ArticleThe journal of physical chemistry. B2012
Intramolecular base stacking of dinucleoside monophosphate anions in aqueous solution.
Article in The journal of physical chemistry. B, 2012. 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, 50 citations in OpenAlex.
- A narrow ratio of nucleic acid to SARS-CoV-2 N-protein enables phase separation.bioRxiv : the preprint server for biology · 2024Article
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations.Journal of chemical theory and computation · 2022Article
- Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip.Nucleic acids research · 2021Article
- Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer.The journal of physical chemistry. B · 2021Article
- Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids.Journal of the American Chemical Society · 2020Article
- Mechanism of premature translation termination on a sense codon.The Journal of biological chemistry · 2018Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The impact of base stacking on the conformations and electrostatics of single-stranded DNA.Nucleic acids research · 2017Article
- Free energy analysis and mechanism of base pair stacking in nicked DNA.Nucleic acids research · 2016Article
- Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations.Journal of chemical theory and computation · 2015Article
- Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment.Journal of chemical theory and computation · 2015Article
- Free-energy landscape and characteristic forces for the initiation of DNA unzipping.Biophysical journal · 2015Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Time-dependent motions of 32 deoxyribodinucleoside and ribodinucleoside monophosphate anions in aqueous solution at 310 K were monitored during 40 ns using classical molecular dynamics (MD). In all studied molecules, spontaneous stacking/unstacking transitions occurred on a time-scale of 10 ns. To facilitate the structural analysis of the sampled configurations we defined a reaction coordinate for the nucleobase stacking that considers both the angle between the planes of the two nucleobases and the distance between their mass-centers. Additionally, we proposed a physically meaningful transient point on this coordinate that separates the stacked and unstacked states. We applied this definition to calculate free energies for stacking of all pairwise combinations of adenine, thymine (uracil), cytosine and guanine moieties embedded in studied dinucleosides monophosphate anions. The stacking equilibrium constants decreased in the order 5'-AG-3' > GA ~ GG ~ AA > GT ~ TG ~ AT ~ GC ~ AC > CG ~ TA > CA ~ TC ~ TT ~ CT ~ CC. The stacked conformations of AG occurred 10 times more frequently than its unstacked conformations. On the other hand, the last five base combinations showed a greater preference for the unstacked than the stacked state. The presence of an additional 2'-OH group in the RNA-based dinucleoside monophosphates increased the fraction of stacked complexes but decreased the compactness of the stacked state. The calculated MD trajectories were also used to reveal prevailing mutual orientation of the nucleobase dipoles in the stacked state.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.