ArticleNucleic acids research2008
Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 54 citations in OpenAlex.
- Molecular Dynamics Simulations Predict That rSNP Located in theBiomolecules · 2020Article
- Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.Frontiers in molecular biosciences · 2020Article
- Genome reading by the NF-κB transcription factors.Nucleic acids research · 2019Review
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.ACS central science · 2019Article
- Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin.Journal of molecular modeling · 2018Article
- Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site.PloS one · 2018Article
- Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations.Biophysical journal · 2016Article
- Article
- Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.Journal of molecular modeling · 2016Article
- Identification of a pKa-regulating motif stabilizing imidazole-modified double-stranded DNA.Nucleic acids research · 2015Article
- DNA Duplex Formation with a Coarse-Grained Model.Journal of chemical theory and computation · 2014Article
- Triple helical DNA in a duplex context and base pair opening.Nucleic acids research · 2014Article
- Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.PloS one · 2014Article
- Hidden Conformation Events in DNA Base Extrusions: A Generalized Ensemble Path Optimization and Equilibrium Simulation Study.Journal of chemical theory and computation · 2013Article
- PELE web server: atomistic study of biomolecular systems at your fingertips.Nucleic acids research · 2013Article
- Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.Nucleic acids research · 2013Article
- Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.Biochemistry · 2012Article
- The transcriptional specificity of NF-κB dimers is coded within the κB DNA response elements.Cell reports · 2012Article
- NF-κB regulation: lessons from structures.Immunological reviews · 2012Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein...DNA recognition in the 'kappaB' family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate kappaB site recognized by the proto-oncogenic 'c-Rel' subfamily of NF-kappaB transcription factors. Simulations of the kappaB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation-including a peculiar state arising at approximately 0.7 micros and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at approximately 1 micros) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-kappaB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
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Registered trials
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.