 2022Article
- Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex.Chemical science · 2021Article
- Effect of N7-methylation on base pairing patterns of guanine: a DFT study.Journal of molecular modeling · 2021Article
- A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions.Nucleic acids research · 2021Article
- Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study.Molecules (Basel, Switzerland) · 2021Article
- Role of the backbone of nucleic acids in the stability of HgRSC advances · 2020Article
- Sequence specificity in DNA-drug intercalation: MD simulation and density functional theory approaches.Journal of computer-aided molecular design · 2020Article
- Theoretical modelling of epigenetically modified DNA sequences.F1000Research · 2015Article
- Understanding the structural and dynamic consequences of DNA epigenetic modifications: computational insights into cytosine methylation and hydroxymethylation.Epigenetics · 2014Article
- Contribution of phenylalanine side chain intercalation to the TATA-box binding protein-DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies.Journal of molecular modeling · 2014Article
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3 authors.
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Abstract
We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2'-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson-Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2 <d(CpA)2 <d(ApT)2 <d(ApA)2 <d(GpT)2 <d(GpA)2 <d(ApG)2 <d(CpG)2 <d(GpG)2 <d(GpC)2, where the energy differences between the last four dimers, d(ApG)2, d(CpG)2, d(GpG)2 and d(GpC)2, is within 4.0 kcal mol(-1), and the energy between the most and the least stable isomers is 13.4 kcal mol(-1). This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5'- to the 3'-end.
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