help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Okonogi, T. M.
Right arrow Articles by Robinson, B. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Okonogi, T. M.
Right arrow Articles by Robinson, B. H.

Biophys J, December 1999, p. 3256-3276, Vol. 77, No. 6

Flexibility of Duplex DNA on the Submicrosecond Timescale

T. M. Okonogi,* A. W. Reese,* S. C. Alley,*# P. B. Hopkins,* and B. H. Robinson*

 *Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, and  #Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802

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 Å 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 Å, approximately 1500 Å is accounted for by static bends and 750 Å by fluctuating bends. A measured dynamic persistence length of around 1500 Å 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.

Biophys J, December 1999, p. 3256-3276, Vol. 77, No. 6
© 1999 by the Biophysical Society   0006-3495/99/12/3256/21  $2.00


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
P. Cekan, A. L. Smith, N. Barhate, B. H. Robinson, and S. Th. Sigurdsson
Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation
Nucleic Acids Res., October 1, 2008; 36(18): 5946 - 5954.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. K. Mazur
Evaluation of Elastic Properties of Atomistic DNA Models
Biophys. J., December 15, 2006; 91(12): 4507 - 4518.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
B. S. Fujimoto, G. P. Brewood, and J. M. Schurr
Torsional Rigidities of Weakly Strained DNAs
Biophys. J., December 1, 2006; 91(11): 4166 - 4179.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. Sakamoto, A. Mahara, K. Yamagata, R. Iwase, T. Yamaoka, and A. Murakami
Evaluation of Dynamic Features of Escherichia coli 16S Ribosomal RNA in Homogeneous Physiological Solution
Biophys. J., December 1, 2005; 89(6): 4122 - 4128.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. M. Somoza, D. Andreatta, C. J. Murphy, R. S. Coleman, and M. A. Berg
Effect of lesions on the dynamics of DNA on the picosecond and nanosecond timescales using a polarity sensitive probe
Nucleic Acids Res., May 6, 2004; 32(8): 2494 - 2507.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
T. M. Okonogi, S. C. Alley, A. W. Reese, P. B. Hopkins, and B. H. Robinson
Sequence-Dependent Dynamics of Duplex DNA: The Applicability of a Dinucleotide Model
Biophys. J., December 1, 2002; 83(6): 3446 - 3459.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. M. Okonogi, S. C. Alley, E. A. Harwood, P. B. Hopkins, and B. H. Robinson
Phosphate backbone neutralization increases duplex DNA flexibility: A model for protein binding
PNAS, April 2, 2002; 99(7): 4156 - 4160.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. Wu, K. M. Parkhurst, R. M. Powell, M. Brenowitz, and L. J. Parkhurst
DNA Bends in TATA-binding Protein{middle dot}TATA Complexes in Solution Are DNA Sequence-dependent
J. Biol. Chem., April 27, 2001; 276(18): 14614 - 14622.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 1999 by the Biophysical Society.