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1: Nucleic Acids Res. 2005 Jul 25;33(13):4090-5. Print 2005.
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Topological constraints in nucleic acid hybridization kinetics.

Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA.

Department of Chemical Engineering, California Institute of Technology Pasadena, CA 91125, USA.

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.

Publication Types:
PMID: 16043632 [PubMed - indexed for MEDLINE]

PMCID: PMC1180668