Hybridization Chain Reaction Design and Biosensor Implementation

Abstract

DNA biosensors could overcome some of the common drawbacks of lab-based techniques for nucleic acids detection for diagnostics purposes. One of the main impediments for such applications of DNA biosensors is their lack of sensitivity: this can prevent their full exploitation in the diagnostic analytical field. DNA nanotechnology could enhance DNA biosensors and let them perform at the required high sensitivity. Well-designed, programmable self-assembly reactions can be triggered by a specific nucleic acid target. The Hybridization Chain Reaction (HCR) is a self-assembly strategy in which the target nucleic acid sequence triggers the formation of long nicked double-stranded DNA nanostructures. This can be performed in solution or on a surface, and the process can be coupled to different signal transduction schemes. We here describe the methods to design and test HCR reactions for the detection of different nucleic acid targets in solution and the procedures to exploit this strategy on surfaces with an electrochemical biosensing platform.

A miRNA biosensor based on localized surface plasmon resonance enhanced by surface-bound hybridization chain reaction

“…Consequently, the recognition-dependent HCR reaction is triggered only in the case of complete sequence-specific hairpin unfolding, not simply upon binding of any sequence to the probe (see Scheme 1 ). The hairpin probe was designed in the context of the guidelines for HCR ( Miti and Zuccheri, 2018 ), and it was merely a thiolated version of one of the two HCR hairpin components. The probe-derivatized chips were passivated with mercaptohexanol (MCH) and salmon sperm DNA.…”

“…The specific hairpin monomers H1 and H2 here employed were designed for miR-17 detection ( Miti and Zuccheri, 2018 ). Their self-assembly was first demonstrated by us through experiments in solution (see section S4 in SI).…”

Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays

“…71 HCR is a signal-enhancing technique that relies on the autonomous self-assembly of two substable hairpin structures (short DNA fragments) through specific interaction for the generation of long nicked DNA double helices, 72 the reaction involves only two hairpins of equal concentration of a certain base length, which coexist stably in solution. 73 HCR is a simple and efficient enzyme-free isothermal amplification reaction, and the design and characterization of a highly specific and efficient HCR will be useful for biosensor applications. An isothermal autocatalytic hybridization reaction (AHR) circuit for sensitive detection of DNA methyltransferase and inhibitors assay was developed by Li and others, 74 by combining the catalytic hairpin assembly (CHA) converter with the hybridization chain reaction (HCR) amplifier, and the schematic diagram of the reaction is shown in Fig.…”

Designer, Programmable DNA‐peptide hybrid materials with emergent properties to probe and modulate biological systems

“…The poor stability in biological medium is due to the fact that order to compensate for the electrostatic repulsion between neighboring DNA helices in nanostructures, relatively high concentrations of Mg +2 ions are used. The corresponding concentration of Mg +2 in biological media such as serum is much lower [85,90,91] . Mg +2 is used over other ions owing to certain site‐specific interactions and binding affinities that allows these DNA nanostructures to be transferred to Mg +2 ‐free buffers without any loss of integrity.…”

“…The corresponding concentration of Mg + 2 in biological media such as serum is much lower. [85,90,91] Mg + 2 is used over other ions owing to certain site-specific interactions and binding affinities that allows these DNA nanostructures to be transferred to Mg + 2 -free buffers without any loss of integrity. The issue however is other media components such as phosphate ions which tend to interfere with the Mg + 2 -bound DNA nanostructures, leading to denaturation.…”