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Biophys. J. BioFAST: First Published April 27, 2007. doi:10.1529/biophysj.106.100511
© 2007 by the Biophysical Society.

A more recent version of this article appeared on August 15, 2007.
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Gregor Neuert
Christian Albrecht
Hermann E Gaub
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NUCLEIC ACIDS

PREDICTING THE RUPTURE PROBABILITIES OF MOLECULAR BONDS IN SERIES

Gregor Neuert 1*, Christian Albrecht 2 and Hermann E Gaub 3

1 Ludwig-Maximilians-University Munich
2 Munich University
3 Ludwig-Maximilians-University Munich, chair for applied physics & Center for Nano Science

* To whom correspondence should be addressed. E-mail: gneuert{at}mit.edu.

Submitted on November 6, 2006
Revised on December 18, 2006
Accepted on 13 March 2007


  Abstract
An assembly of two receptor ligand bonds in series will typically break at the weaker complex upon application of an external force. The rupture site depends highly on the binding potentials of both bonds and on the loading rate of the applied force. A model is presented that allows simulations of force induced rupture of bonds in series at a given force and loading rate based on the natural dissociation rates kR0,S0 and the potential width {Delta}XR,S of the reference and sample bonds. The model is especially useful for the analysis of differential force assay experiments. This is illustrated by experiments on molecular force balances consisting of two 30 bp oligonucleotide duplexes where kR0,S0 and {Delta}XR,S have been determined for different single nucleotide mismatches. Furthermore, prediction of the rupture site of two bonds in series is demonstrated for DNA duplexes in combination with streptavidin / biotin and anti-digoxigenin / digoxigenin respectively.

Key Words: DNA, biotin streptavidin, differential force assay, digoxigenin, force spectroscopy, unbinding pathway




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Copyright © 2007 by the Biophysical Society.