title: Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction.
abstract: We describe a method for sensitive monitoring of restriction endonuclease kinetics and activity by use of a universal molecular beacon (U-MB) coupled with real-time polymerase chain reaction (PCR). The method is used to monitor the progress of DNA cleavage in a sealed reaction tube and offers more accurate and high-throughput detection. The template has a universal tail hybridized with the U-MB and the remaining sequence is complementary to one of the restriction endonuclease digestion products. The U-MB is replaced by the extension of digested product and the fluorescence quenches. With this concept, one universal fluorescence probe can be used in different enzyme analytical systems. In the work described here, homogenous assays were performed with the restriction endonucleases AluI, EcoRI, XhoI, and SacI at smoothly controlled temperature. Cleavage efficiencies were determined, and the potential applications of this method were discussed. Furthermore, the AluI and EcoRI cleavage reactions were monitored online at varying substrate concentrations at the molecular level, and K(m), V(max), and K(cat) values were calculated. The results suggest that U-MB monitoring of restriction endonuclease assays based on real-time PCR will be very useful for high-throughput, sensitive, and precise assays for enzyme activity screening and evolutionary biotechnology analysis.
authors.affiliation: Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Chengfu Road 202, Haidian District, Beijing 100871, China.
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Li
authors.forename: Chen
authors.initials: C
authors.lastname: Song
authors.forename: Meiping
authors.initials: M
authors.lastname: Zhao
authors.forename: Yuanzong
authors.initials: Y
authors.lastname: Li
mesh_terms: D002384:Catalysis / Q000528:radiation effects; D002851:Chromatography, High Pressure Liquid; D004247:DNA / Q000378:metabolism*; D004262:DNA Restriction Enzymes / Q000378:metabolism*; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D006868:Hydrolysis / Q000528:radiation effects; D007700:Kinetics; D008027:Light; D015336:Molecular Probe Techniques; D016133:Polymerase Chain Reaction / Q000379:methods*; D013997:Time Factors
chemical_list: D004247:DNA; D004262:DNA Restriction Enzymes; D015246:Deoxyribonuclease EcoRI; C024669:endodeoxyribonuclease AluI; C024408:endodeoxyribonuclease SacI; C034510:CTCGAG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific