ArticleBiophysical journal2000
Sequence-dependent dynamics in duplex DNA.
Article in Biophysical journal, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography.Journal of biomolecular structure & dynamics · 2018Article
- Diverse p53/DNA binding modes expand the repertoire of p53 response elements.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.The journal of physical chemistry. B · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
- Molecular origins of DNA flexibility: sequence effects on conformational and mechanical properties.Physical review letters · 2011Article
- Sequence dependencies of DNA deformability and hydration in the minor groove.Biophysical journal · 2009Article
- Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation.Nucleic acids research · 2008Article
- Site-directed spin labeling studies on nucleic acid structure and dynamics.Progress in nucleic acid research and molecular biology · 2008Review
- Torsional rigidities of weakly strained DNAs.Biophysical journal · 2006Article
- Mismatch-induced DNA unbending upon duplex opening.Biophysical journal · 2005Article
- The relative flexibility of B-DNA and A-RNA duplexes: database analysis.Nucleic acids research · 2004Article
- DNA basepair step deformability inferred from molecular dynamics simulations.Biophysical journal · 2003Article
- High-throughput approach for detection of DNA bending and flexibility based on cyclization.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.Biophysical journal · 2002Article
- Dynamics of supercoiled and relaxed pTZ18U plasmids probed with a long-lifetime metal-ligand complex.Journal of biochemistry and molecular biology · 2002Article
- Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The submicrosecond bending dynamics of duplex DNA were measured at a single site, using a site-specific electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of the mean squared amplitude of bending relative to the end-to-end vector defined by the weakly bending rod model. The bending dynamics monitored at the single site varied when the length and position of a repeated AT sequence, distant from the spin probe, were changed. As the distance between the probe and the AT sequence was increased, the mean squared amplitude of bending seen by the probe due to that sequence decreased. A model for the sequence-dependent internal flexural motion of duplex DNA, which casts the mean squared bending amplitudes in terms of sequence-dependent bending parameters, has been developed. The best fit of the data to the model occurs when the (AT)(n) basepairs are assumed to be 20% more flexible than the average of the basepairs within the control sequence. These findings provide a quantitative basis for interpreting the kinetics of biological processes that depend on duplex DNA flexibility, such as protein recognition and chromatin packaging.
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