Speeding up a single-molecule DNA device with a simple catalyst

Abstract

Recently, several groups have designed and synthesized single-molecule devices based on DNA that can switch between different configurations in response to sequential addition of fuel DNA strands. There is considerable interest in improving the speed of these "nanomotors." One approach is the use of rationally designed DNA catalysts to promote hybridization of complementary oligonucleotides. A particularly simple and robust DNA device reported by Li and Tan is comprised of a single-strand 17-base oligomer that folds into a chairlike quadruplex structure. We have identified the key rate-limiting barrier in this device as the tendency for one of the fuel strands B to fold into the quadruplex configuration of the device strand. This seriously impedes the restoration reaction. We have designed a catalytic strand to inhibit the folding of B and shown that the catalyst speeds up the restoration reaction by roughly a factor of 2. The catalyst remains effective even after repeated cycling