title: Kinetics of Proximity-Induced Intramolecular DNA Strand Displacement.
abstract: Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechanisms involved in many DNA-mediated proximity assays and protein-responsive DNA devices. However, the kinetic profile of PiDSD has never been systematically examined before. Herein, we report a systematic study to explore the kinetics of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolecular DNA strand-exchange strategy to measure a set of key kinetic parameters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals for the real-time monitoring of PiDSD. By using this approach, we have successfully revealed the kinetic profiles of PiDSD, determined the enhanced local effective concentrations of DNA probes that are involved in PiDSD, and identified a number of key factors that influence the kinetics of PiDSD. Our study on PiDSD establishes knowledge and strategies that can be used to guide the design and operation of various DNA-mediated proximity assays and protein-triggered DNA devices.
authors.affiliation: Department of Chemistry and Center for Biotechnology, Brock University , St. Catharines, Ontario L2S 3A1, Canada.
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton, Alberta T6G 2G3, Canada.
authors.forename: Yanan
authors.initials: Y
authors.lastname: Tang
authors.affiliation: Department of Chemistry and Center for Biotechnology, Brock University , St. Catharines, Ontario L2S 3A1, Canada.
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Traynor
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton, Alberta T6G 2G3, Canada.
authors.forename: Xing-Fang
authors.initials: XF
authors.lastname: Li
authors.affiliation: Department of Laboratory Medicine and Pathology, University of Alberta , Edmonton, Alberta T6G 2G3, Canada.
authors.forename: X Chris
authors.initials: XC
authors.lastname: Le
mesh_terms: D001710:Biotin / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D015342:DNA Probes / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry; D007700:Kinetics; D009693:Nucleic Acid Hybridization; D013050:Spectrometry, Fluorescence; D019809:Streptavidin / Q000737:chemistry / Q000378:metabolism
chemical_list: D015342:DNA Probes; D005456:Fluorescent Dyes; D001710:Biotin; D004247:DNA; D019809:Streptavidin