FRET-based kinetic analysis of highly reactive heterochiral DNA toward EcoRI endonuclease

Biochemical and Biophysical Research Communications

Volumn 390, Issue 2, 2009, Pages 192-195

  Urata, Hidehito ^a   Tamaki, Chihiro ^a   Matsuno, Miki ^a   Wada, Shun ichi ^a   Akagi, Masao ^a  

^a OSAKA MEDICAL COLLEGE   (Japan)

Author keywords

DNA; EcoRI promoted hydrolysis; FRET; Heterochiral; Kinetics

Indexed keywords

DEOXYRIBONUCLEOTIDE; DNA; DODECADEOXYNUCLEOTIDE; ECORI ENDONUCLEASE; ENDONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CHEMICAL REACTION KINETICS; CHIRALITY; CONFORMATIONAL TRANSITION; DNA CONFORMATION; DNA FLANKING REGION; DNA MODIFICATION; DNA SEQUENCE; DNA SYNTHESIS; ENZYME MECHANISM; ENZYME SUBSTRATE COMPLEX; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYDROLYSIS; PARAMETER; PRIORITY JOURNAL; PROTEIN DNA BINDING;

BASE SEQUENCE; DEOXYRIBONUCLEASE ECORI; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYDROLYSIS; KINETICS;

EID: 70350126915     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2009.08.164     Document Type: Article

References (23)

1. Urata H., Shinohara K., Ogura E., Ueda Y., and Akagi M. Mirror-image DNA. J. Am. Chem. Soc. 113 (1991) 8174-8175
2. Urata H., Shimizu H., Hiroaki H., Kohda D., and Akagi M. Thermodynamic study of hybridization properties of heterochiral nucleic acids. Biochem. Biophys. Res. Commun. 309 (2003) 79-83
3. Urata H., and Akagi M. Sequence dependence of thermodynamic stability of heterochiral DNA. Tetrahed. Lett. 37 (1996) 5551-5554
4. Urata H., Ueda Y., Suhara H., Nishioka E., and Akagi M. NMR study of a heterochiral DNA: stable Watson-Crick-type base-pairing between the enantiomeric residues. J. Am. Chem. Soc. 115 (1993) 9852-9853
5. 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
6. Lesser D.R., Kurpiewski M.R., Waters T., Connolly B.A., and Jen-Jacobson L. Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. Proc. Natl. Acad. Sci. USA 90 (1993) 7548-7552
7. 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
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. Lu A.L., Jack W.E., and Modrich P. DNA determinants important in sequence recognition by EcoRI endonuclease. J. Biol. Chem. 256 (1981) 13200-13206
10. Becker M.M., Lesser D., Kurpiewski M., Baranger A., and Jen-Jacobson L. "Ultraviolet footprinting" accurately maps sequence-specific contacts and DNA kinking in the EcoRI endonuclease-DNA complex. Proc. Natl. Acad. Sci. USA 85 (1988) 6247-6251
11. Frederick C.A., Grable J., Melia M., Samudzi C., Jen-Jacobson L., Wang B.C., Greene P., Boyer H.W., and Rosenberg J.M. Kinked DNA in crystalline complex with EcoRI endonuclease. Nature 309 (1984) 327-331
12. Kim Y., Grable J.C., Love R., Greene P.J., and Rosenberg J.M. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249 (1990) 1307-1309
13. McClarin J.A., Frederick C.A., Wang B.C., Greene P., Boyer H.W., Grable J., and Rosenberg J.M. Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution. Science 234 (1986) 1526-1541
14. Urata H., Ueda Y., and Akagi M. Effects of breaking homochirality on DNA structure and stability: Introduction of an l-nucleotide into DNA induces some decrease of helical stability but not critical helical distortion. Viva Origino 31 (2004) 233-242
15. Urata H., Ogura E., Shinohara K., Ueda Y., and Akagi M. Synthesis and properties of mirror-image DNA. Nucleic Acids Res. 20 (1992) 3325-3332
16. In: Fasman G.D. (Ed). Handbook of Biochemistry and Molecular Biology. third ed. Nucleic Acids vol. 1. (1975), CRC Press, Boca Raton, FL 589
17. Piatek A.S., Tyagi S., Pol A.C., Telenti A., Miller L.P., Kramer F.R., and Alland D. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 16 (1998) 359-363
18. Sokol D.L., Zhang X., Lu P., and Gewirtz A.M. Real time detection of DNA•RNA hybridization in living cells. Proc. Natl. Acad. Sci. USA 95 (1998) 11538-11543
19. Ranasinghe R.T., and Brown T. Fluorescence based strategies for genetic analysis. Chem. Commun. (2005) 5487-5502
20. Biggins J.B., Prudent J.R., Marshall D.J., Ruppen M., and Thorson J.S. A continuous assay for DNA cleavage: the application of "break lights" to enediynes, iron-dependent agents, and nucleases. Proc. Natl. Acad. Sci. USA 97 (2000) 13537-13542
21. m and Kcat for BamHI restriction endonuclease: an empirical and iterative approach. Anal. Biochem. 220 (1994) 160-164
22. Heitman J. How the EcoRI endonuclease recognizes and cleaves DNA. BioEssays 14 (1992) 445-454
23. 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