Topological constraints in nucleic acid hybridization kinetics

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex

An autonomous polymerization motor powered by DNA hybridization

We present a synthetic molecular motor capable of autonomous nanoscale transport in solution. Inspired by bacterial pathogens such as Rickettsia rickettsii, which locomote by inducing the polymerization of the protein actin at their surfaces to form 'comet tails', the motor operates by polymerizing a double-helical DNA tail. DNA strands are propelled processively at the living end of the growing polymers, demonstrating autonomous locomotion powered by the free energy of DNA hybridization