Continuous monitoring of restriction endonuclease cleavage activity by universal molecular beacon light quenching coupled with real-time polymerase chain reaction

Analytical Biochemistry

Volumn 381, Issue 1, 2008, Pages 1-7

  Li, Xiaomin ^a   Song, Chen ^a   Zhao, Meiping ^a   Li, Yuanzong ^a  

^a PEKING UNIVERSITY   (China)

Author keywords

Real time polymerase chain reaction; Restriction endonucleases; Universal molecular beacon

Indexed keywords

ENZYME ACTIVITY; FLUORESCENCE; REACTION KINETICS;

CLEAVAGE ACTIVITIES; CONTINUOUS MONITORING; CONTROLLED TEMPERATURE; HIGH-THROUGHPUT DETECTION; MOLECULAR BEACON; REAL TIME POLYMERASE CHAIN REACTIONS; RESTRICTION ENDONUCLEASES; SUBSTRATE CONCENTRATIONS;

POLYMERASE CHAIN REACTION;

ALUI; ECORI; RESTRICTION ENDONUCLEASE; SACI; XHOI;

ARTICLE; BIOTECHNOLOGY; CONCENTRATION (PARAMETERS); DNA CLEAVAGE; ENZYME ACTIVATION; ENZYME ANALYSIS; ENZYME SUBSTRATE; MONITORING; NUCLEIC ACID PROBE; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; TEMPERATURE; UNIVERSAL MOLECULAR BEACON;

EID: 49049120669     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.06.027     Document Type: Article

References (42)

