A study on endonuclease BspD6I and its stimulus-responsive switching by modified oligonucleotides

Chemiluminescent heterogeneous and homogeneous-heterogeneous assays for determination of nicking endonuclease activity

Homogeneous-heterogeneous and heterogeneous formats of a simple and sensitive assay for the determination of nicking endonuclease (NE) Nt.Bst9I activity was developed. The duplex of two 26-membered biotinylated DNA oligonucleotides was used as a substrate of Nt.Bst9I. To improve the assay sensitivity the chemiluminescent detection system based on the use of conjugate of streptavidin and polyperoxidase and enhanced chemiluminescence reaction was used. Both proposed assay formats were constructed using microtiter plates as a solid support, allowing for easy automation of NE analysis using ELISA equipment. Varying the acidity, concentration of KCl and NaCl, and temperature of the reaction medium, favorable conditions were found. Although both formats of the proposed assay can be applied to estimate Nt.Bst9I activity, the heterogenous assay was more sensitive than the homogeneous-heterogeneous one.

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification

Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.

Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA

Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is 'nicked' rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I-DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I's binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.