Electrochemical detection of Nanog in cell extracts via target-induced resolution of an electrode-bound DNA pseudoknot

Signal-on electrogenerated chemiluminescence detection of gonyautoxin 1/4 based on proximity ligation-induced an electrode-bound pseudoknot DNA

A "signal on" electrogenerated chemiluminescence (electrochemiluminescence, ECL) aptasensor based on proximity ligation-induced an electrode-bound pseudoknot DNA for sensitive detection of gonyautoxin 1/4 (GTX1/4) was developed on basis of the competitive type reaction mode. Aptamer was adopted as recognition element. Ru(bpy)32+ as ECL signal, was attached on the glassy carbon electrode (GCE) surface modified with nafion and gold nanoparticles (AuNPs) by electrostatic attraction to obtain the ECL platform. The pseudoknot DNA as capture probe, was immobilized onto the ECL platform via Au-S bond to obtain the ECL aptasensor. In the absence of GTX1/4, Y-shape proximate cooperative complex among aptamer, pseudoknot DNA and DNA1 was formed, drawing the ferrocene groups Fc, as ECL quencher) of both pseudoknot DNA and DNA1 near the electrode surface and resulting in low ECL signal. In the presence of GTX1/4, GTX1/4 competed with pseudoknot DNA and DNA1 for aptamer in homogeneous solution, preventing the formation of proximate cooperative complex and keeping the capture DNA in the pseudoknot conformation with Fc groups far away from the electrode surface, generating a high ECL signal. The recovery of ECL intensity increased with the GTX1/4 concentration and allowed the detection of GTX1/4 in the range of 0.01 ng/mL to 10 ng/mL with a detection of limit as low as 6.56 pg/mL. Additionally, the accuracy of this method was validated for analysis of spiked sea water samples with good recoveries, which indicates great potential in commercial application.

A CRISPR-derived biosensor for the sensitive detection of transcription factors based on the target-induced inhibition of Cas12a activation

Transcription factors (TFs) are the key proteins for the decision of cell fates, and they have been recognized as potent markers for diagnostic and treatment of diseases. Herein, we report on a highly sensitive biosensor for the detection of TFs based on the CRISPR/Cas12a system. This biosensor was accomplished based on the competitive binding of the Cas12a-crRNA and TFs towards a dsDNA referred to as activator. Without TFs, the activator can be recognized by Cas12a-crRNA and cause the activation of the DNase activity of Cas12a. When TFs were added, the TFs can bind with the activator because the activator was designed to contain the specific binding sites of target TFs. We find that this binding can inhibit the association between Cas12a-crRNA and the activator, which hinders the activation of Cas12a. As a proof-of-concept, the rapid detection of five kinds of TFs was presented, and the detection was extended to the analysis of TFs expression in xenograft solid tumors from mice. This investigation is the first attempt to apply CRISPR technology in the sensing of TFs, and it discloses that the blocking of activator can be applied as a new sensing mechanism for the development of CRISPR-based biosensor.

Target-Induced Cascade Amplification for Homogeneous Virus Detection

Detection of viruses with high sensitivity is critical for the prevention and treatment of the related disease. Two homogeneous target-induced cascade amplification methods were proposed for the detection of enterovirus 71 and coxsackievirus B3. These methods both employ DNAzyme but differ in the way in which the DNAzyme is amplified. In the hybridization chain reaction (HCR)-based strategy, the DNAzyme is assembled by hairpin DNA strands, while in the rolling circle amplification (RCA)-based strategy, the DNAzyme is synthesized by the polymerase. On the basis of the virion structure, we investigated the effects of using only VP1-antibody or VP1-antibody and VP2-antibody on the detection. And the combination of two kinds of antibodies was found to further improve the performance of the detection. Subsequently, the simultaneous detection of EV71 and CVB3 was achieved by the RCA-based strategy. And the proposed methods were also applied in clinical samples analysis with a satisfactory result, showing great potential for applications in virus detection.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.