Self-Replication-Assisted Rapid Preparation of DNA Nanowires at Room Temperature and Its Biosensing Application

Abstract

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.

Smart Catalyzed Hairpin Assembly-Induced DNAzyme Nanosystem for Intracellular UDG Imaging

“…Recently, several isothermal signal amplification technologies, such as rolling circle amplification and nuclease-based target recycling amplification, − have yielded for amplifying and enhancing the detection sensitivity of targets. Alternatively, the strand displacement amplification, hybridization chain reaction, and catalyzed hairpin assembly (CHA) as enzyme-free amplification strategies with high signal-to-background ratios have been engineered to power ultrasensitive intracellular measurement, avoiding the disadvantages of enzymatic processes. Among them, the typical CHA reaction, which was originally introduced by Yin et al in 2008, could generate plenty of branched DNA junction architectures from three metastable hairpin probes to recycle the DNA initiators at a constant temperature without the involvement of enzymes and obtain an amplified readout signal by 100-fold. , Because of their satisfactory features such as simple design and easy operation, the stable CHA systems have been naturally adapted for detecting a wide spectrum of biomarkers. − However, as we know, most of the abovementioned DNA reactants are made up of separate building elements.…”

Signal Extraction, Transformation, and Magnification for Ultrasensitive and Specific Detection of Nucleic Acids

“…32 In addition, H2 is chosen as the signal unit labeled with a fluorophore reporter (FAM) and a quencher (BHQ1). 33 As shown in Figure 2B, LAMP initiation forms a dumbbelllike structure for designing ET-Combo specifically related to the target sequence (step 1). 16,29 Subsequently, EP, as the specific signal extractor, can hybridize with the loop region of the dumbbell-like structure and be extended by DNA polymerase to form a complementary strand (steps 2 and 3).…”

“…To avoid extension by a DNA polymerase, trigger, H1 and H2 are blocked with a phosphate group at the 3′ end (marked by “x” in dark blue) . In addition, H2 is chosen as the signal unit labeled with a fluorophore reporter (FAM) and a quencher (BHQ1) …”

On the Interaction between 1D Materials and Living Cells

“…Then, the DNAzyme can play its role of functional element for the chemiluminescence-based detection, by catalyzing the oxidation of luminol or 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid by H 2 O 2 . This biosensing platform was optimized for BRCA1 oncogene sensing down to of 10 −13 M. Furthermore, He et al have optimized a rapid DNA NWs assembly protocol at room temperature, and used it as a biosensor device for adenosine triphosphate detection [ 222 ]. A self-replicating catalysed hairpin assembly (SRCHA) was exploited to prepare DNA nanowires, starting from numerous target DNA replicas, that were produced with sticky ends allowing the double-stranded DNA single fibres to elongate and interact to induce the NW formation ( Figure 12 a–d).…”