1. Pingoud A., and Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29 (2001) 3705-3727
2. Bhagwat A.S. Restriction enzymes: properties and use. Methods Enzymol. 216 (1992) 199-224
3. Pingoud A., and Jeltsch A. Recognition and cleavage of DNA by type II restriction endonuclease. Eur. J. Biochem. 246 (1997) 1-22
4. Guttman A., Ronai Z., Barta C., Hou Y.M., Sasvari-Szekely M., Wang X., and Briggs S.P. Membrane-mediated ultrafast restriction digestion and subsequent rapid gel microchip electrophoresis of DNA. Electrophoresis 23 (2002) 1524-1530
5. Roberts R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331-2365
6. Botstein D., White R.L., Skolnick M., and Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32 (1980) 314-331
7. Halford S., and Goodall A. Modes of DNA cleavage by the EcoRV restriction endonuclease. Biochemistry 27 (1988) 1771-1777
8. McLaughlin L.W., Benseler F., Graeser E., Piel N., and Scholtissek S. Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease. Biochemistry 26 (1987) 7238-7245
9. Alves J., Ruter T., Geiger R., Fliess A., Maass G., and Pingoud A. Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymic activity, not, however, the preference of this restriction endonuclease for cleavage within the site -GAATTC-. Biochemistry 28 (1989) 2678-2684
10. Waters T.R., and Connolly B.A. Continuous spectrophotometric assay for restriction endonucleases using synthetic oligodeoxynucleotides and based on the hyperchromic effect. Anal. Biochem. 204 (1992) 204-209
11. Jeltsch A., Fritz A., Alves J., Wolfes H., and Pingoud A. A fast and accurate enzyme-linked immunosorbent assay for the determination of the DNA cleavage activity of restriction endonucleases. Anal. Biochem. 213 (1993) 234-240
12. Lee S.P., and Han M.K. Fluorescence assay for DNA cleavage. Methods Enzymol. 278 (1997) 343-363
13. Roddy E.S., Price M., and Ewing A.G. Continuous monitoring of a restriction enzyme digest of DNA on a microchip with automated capillary sample introduction. Anal. Chem. 75 (2003) 3704-3711
14. Ghosh S.S., Eis P.S., Blumeyer K., Fearon K., and Millar D.P. Real-time kinetics of restriction endonuclease cleavage monitored by fluorescence resonance energy transfer. Nucleic Acids Res. 22 (1994) 3155-3159
15. Eisenschmidt K., Lanio T., Jeltsch A., and Pingoud A. A fluorimetric assay for on-line detection of DNA cleavage by restriction endonucleases. J. Biotechnol. 96 (2002) 185-191
16. Li J.J., Geyer R., and Tan W.H. Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA. Nucleic Acids Res. 28 (2000) e52
17. Tyagi S., and Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14 (1996) 303-308
18. Piatek A.S., Tyagi S., Pol A.C., Miller L.P., Kramer F.R., and Alland D. Molecular beacon sequence analysis for detecting drug resistant in Mycobacterium tuberculosis. Nat. Biotechnol. 16 (1998) 359-363
19. Li X.M., Huang Y., Guan Y., Zhao M.P., and Li Y.Z. Universal molecular beacon-based tracer system for real-time polymerase chain reaction. Anal. Chem. 78 (2006) 7886-7890
20. Li X.M., Huang Y., Song C., Zhao M.P., and Li Y.Z. Several concerns about the primer design in the universal molecular beacon real-time PCR assay and its application in HBV DNA detection. Anal. Bioanal. Chem. 388 (2007) 979-985
21. Lee S.P., Porter D., Chirikjian J.G., Knutson J.R., and Han M.K. A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease. Anal. Biochem. 220 (1994) 377-383
22. Lehninger A.L., Nelson D.L., and Cox M.M. Principles of Biochemistry (1993), Worth, New York
23. Brennan C.A., Van Cleve M.D., and Gumport R.I. The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261 (1986) 7270-7278
24. Alves J., Urbanke C., Fliess A., Maass G., and Pingoud A. Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease. Biochemistry 28 (1989) 7879-7888
25. Ma C.B., Tang Z.W., Wang K.M., Tan W.H., Yang X.H., Li W., Li Z.H., and Lv X.Y. Real-time monitoring of restriction endonuclease activity using molecular beacon. Anal. Biochem. 363 (2007) 294-296
26. Mark D., Van C., and Richard I.G. Influence of enzyme-substrate contacts located outside the EcoRI recognition site on cleavage of duplex oligodeoxyribonucleotide substrates by EcoRI endonuclease. Biochemistry 31 (1992) 334-339
27. Terry B., Jack W., and Modrich P. Mechanism of specific site location and DNA cleavage by EcoRI endonuclease. Gene Amplif. Anal. 5 (1987) 103-118
28. Cleavage close to the end of DNA fragments (oligonucleotides). New England Biolabs technical reference (2005-2006)
29. Lesser D.R., Kurpiewski M.R., and Jen-Jacobson L. The energetic basis of specificity in the EcoRI endonuclease-DNA interaction. Science 250 (1990) 776-786
30. Wenz C., Hahn M., and Pingoud A. Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site. Biochemistry 37 (1998) 2234-2242
31. Wenz C., Jeltsch A., and Pingoud A. Probing the indirect readout of the restriction enzyme EcoRV. J. Biol. Chem. 271 (1996) 5565-5573
32. Yang C.C., and Topal D. Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site. Biochemistry 31 (1992) 9657-9664
33. Taylor J.D., and Halford S.E. The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex. Biochemistry 31 (1992) 90-97
34. Terry B.J., Jack W.E., and Modrich P. Facilitated diffusion during catalysis by EcoRI endonuclease: nonspecific interactions in EcoRI catalysis. J. Biol. Chem. 260 (1985) 13130-13137
35. Kettling U., Koltermann A., Schwille P., and Eigen M. Real-time enzyme kinetics monitored by dual-color fluorescence cross-correlation spectroscopy. Proc. Natl. Acad.Sci. USA 95 (1998) 1416-1420
36. Nordlund T.M., Andersson S., Nilsson L., Rigler R., Graslund A., and McLaughlin L.W. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry 28 (1989) 9095-9103
37. Greene P.J., Gupta M., Boyer H.W., Brown W.E., and Rosenberg J.M. Sequence analysis of the DNA encoding the EcoRI endonuclease and methylase. J. Biol. Chem. 256 (1981) 2143-2153
38. Halford S.E., Johnson N.P., and Grinsted J. The reactions of the EcoRΙ and other restriction endonucleases. Biochem. J. 179 (1979) 353-365
39. Halford S.E., Johnson N.P., and Grinsted J. The EcoRI restriction endonuclease with bacteriophage lambda DNA: kinetic studies. Biochem. J. 191 (1980) 581-592
40. Halford S.E., and Johnson N.P. The EcoRI restriction endonuclease covalently closed DNA and ethidium bromide. Biochem. J. 199 (1981) 767-777
41. Jack W.E., Terry B.J., and Modrich P. Involvement of outside DNA sequences in the major kinetic path by which EcoRI endonuclease locates and leaves its recognition sequence. Proc. Natl. Acad. Sci. USA 79 (1982) 4010-4014
42. Wright D.J., Jack W.E., and Modrich P. The kinetic mechanism of EcoRI endonuclease. J. Biol. Chem. 274 (1999) 31896-31902