DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants

Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.

Anodic Electrogenerated Chemiluminescence of Ru(bpy)3(2+) with CdSe Quantum Dots as Coreactant and Its Application in Quantitative Detection of DNA

In the present paper, we report that CdSe quantum dots (QDs) can act as the coreactant of Ru(bpy)₃²⁺ electrogenerated chemiluminescence (ECL) in neutral condition. Strong anodic ECL signal was observed at ~1.10 V at CdSe QDs modified glassy carbon electrode (CdSe/GCE), which might be mainly attributed to the apparent electrocatalytic effect of QDs on the oxidation of Ru(bpy)₃²⁺. Ru(bpy)₃²⁺ can be intercalated into the loop of hairpin DNA through the electrostatic interaction to fabricate a probe. When the probe was bound to the CdSe QDs modified on the GCE, the intense ECL signal was obtained. The more Ru(bpy)₃²⁺ can be intercalated when DNA loop has larger diameter and the stronger ECL signal can be observed. The loop of hairpin DNA can be opened in the presence of target DNA to release the immobilized Ru(bpy)₃²⁺, which can result in the decrease of ECL signal. The decreased ECL signal varied linearly with the concentration of target DNA, which showed the ECL biosensor can be used in the sensitive detection of DNA. The proposed ECL biosensor showed an excellent performance with high specificity, wide linear range and low detection limit.

Spectrophotometric and ultrasensitive DNA bioassay by circular-strand displacement polymerization reaction

We demonstrated a new spectrophotometric DNA detection approach based on a circular strand-displacement polymerization reaction for the quantitative detection of sequence specific DNA. In this assay, the hybridization of an immobilized hairpin probe on the microtiter plate, to target DNA, results in a conformational change and leads to a stem separation. A short primer thus anneals with the open stem and triggers a polymerization reaction, allowing a cyclic reaction comprising the release of target DNA and hybridization of the target with the remaining immobilized hairpin probe. Through this cyclical process, a large number of duplex DNA complexes are produced. Finally, the biotin modified duplex DNA products can be detected via the HRP catalyzed substrate 3,3',5,5'-tetramethylbenzidine using a spectrophotometer. As a proof of concept, a short DNA sequence (20-nt) related to the South East Asia (SEA) type deletion of α-thalassemia was chosen as the model target. This proposed assay has a very high sensitivity and selectivity with a dynamic response ranging from 0.1 fM to 10 nM and the detection limit was 8 aM. It can be performed within 2 hours, and it can differentiate target SEA DNA from wild-type DNA. By substituting the hairpin probes used in the present work, this assay can be used to detect other subtypes of genetic disorders.