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Nucleic Acids Research, 2003, Vol. 31, No. 4 1311-1318
© 2003 Oxford University Press

Discrimination among individual Watson–Crick base pairs at the termini of single DNA hairpin molecules

Wenonah A. Vercoutere1,2, Stephen Winters-Hilt1,3, Veronica S. DeGuzman1,2, David Deamer1,2, Sam E. Ridino1, Joseph T. Rodgers1, Hugh E. Olsen2, Andre Marziali4 and Mark Akeson*,1,2,3

1 Center for Biomolecular Science and Engineering, 2 Department of Chemistry and Biochemistry, and 3 Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA and 4 Department of Physics and Astronomy, University of British Columbia, Vancouver, Canada

*To whom correspondence should be addressed. Tel: +1 831 459 5157; Fax: +1 831 459 2935; Email: makeson{at}chemistry.ucsc.edu

Nanoscale {alpha}-hemolysin pores can be used to analyze individual DNA or RNA molecules. Serial examination of hundreds to thousands of molecules per minute is possible using ionic current impedance as the measured property. In a recent report, we showed that a nanopore device coupled with machine learning algorithms could automatically discriminate among the four combinations of Watson–Crick base pairs and their orientations at the ends of individual DNA hairpin molecules. Here we use kinetic analysis to demonstrate that ionic current signatures caused by these hairpin molecules depend on the number of hydrogen bonds within the terminal base pair, stacking between the terminal base pair and its nearest neighbor, and 5' versus 3' orientation of the terminal bases independent of their nearest neighbors. This report constitutes evidence that single Watson–Crick base pairs can be identified within individual unmodified DNA hairpin molecules based on their dynamic behavior in a nanoscale pore.


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