title: Topological constraints in nucleic acid hybridization kinetics.
abstract: 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.
authors.affiliation: Department of Chemical Engineering, California Institute of Technology Pasadena, CA 91125, USA.
authors.forename: Justin S
authors.initials: JS
authors.lastname: Bois
authors.forename: Suvir
authors.initials: S
authors.lastname: Venkataraman
authors.forename: Harry M T
authors.initials: HM
authors.lastname: Choi
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Spakowitz
authors.forename: Zhen-Gang
authors.initials: ZG
authors.lastname: Wang
authors.forename: Niles A
authors.initials: NA
authors.lastname: Pierce
mesh_terms: D020029:Base Pairing; D004277:DNA, Single-Stranded / Q000737:chemistry*; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D012313:RNA / Q000737:chemistry*
chemical_list: D004277:DNA, Single-Stranded; D012313:RNA