title: Design and Analysis of Localized DNA Hybridization Chain Reactions.
abstract: Theoretical models of localized DNA hybridization reactions on nanoscale substrates indicate potential benefits over conventional DNA hybridization reactions. Recently, a few approaches have been proposed to speed-up DNA hybridization reactions; however, experimental confirmation and quantification of the acceleration factor have been lacking. Here, a system to investigate localized DNA hybridization reactions on a nanoscale substrate is presented. The system consists of six metastable DNA hairpins that are tethered to a long DNA track. The localized DNA hybridization reaction of the proposed system is triggered by a DNA strand which initiates the subsequent self-assembly. Fluorescence kinetics indicates that the half-time completion of a localized DNA hybridization chain reaction is six times faster than the same reaction in the absence of the substrate. The proposed system provides one of the first known quantification of the speed-up of DNA hybridization reactions due to the locality effect.
authors.affiliation: Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA.
authors.forename: Hieu
authors.initials: H
authors.lastname: Bui
authors.affiliation: Department of Biomedical Engineering, Duke University, 101 Science Drive, Campus Box, 90281, 27708, USA.
authors.forename: Vincent
authors.initials: V
authors.lastname: Miao
authors.affiliation: Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA.
authors.forename: Sudhanshu
authors.initials: S
authors.lastname: Garg
authors.affiliation: Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA.
authors.forename: Reem
authors.initials: R
authors.lastname: Mokhtar
authors.affiliation: Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA.
authors.forename: Tianqi
authors.initials: T
authors.lastname: Song
authors.affiliation: Department of Computer Science, Duke University, 308 Research Drive, Campus Box, 90129, 27708, USA.
authors.forename: John
authors.initials: J
authors.lastname: Reif
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D005453:Fluorescence; D007700:Kinetics; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D004247:DNA
keywords: DNA hairpins; DNA nanotechnology; DNA self-assembly; localized reactions; speed-up