ArticleBiophysical journal2002
Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 70 citations in OpenAlex.
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- Deciphering the mechanical code of the genome and epigenome.Nature structural & molecular biology · 2022Article
- Evolutionary Invariant of the Structure of DNA Double Helix in RNAP II Core Promoters.International journal of molecular sciences · 2022Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
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- The complex architecture of p53 binding sites.Nucleic acids research · 2021Article
- A Conformational Switch in the Zinc Finger Protein Kaiso Mediates Differential Readout of Specific and Methylated DNA Sequences.Biochemistry · 2020Article
- σJournal of bacteriology · 2018Article
- μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA.Nucleic acids research · 2014Article
- Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.Nucleic acids research · 2014Article
- DNA bending propensity in the presence of base mismatches: implications for DNA repair.The journal of physical chemistry. B · 2013Article
- Effect of Bending Rigidity on the Knotting of a Polymer under Tension.ACS macro letters · 2012Article
- 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
- Sequence-specific ultrasonic cleavage of DNA.Biophysical journal · 2011Article
- Sequence dependence of DNA bending rigidity.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Base sequence context effects on nucleotide excision repair.Journal of nucleic acids · 2010Article
- Distant neighbor base sequence context effects in human nucleotide excision repair of a benzo[a]pyrene-derived DNA lesion.Journal of molecular biology · 2010Article
- Local and global effects of strong DNA bending induced during molecular dynamics simulations.Nucleic acids research · 2009Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The short-time (submicrosecond) bending dynamics of duplex DNA were measured to determine the effect of sequence on dynamics. All measurements were obtained from a single site on duplex DNA, using a single, site-specific modified base containing a rigidly tethered, electron paramagnetic resonance active spin probe. The observed dynamics are interpreted in terms of single-step sequence-dependent bending force constants, determined from the mean squared amplitude of bending relative to the end-to-end vector using the modified weakly bending rod model. The bending dynamics at a single site are a function of the sequence of the nucleotides constituting the duplex DNA. We developed and examined several dinucleotide-based models for flexibility. The models indicate that the dominant feature of the dynamics is best explained in terms of purine- and pyrimidine-type steps, although distinction is made among all 10 unique steps: It was found that purine-purine steps (which are the same as pyrimidine-pyrimidine steps) were near average in flexibility, but the pyrimidine-purine steps (5' to 3') were nearly twice as flexible, whereas purine-pyrimidine steps were more than half as flexible as average DNA. Therefore, the range of stepwise flexibility is approximately fourfold and is characterized by both the type of base pair step (pyrimidine/purine combination) and the identity of the bases within the pair (G, A, T, or C). All of the four models considered here underscore the complexity of the dependence of dynamics on DNA sequence with certain sequences not satisfactorily explainable in terms of any dinucleotide model. These findings provide a quantitative basis for interpreting the dynamics and kinetics of DNA-sequence-dependent biological processes, including protein recognition and chromatin packaging.
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