title: Optically Controlled Signal Amplification for DNA Computation.
abstract: The hybridization chain reaction (HCR) and fuel-catalyst cycles have been applied to address the problem of signal amplification in DNA-based computation circuits. While they function efficiently, these signal amplifiers cannot be switched ON or OFF quickly and noninvasively. To overcome these limitations, a light-activated initiator strand for the HCR, which enabled fast optical OFF → ON switching, was developed. Similarly, when a light-activated version of the catalyst strand or the inhibitor strand of a fuel-catalyst cycle was applied, the cycle could be optically switched from OFF → ON or ON → OFF, respectively. To move the capabilities of these devices beyond solution-based operations, the components were embedded in agarose gels. Irradiation with customizable light patterns and at different time points demonstrated both spatial and temporal control. The addition of a translator gate enabled a spatially activated signal to travel along a predefined path, akin to a chemical wire. Overall, the addition of small light-cleavable photocaging groups to DNA signal amplification circuits enabled conditional control as well as fast photocontrol of signal amplification.
authors.affiliation: Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15217, United States.
authors.forename: Alexander
authors.initials: A
authors.lastname: Prokup
authors.affiliation: Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15217, United States.
authors.forename: James
authors.initials: J
authors.lastname: Hemphill
authors.affiliation: Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15217, United States.
authors.forename: Qingyang
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15217, United States.
authors.forename: Alexander
authors.initials: A
authors.lastname: Deiters
mesh_terms: D002384:Catalysis; D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry*; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization; D010777:Photochemistry / Q000379:methods
chemical_list: D004247:DNA
keywords: DNA computation; fuel−catalyst cycle; hybridization chain reaction; photochemistry; signal amplification