ArticleNucleic acids research2015
Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Article
- Experimental detection of conformational transitions between forms of DNA: problems and prospects.Biophysical reviews · 2023Review
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA.Journal of chemical information and modeling · 2022Article
- Alchemical Free-Energy Calculations of Watson-Crick and Hoogsteen Base Pairing Interconversion in DNA.Journal of chemical theory and computation · 2022Article
- Transient Hoogsteen Base Pairs Observed in Unbiased Molecular Dynamics Simulations of DNA.The journal of physical chemistry letters · 2022Article
- Sequence dependence of transient Hoogsteen base pairing in DNA.PLoS computational biology · 2022Article
- Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks.Journal of chemical theory and computation · 2021Article
- Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.Biophysical journal · 2020Article
- Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA.Nucleic acids research · 2019Article
- New insights into protein-DNA binding specificity from hydrogen bond based comparative study.Nucleic acids research · 2019Article
- Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.Biophysical journal · 2019Article
- Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms.Scientific reports · 2018Article
- Modulation of Hoogsteen dynamics on DNA recognition.Nature communications · 2018Article
- The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwRSC advances · 2018Article
- Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.Frontiers in chemistry · 2018Article
- Unexpected Routes of the Mutagenic Tautomerization of the T Nucleobase in the Classical A·T DNA Base Pairs: A QM/QTAIM Comprehensive View.Frontiers in chemistry · 2018Article
- How accurate are accurate force-fields for B-DNA?Nucleic acids research · 2017Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events.
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