title: Catalytic molecular logic devices by DNAzyme displacement.
abstract: Chemical reactions catalyzed by DNAzymes offer a route to programmable modification of biomolecules for therapeutic purposes. To this end, we have developed a new type of catalytic DNA-based logic gates in which DNAzyme catalysis is controlled via toehold-mediated strand displacement reactions. We refer to these as DNAzyme displacement gates. The use of toeholds to guide input binding provides a favorable pathway for input recognition, and the innate catalytic activity of DNAzymes allows amplification of nanomolar input concentrations. We demonstrate detection of arbitrary input sequences by rational introduction of mismatched bases into inhibitor strands. Furthermore, we illustrate the applicability of DNAzyme displacement to compute logic functions involving multiple logic gates. This work will enable sophisticated logical control of a range of biochemical modifications, with applications in pathogen detection and autonomous theranostics.
authors.affiliation: Center for Biomedical Engineering, MSC01 1141, 1 University of New Mexico, Albuquerque, NM 87131 (USA).
authors.forename: Carl W
authors.initials: CW
authors.lastname: Brown
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Lakin
authors.forename: Darko
authors.initials: D
authors.lastname: Stefanovic
authors.forename: Steven W
authors.initials: SW
authors.lastname: Graves
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D002384:Catalysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D021881:DNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism
chemical_list: D021881:DNA, Catalytic; D009841:Oligonucleotides; D004247:DNA
keywords: DNA strand displacement; DNAzymes; molecular logic; nucleic acids; sensors