A rapid signal amplification system based on the self-replicating catalyzed hairpin assembly is reported in which two hairpins, H1 and H2, were well-designed in which two split target/trigger DNA and two split G-quadruplex sequences were respectively integrated into H1 and H2. Target/trigger DNA can be cyclically used in this system to form the duplex DNA assemblies (H1-H2), which will bring the two G-quadruplex fragments into close-enough proximity to induce the formation of intact G-quadruplex as a colorimetric signal readout. Similarly, the two split target/trigger DNA sequences will reunite into a DNA sequence that is identical to the target/trigger DNA; then, the obtained replica can also be cyclically used as a new activator unit to trigger the CHA reaction, leading to the rapidly and significantly enhanced formation of target/trigger DNA replicas with the concomitant generation of a higher signal. This self-replication-based autocatalytic signal amplified approach has been successfully used to develop a rapid and visual assay for DNA and small molecule detection.

It is known that the adsorption of short single-stranded DNA (ssDNA) on unmodified gold nanoparticles (AuNPs) is much faster than that for long ssDNA, and thus leads to length-dependent AuNPs aggregation after addition of salt, the color of the solutions sequentially changed from red to blue in accordance with the increase of ssDNA length. However, we found herein that the ssDNA sticky end of hairpin DNA exhibited a completely different adsorption behavior compared to ssDNA, an inverse blue-to-red color variation was observed in the colloid solution with the increase of sticky end length when the length is within a certain range. This unusual sequence length-dependent AuNPs aggregation might be ascribed to the effect of the stem of hairpin DNA. On the basis of this unique phenomenon and catalytic hairpin assembly (CHA) based signal amplification, a novel AuNPs-based colorimetric DNA assay with picomolar sensitivity and specificity was developed. This unusual sequence length-dependent AuNPs aggregation of the ssDNA sticky end introduces a new direction for the AuNPs-based colorimetric assays.

No abstract

One-dimensional DNA polymer chains were obtained based on the catalyzed hairpin assembly and sticky end self-assembly, which led to a signal amplified colorimetric nucleic acid assay.

A rapid room-temperature DNA nanowires preparation strategy on the basis of self-replicating catalyzed hairpin assembly (SRCHA) was reported. In this system, three hairpin probes (P1, P2, and P3) were well-designed and partially hybridize to each other, and two split trigger DNA sequences were integrated into P1 and P3, respectively. When the SRCHA was initiated by the trigger DNA, a series of DNA assembly steps based on the toehold-mediated DNA strand displacement were activated, and the Y shaped DNA (P1−P2− P3) was formed. In that case, the two split trigger DNA sequences will come into close-enough proximity to form the trigger DNA replicas, which can initiate the additional SRCHA reaction cycles for DNA nanowire preparation, and eventually a rapid room-temperature DNA nanowires preparation strategy without need of fuel strands was successfully developed. Furthermore, the prepared DNA nanowires have been used to develop a rapid and signal amplified sensing platform for sensitive adenosine triphosphate (ATP) detection.