Expanding the Rule Set of DNA Circuitry with Associative Toehold Activation

Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin Texas 78712, USA.
Journal of the American Chemical Society (Impact Factor: 12.11). 11/2011; 134(1):263-71. DOI: 10.1021/ja206690a
Source: PubMed


Toehold-mediated strand displacement has proven extremely powerful in programming enzyme-free DNA circuits and DNA nanomachines. To achieve multistep, autonomous, and complex behaviors, toeholds must be initially inactivated by hybridizing to inhibitor strands or domains and then relieved from inactivation in a programmed, timed manner. Although powerful and reasonably robust, this strategy has several drawbacks that limit the architecture of DNA circuits. For example, the combination between toeholds and branch migration (BM) domains is 'hard wired' during DNA synthesis thus cannot be created or changed during the execution of DNA circuits. To solve this problem, I propose a strategy called 'associative toehold activation', where the toeholds and BM domains are connected via hybridization of auxiliary domains during the execution of DNA circuits. Bulged thymidines that stabilize DNA three-way junctions substantially accelerate strand displacement reactions in this scheme, allowing fast strand displacement initiated by reversible toehold binding. To demonstrate the versatility of the scheme, I show (1) run-time combination of toeholds and BM domains, (2) run-time recombination of toeholds and BM domains, which results in a novel operation 'toehold switching', and (3) design of a simple conformational self-replicator.

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    • "Toehold-driven systems can usually be operated in a reversible fashion, but they underlie certain experimental restrictions, such as the gradual dilution of the sample. Recent developments in toehold-mediated strand displacement like the remote toehold approach (19) or the associative toehold activation (20) direct towards improved control of the displacement kinetics. "
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