ArticleBiophysical journal1999
Flexibility of duplex DNA on the submicrosecond timescale.
Article in Biophysical journal, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin.Faraday discussions · 2016Article
- Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC).Biochimica et biophysica acta · 2015Article
- On the absence of intrahelical DNA dynamics on the μs to ms timescale.Nature communications · 2014Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
- Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes.Biochemistry · 2009Article
- Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy.The journal of physical chemistry. B · 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
- Evaluation of elastic properties of atomistic DNA models.Biophysical journal · 2006Article
- Torsional rigidities of weakly strained DNAs.Biophysical journal · 2006Article
- A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns.Chemical research in toxicology · 2006Review
- Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.Molecular genetics and genomics : MGG · 2005Article
- Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution.Biophysical journal · 2005Article
- Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe.Nucleic acids research · 2004Article
- Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model.Biophysical journal · 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
- Sequence-dependent dynamics in duplex DNA.Biophysical journal · 2000Article
- Dynamic bending rigidity of a 200-bp DNA in 4 mM ionic strength: a transient polarization grating study.Biophysical journal · 2000Article
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Authors and funding
5 authors.
Funding
Abstract
Using a site-specific, Electron Paramagnetic Resonance (EPR)-active spin probe that is more rigidly locked to the DNA than any previously reported, the internal dynamics of duplex DNAs in solution were studied. EPR spectra of linear duplex DNAs containing 14-100 base pairs were acquired and simulated by the stochastic Liouville equation for anisotropic rotational diffusion using the diffusion tensor for a right circular cylinder. Internal motions have previously been assumed to be on a rapid enough time scale that they caused an averaging of the spin interactions. This assumption, however, was found to be inconsistent with the experimental data. The weakly bending rod model is modified to take into account the finite relaxation times of the internal modes and applied to analyze the EPR spectra. With this modification, the dependence of the oscillation amplitude of the probe on position along the DNA was in good agreement with the predictions of the weakly bending rod theory. From the length and position dependence of the internal flexibility of the DNA, a submicrosecond dynamic bending persistence length of around 1500 to 1700 A was found. Schellman and Harvey (Biophys. Chem. 55:95-114, 1995) have estimated that, out of the total persistence length of duplex DNA, believed to be about 500 A, approximately 1500 A is accounted for by static bends and 750 A by fluctuating bends. A measured dynamic persistence length of around 1500 A leads to the suggestion that there are additional conformations of the DNA that relax on a longer time scale than that accessible by linear CW-EPR. These measurements are the first direct determination of the dynamic flexibility of duplex DNA in 0.1 M salt.
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