Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, University of Texas at Austin, Austin Texas 78712, USA.
J Am Chem Soc. 2012 Jan 11;134(1):263-71. doi: 10.1021/ja206690a. Epub 2011 Dec 14.
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.
适体介导的链位移已被证明在编程无酶 DNA 回路和 DNA 纳米机器方面非常强大。为了实现多步骤、自主和复杂的行为，适体必须通过与抑制剂链或结构域杂交来最初失活，然后以编程、定时的方式从失活中解脱出来。尽管这种策略功能强大且相当稳健，但它有几个缺点，限制了 DNA 回路的架构。例如，在 DNA 合成过程中，适体和分支迁移 (BM) 结构域之间的结合是“硬连线”的，因此在 DNA 回路的执行过程中无法创建或改变。为了解决这个问题，我提出了一种称为“关联适体激活”的策略，其中在 DNA 回路的执行过程中，通过辅助结构域的杂交将适体和 BM 结构域连接起来。在这个方案中，稳定 DNA 三链结的膨出胸腺嘧啶显著加速了链置换反应，允许通过可逆适体结合快速启动链置换。为了展示该方案的多功能性，我展示了 (1) 适体和 BM 结构域的运行时组合，(2) 适体和 BM 结构域的运行时重组，这导致了一种新的操作“适体切换”，以及 (3) 简单构象自我复制子的设计。
