Colorimetric detection of gene transcript by target-induced three-way junction formation

Expanding the analytical applications of nucleic acid hybridization using junction probes

Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.

Toehold integrated molecular beacon system for a versatile non-enzymatic application

A molecular beacon (MB) is an oligonucleotide hybridization probe with a hairpin-shaped structure that leads to specific and instantaneous nucleic acid hybridization, enabling a variety of applications. However, integration of additional module sequences interferes with the performance of MBs and increases the complexity of sequence design. Herein, we develop and characterize a toehold integrated molecular beacon (ToMB) strategy for nucleic acid hybridization, where the reaction rate can be flexibly regulated by a target-induced MB conformational switch. Using this basic mechanism, the ToMB is capable of identifying nucleic acids with high specificity and a wider linearity range compared with the conventional molecular beacon system. We further applied the ToMB to the construction of a hybridization chain reaction system and a basic OR logic gate VJHto explore its programmability and versatility. Our results strongly suggest that the novel ToMB can act as a powerful nano-module to construct universal and multifunctional biosensors or molecular computations. Graphical abstract Molecular beacon is employed as a flexible and switchable spacer to control the toehold-mediated strand displacement reaction.

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.