ArticleNucleic acids research2016
Long-timescale dynamics of the Drew-Dickerson dodecamer.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Role of Charge Density of Polycations in DNA Complexation and Condensation.Biomolecules · 2025Article
- Combining Cyclic Triimidazo Triazine Core With Ethynyl-N-Methyl-Pyridinium Groups for Targeting G-Quadruplex Structures.Archiv der Pharmazie · 2025Article
- Naphthalene diimide-naphthalimide dyads promote telomere damage by selectively targeting multimeric G-quadruplexes.Nucleic acids research · 2025Article
- Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer-promoter communication.The Journal of chemical physics · 2024Article
- modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.Journal of chemical theory and computation · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- Histone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair.Nature communications · 2023Article
- Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA.RSC chemical biology · 2023Article
- Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM.Nucleic acids research · 2023Article
- Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif.Biophysical journal · 2022Article
- Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes.The journal of physical chemistry. B · 2022Article
- Self-Consistent Parameterization of DNA Residues for the Non-Polarizable AMBER Force Fields.Life (Basel, Switzerland) · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function.PLoS computational biology · 2021Article
- Molecular dynamics study of the competitive binding of hydrogen peroxide and water molecules with DNA phosphate groups.European biophysics journal : EBJ · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC)2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na(+)Cl(-) or K(+)Cl(-) The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 μs) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 μs of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.
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