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Nucleic Acids Research 2004 32(16):4876-4883; doi:10.1093/nar/gkh826
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Published online 14 September 2004

Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved

DNA base pair resolution by single molecule force spectroscopy

Bernie D. Sattin, Andrew E. Pelling and M. Cynthia Goh*

Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada

* To whom correspondence should be addressed. Tel: +1 416 978 6254; Email: cgoh{at}chem.utoronto.ca
Present address: Andrew E. Pelling, UCLA, Department of Chemistry and Biochemistry, 607 Charles E. Young Dr East, Los Angeles, CA 90095, USA

Received June 1, 2004; Revised July 23, 2004; Accepted August 26, 2004

The forces that hold complementary strands of DNA together in a double helix, and the role of base mismatches in these, are examined by single molecule force spectroscopy using an atomic force microscope (AFM). These forces are important when considering the binding of proteins to DNA, since these proteins often mechanically stretch the DNA during their action. In AFM measurement of forces, there is an inherent instrumental limitation that makes it difficult to compare results from different experimental runs. This is circumvented by using an oligonucleotide microarray, which allowed a direct comparison of the forces between perfectly matched short oligonucleotides and those containing a single or double mismatch. Through this greatly increased sensitivity, the force contribution of a single AT base pair was derived. The results indicate that the contribution to forces from the stacking interactions is more important than that from hydrogen bonding.


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