title: Robustness and modularity properties of a non-covalent DNA catalytic reaction.
abstract: The biophysics of nucleic acid hybridization and strand displacement have been used for the rational design of a number of nanoscale structures and functions. Recently, molecular amplification methods have been developed in the form of non-covalent DNA catalytic reactions, in which single-stranded DNA (ssDNA) molecules catalyze the release of ssDNA product molecules from multi-stranded complexes. Here, we characterize the robustness and specificity of one such strand displacement-based catalytic reaction. We show that the designed reaction is simultaneously sensitive to sequence mutations in the catalyst and robust to a variety of impurities and molecular noise. These properties facilitate the incorporation of strand displacement-based DNA components in synthetic chemical and biological reaction networks.
authors.affiliation: California Institute of Technology, MC 136-93, 1200 E. California Blvd., Pasadena, CA 91125, USA. dzhang@dna.caltech.edu
authors.forename: David Yu
authors.initials: DY
authors.lastname: Zhang
authors.forename: Erik
authors.initials: E
authors.lastname: Winfree
mesh_terms: D002384:Catalysis; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D008954:Models, Biological; D013379:Substrate Specificity
chemical_list: D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D004247:DNA