The Design And Characteristic Study Of New Type Catalytic Molecular Beacons

Catalytic molecular beacon is single-strand oligonucleotide that possesses catalytic function. Antisense conformational triggers based on molecular beacons can be used to initiate catalytic events. Generally, the catalytic molecular beacons consist of: (a) catalytic domain, which is deoxyribozyme and cleave substrate, (b) reporting domain, which is molecular beacons and report fluorescent signal. In one project, someone has constructed catalytic molecular beacons from a hammerhead-type deoxyribozyme by a modular design. The deoxyribozyme was engineered to contain a molecular beacon stem-loop module that, when closed, inhibits the deoxyribozyme module and is complementary to a target oligonucleotide. Binding of target oligonucleotides opens the beacon stem-loop and allosterically activates the deoxyribozyme module, which amplifies the recognition event through cleavage of a doubly labeled fluorescent substrate. The customized modulardesign of catalytic molecular beacons allows for any two single-stranded oligonucleotide sequences to be distinguished in homogenous solution in a single step. In further research, some team report herein a set of deoxyribozyme-based logic gates capable of generating any Boolean function. They construct basic NOT and AND gates, followed by the more complex XOR gate. These gates were constructed through a modular design that combines molecular beacon stem-loops with hammerhead-type deoxyribozymes. Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in solution. The operation of these gates is conveniently connected to a fluorescent readout. According to above research, we believe in that Catalytic molecular beacons will have comprehensive applied value, it can recognize and report the presence of specific nucleic acids in homogeneous solution. It also is used to act as molecular computer.We construct a new type Catalytic molecular beacons, it form a stem-and-loop structure. The stem is made of complementary base pair. A fluorophore and a quencher are covalently linked to the end of the stem. The stem is reporting element. The loop contains a 10-23 deoxyribozymes that can recognize the substrate through two watson-crick binding domains and cleave binding substrate, it is a catalytic element. When the 10-23 deoxyribozymes which is embedded in the loop binds a complete matched substrate, the stem-and-loop structure is destroyed and the fluorescent signal appears simultaneously. 'The catalytic efficiency of the 10-23 deoxyribozymes is limited by the presence of the stem-and-loop structure. The catalytic molecular beacons display a high level of substrate specificity, discriminating against substrate that contains a single base mismatch within either of the two substrate-recognition domains. After any single base of complete matched substrate is substituted by other nucleotide, it can't be recognized and cleaved by 10-23deoxyribozymes which is embedded in the loop. The new type Catalytic molecular beacons could be applied to the domain of antisense therapy and the modular design of the molecular computer in the future.