title: Mismatches improve the performance of strand-displacement nucleic Acid circuits.
abstract: Catalytic hairpin assembly (CHA) has previously proven useful as a transduction and amplification method for nucleic acid detection. However, the two hairpin substrates in a CHA circuit can potentially react non-specifically even in the absence of a single-stranded catalyst, and this non-specific background degrades the signal-to-noise ratio. The introduction of mismatched base pairs that impede uncatalyzed strand exchange reactions led to a significant decrease of the background signal, while only partially damping the signal in the presence of a catalyst. Various types and lengths of mismatches were assayed by fluorimetry, and in many instances, our MismatCHA designs yielded 100-fold increased signal-to-background ratios compared to a ratio of 4:1 with the perfectly matched substrates. These observations could be of general utility for the design of non-enzymatic nucleic acid circuits.
authors.affiliation: Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, 2500 Speedway, Austin, TX (USA).
authors.forename: Yu Sherry
authors.initials: YS
authors.lastname: Jiang
authors.forename: Sanchita
authors.initials: S
authors.lastname: Bhadra
authors.forename: Bingling
authors.initials: B
authors.lastname: Li
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
mesh_terms: D000595:Amino Acid Sequence; D002384:Catalysis; D004247:DNA / Q000737:chemistry*; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*
chemical_list: D004247:DNA
keywords: DNA structures; bioanalysis; hairpin loops; mismatch; nanobiotechnology