"DNA hairpins: fuel for autonomous DNA devices".

Simon J Green ^1, *, Daniel Lubrich ¹, and Andrew J Turberfield ¹

¹ Department of Physics, Clarendon Laboratory,University of Oxford, Parks Road, OX1 3PU, U.K.

* To whom correspondence should be addressed. E-mail: simon.green@physics.ox.ac.uk

Abstract:

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

Additional References:

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Links to RNA and Biological Causality:

A Brief History of  Activator RNA:

Links to Euchromatin Activator RNA Reviews:
Links to Euchromatin Activator RNA Research:
Links to Ultrastructural Probes of DNase I-Sensitive Sites:
Links to RNA as a Therapeutic Agent:
Links to Hodgkin Lymphoma Immuno-Pathology:
Links to Activated T-Lymphocyte Immunotherapy:
Links to Medical Systems Biology:
Links to Selective Gene Transcription:
Links to RNA-Induced Epigenetics:
Links to RNA-Induced Embryogenesis:
Links to RNA and Biological Causality:
Links to Reprogramming and Neoplasia:

"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".