Design and analysis of linear cascade DNA hybridization chain reactions using DNA hairpins


Journal Article

© 2017 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft. DNA self-assembly has been employed non-conventionally to construct nanoscale structures and dynamic nanoscale machines. The technique of hybridization chain reactions by triggered self-assembly has been shown to form various interesting nanoscale structures ranging from simple linear DNA oligomers to dendritic DNA structures. Inspired by earlier triggered self-assembly works, we present a system for controlled self-assembly of linear cascade DNA hybridization chain reactions using nine distinct DNA hairpins. NUPACK is employed to assist in designing DNA sequences and Matlab has been used to simulate DNA hairpin interactions. Gel electrophoresis and ensemble fluorescence reaction kinetics data indicate strong evidence of linear cascade DNA hybridization chain reactions. The half-time completion of the proposed linear cascade reactions indicates a linear dependency on the number of hairpins.

Full Text

Duke Authors

Cited Authors

  • Bui, H; Garg, S; Miao, V; Song, T; Mokhtar, R; Reif, J

Published Date

  • January 1, 2017

Published In

Volume / Issue

  • 19 / 1

International Standard Serial Number (ISSN)

  • 1367-2630

Digital Object Identifier (DOI)

  • 10.1088/1367-2630/aa53d0

Citation Source

  • Scopus