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This article is part of the supplement: Proceedings of the Fourth Annual MCBIOS Conference. Computational Frontiers in Biomedicine

Open Access Proceedings

Preliminary nanopore cheminformatics analysis of aptamer-target binding strength

Karen Thomson12, Iftekhar Amin12, Eric Morales2 and Stephen Winters-Hilt12*

Author Affiliations

1 Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA

2 Research Institute for Children, Children's Hospital, New Orleans, LA 70118, USA

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BMC Bioinformatics 2007, 8(Suppl 7):S11  doi:10.1186/1471-2105-8-S7-S11

Published: 1 November 2007



Aptamers are nucleic acids selected for their ability to bind to molecules of interest and may provide the basis for a whole new class of medicines. If the aptamer is simply a dsDNA molecule with a ssDNA overhang (a "sticky" end) then the segment of ssDNA that complements that overhang provides a known binding target with binding strength adjustable according to length of overhang.


Two bifunctional aptamers are examined using a nanopore detector. They are chosen to provide sensitive, highly modulated, blockade signals with their captured ends, while their un-captured regions are designed to have binding moieties for complementary ssDNA targets. The bifunctional aptamers are duplex DNA on their channel-captured portion, and single-stranded DNA on their portion with binding ability. For short ssDNA, the binding is merely to the complementary strand of DNA, which is what is studied here – for 5-base and 6-base overhangs.


A preliminary statistical analysis using hidden Markov models (HMMs) indicates a clear change in the blockade pattern upon binding by the single captured aptamer. This is also consistent with the hypothesis that significant conformational changes occur during the annealing binding event. In further work the objective is to simply extend this ssDNA portion to be a well-studied ~80 base ssDNA aptamer, joined to the same bifunctional aptamer molecular platform.