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Biophys. J. BioFAST: First Published October 29, 2004. doi:10.1529/biophysj.103.036293
© 2004 by the Biophysical Society.

A more recent version of this article appeared on January 1, 2005.
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Andy Sischka
Katja Toensing
Rainer Eckel
Sven David Wilking
Nobert Sewald
Robert Ros
Dario Anselmetti
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NUCLEIC ACIDS

Molecular mechanisms and kinetics between DNA and DNA binding ligands

Andy Sischka 1, Katja Toensing 1, Rainer Eckel 1, Sven David Wilking 2, Nobert Sewald 2, Robert Ros 1 and Dario Anselmetti 1*

1 Faculty of Physics, Bielefeld University
2 Faculty of Chemistry, Bielefeld University

* To whom correspondence should be addressed. E-mail: dario.anselmetti{at}physik.uni-bielefeld.de.

Submitted on December 17, 2003
Revised on February 20, 2004
Accepted on 13 October 2004


  Abstract
Mechanical properties of single double stranded DNA (dsDNA) in the presence of different binding ligands were analyzed in optical tweezers experiments with sub-piconewton force resolution. The binding of ligands to DNA change the overall mechanic response of the dsDNA molecule. This fundamental property can be used for discrimination and identification of different binding modes and, furthermore, may be relevant for various processes like nucleosome packing or applications like cancer therapy. We compared the effects of the minor groove binder distamycin-A, a major groove binding {alpha}-helical peptide, the intercalator ethidium bromide, YO-1 and daunomycin as well as the bisintercalator YOYO-1 on {lambda}-DNA. Binding of molecules to the minor and major groove of dsDNA induces distinct changes in the molecular elasticity compared to the free dsDNA detectable as a shift of the overstretching transition to higher forces. Intercalating molecules affect the molecular mechanics by a complete disappearance of the overstretching transition and an associated increase in molecular contour length. Significant force hysteresis effects occurring during stretching/relaxation cycles with velocities above 10 nm/s for YOYO-1 and 1,000 nm/s for daunomycin. These indicates structural changes in the timescale of minutes for the YOYO-DNA and of seconds for the daunomycin-DNA complexes, respectively.

Key Words: dsDNA elasticity, hysteresis effects, molecular binding kinetics, optical tweezers, single molecule force spectroscopy, time dependent mechanical properties




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Copyright © 2004 by the Biophysical Society.