ArticlePLoS computational biology2017
Sequence dependency of canonical base pair opening in the DNA double helix.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Nonconsensus flanking sequence of hundreds of base pairs around in vivo binding sites: statistical beacons for transcription factor scanning.Nucleic acids research · 2026Article
- Influence of Membrane Composition on the Passive Membrane Penetration of Industrially Relevant NSO-Heterocycles.International journal of molecular sciences · 2025Article
- Local sequence context atFrontiers in molecular biosciences · 2025Article
- Enhanced Disease Resistance Mechanism of the CmoAP2/ERF Transcription Factor in Pumpkin through Genetic Mutations.ACS omega · 2024Article
- The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations.Molecules (Basel, Switzerland) · 2024Article
- Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range.International journal of molecular sciences · 2022Article
- Energy Landscapes for Base-Flipping in a Model DNA Duplex.The journal of physical chemistry. B · 2022Article
- Carcinogen-induced DNA structural distortion differences in the RAS gene isoforms; the importance of local sequence.BMC chemistry · 2021Article
- First passage time study of DNA strand displacement.Biophysical journal · 2021Article
- Importance of base-pair opening for mismatch recognition.Nucleic acids research · 2020Article
- Slow motions in A·T rich DNA sequence.Scientific reports · 2020Article
- GapR binds DNA through dynamic opening of its tetrameric interface.Nucleic acids research · 2020Article
- Inequality in the Frequency of the Open States Occurrence Depends on SingleMolecules (Basel, Switzerland) · 2020Article
- Article
- Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA.Journal of chemical theory and computation · 2018Article
- Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function.Scientific reports · 2018Article
- Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs.Frontiers in chemistry · 2018Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.
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