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 singles-stranded catalyst, and this non-specific background degrades signal-to-noise. The introduction of mismatched base-pairs that impede uncatalyzed strand exchange reactions greatly decreased background signal while only partially damping signal in the presence of catalyst. Various types and lengths of mismatches were assayed by fluorimetry and in many instances our MismatCHA designs yielded 100-fold signal-to-background ratios compared to a similar ratio of 4 with the perfectly matched substrates. These observations may prove to be of general utility for the design of non-enzymatic nucleic acid circuits.

Hairpin assembly circuit-based fluorescence cooperative amplification strategy for enzyme-free and label-free detection of small molecule

“…That is because the upstream leakage can be amplified by the downstream, generating remarkable background. In toeholdmediated DNA amplified circuits, there are two major sources of leakage: impurities [32] and toehold-independent reactions [33]. That is to say, we can decrease the background by better synthesis or purification methods to improve the purity of DNA sequences.…”

Rational Design of Electrochemical DNA Biosensors for Point‐of‐Care Applications

“…Indeed, the principle of introducing mismatches can also be applied in the leakage issues in CHA cascades mentioned previously. A mismatch can be introduced on the sites where breathing is expected, and the background signal will be significantly lowered …”

Amplified fluorescence detection of DNA based on catalyzed dynamic assembly and host–guest interaction between β-cyclodextrin polymer and pyrene

“…In the past few decades, inspired by the simple rules governing hybridization of metastable DNA molecules, researchers have developed many attractive signal-amplification approaches based on the catalyzed dynamic assembly for biochemical analytical applications [10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27]. For example, Pierce group constructed a kind of in situ amplifier for multiplexed imaging of mRNAs in fixed whole mount and sectioned zebrafish embryos [18].…”