DNA hairpins: fuel for autonomous DNA devices
Simon J Green 1*, Daniel Lubrich 1 and Andrew J Turberfield 1
1 University of Oxford
* To whom correspondence should be addressed. E-mail: s.green{at}physics.ox.ac.uk.
Submitted on March 8, 2006
Revised on April 14, 2006
Accepted on 10 July 2006
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Abstract |
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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.
Key Words:
hairpin loops, hybridization catalysis, kissing, molecular motors, nanotechnology, self-assembly
