Catalyzed relaxation of a metastable DNA fuel

Practically all of lifes molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalysis of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in nucleic-acid-based engineering as it is in biology. Here we report a metastable DNA fuel" and a corresponding DNA catalyst" that improves upon the original hybridization-based catalyst of Ref. [1] by more than two orders of magnitude. This is achieved by identifying and purifying a fuel with a kinetically trapped metastable conguration consisting of a kissing loop" anked by and thus stabilized by helical domains; the catalyst strand acts by opening a helical domain and allowing the complex to relax to its ground state by a multistep pathway involving four-way branch migration. The improved fuel/catalyst system shows a roughly 5000-fold acceleration of the uncatalyzed reaction, with each catalyst molecule capable of turning over in excess of 50 substrates. With kcat/kM = 10^7 /M/min, comparable to many protein enzymes and ribozymes, this fuel system becomes a viable component enabling future DNA-based synthetic molecular machines, signal amplication and logic circuits.