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Biophys. J. BioFAST: First Published June 8, 2007. doi:10.1529/biophysj.107.106112
© 2007 by the Biophysical Society.

A more recent version of this article appeared on October 1, 2007.
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NUCLEIC ACIDS

B-S Transition in Short Oligonucleotides

Julia Morfill 1*, Ferdinand Kühner 1, Kerstin Blank 2, Robert Lugmaier 1, Julia Sedlmair 1 and Hermann E. Gaub 1

1 Lehrstuhl für Angewandte Physik & Center for Nanosciene, LMU München
2 Institut de Science et d'Ingenierie Supramoleculaires (ISIS), Laboratoire de Biologie Chimique

* To whom correspondence should be addressed. E-mail: julia{at}morfill.de.

Submitted on February 7, 2007
Revised on March 21, 2007
Accepted on 29 May 2007


  Abstract
Stretching experiments with long double stranded DNA molecules in physiological ambient revealed a force-induced transition at a force of 65 pN. During this transition between B-DNA and highly overstretched S-DNA the DNA lengthens by a factor of 1.7 of its B-form contour length. Here, we report the occurrence of this so-called B-S transition in short duplexes consisting of 30 base pairs. We employed AFM-based single molecule force spectroscopy to explore the unbinding mechanism of two short duplexes containing 30 or 20 base pairs by pulling at the opposite 5' termini. For a 30 base pair long DNA duplex the B-S transition is expected to cause a length increase of 6.3 nm and should therefore be detectable. Indeed 30 % of the measured force-extension curves exhibit a region of constant force (plateau) at 65 pN, which corresponds to the B-S transition. The observed plateaus show a length between 3 nm and 7 nm. This plateau length distribution indicates, that the dissociation of a 30 base pair duplex mainly occurs during the B-S transition. In contrast, the measured force-extension curves for a 20 base pair DNA duplex exhibited rupture forces below 65 pN and did not show any evidence of a B-S transition.

Key Words: Atomic Force Microscope, B-S transition, DNA, oligonucleotide, single molecule force spectroscopy




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Copyright © 2007 by the Biophysical Society.