This Article Full Text Full Text (PDF) Supplement All Versions of this Article: biophysj.106.084681v1 91/8/2966    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Green, S. J. Articles by Turberfield, A. J. Search for Related Content PubMed PubMed Citation Articles by Green, S. J. Articles by Turberfield, A. J.

DNA Hairpins: Fuel for Autonomous DNA Devices

University of Oxford, Department of Physics, Clarendon Laboratory, Oxford, United Kingdom

Correspondence: Address reprint requests to Simon J. Green, University of Oxford, Dept. of Physics, Clarendon Laboratory, Parks Rd., Oxford OX1 3PU, UK. E-mail: simon.green{at}physics.ox.ac.uk.

We present a study of the hybridization of complementary DNA hairpin loops, with particular reference to their use as fuel for autonomous DNA devices. The rate of spontaneous hybridization between complementary hairpins can be reduced by increasing the neck length or decreasing the loop length. Hairpins with larger loops rapidly form long-lived kissed complexes. Hairpin loops may be opened by strand displacement using an opening strand that contains the same sequence as half of the neck and a "toehold" complementary to a single-stranded domain adjacent to the neck. We find loop opening via an external toehold to be 10–100 times faster than via an internal toehold. We measure rates of loop opening by opening strands that are at least 1000 times faster than the spontaneous interaction between hairpins. We discuss suitable choices for loop, neck, and toehold length for hairpin loops to be used as fuel for autonomous DNA devices.