Mismatches Improve the Performance of Strand-Displacement Nucleic Acid Circuits

• Published in: Angewandte Chemie International Edition Vol. 53; no. 7; pp. 1845 - 1848
• Main Authors: Jiang, Yu Sherry, Bhadra, Sanchita, Li, Bingling, Ellington, Andrew D.
• Format: Journal Article
• Language: English
• Published: Weinheim WILEY-VCH Verlag 10.02.2014; WILEY‐VCH Verlag; Wiley Subscription Services, Inc
• Edition: International ed. in English
• Subjects: Amino Acid Sequence; Amplification; Assembly; bioanalysis; Catalysis; Catalysts; Circuits; Damping; DNA - chemistry; DNA structures; Fluorimetry; hairpin loops; Inverted Repeat Sequences; mismatch; Molecular Sequence Data; nanobiotechnology; Nanotechnology; Nucleic Acid Conformation; Nucleic Acid Hybridization - methods; Nucleic acids; nanobiotechnology; hairpin loops; bioanalysis; DNA structures; mismatch
• ISSN: 1433-7851; 1521-3773
• DOI: 10.1002/anie.201307418

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. Catalytic hairpin assembly (CHA) is a useful amplification method for the detection of nucleic acids. CHA circuits, however, have been shown to execute non‐specifically even in the absence of catalyst, which can make quantitation of lower input concentrations difficult. By introducing two mismatched bases into a specific domain on the circuit, the signal‐to‐background ratio can be improved from less than 10:1 to over 100:1.