Sequence-specific cleavage of RNA by Type II restriction enzymes

Nucleic Acids Research

Volumn 38, Issue 22, 2010, Pages 8257-8268

  Murray, Iain A ^a   Stickel, Shawn K ^a   Roberts, Richard J ^a  

^a NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; OLIGORIBONUCLEOTIDE; PHOSPHODIESTERASE; RESTRICTION ENDONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; BACTERIOPHAGE LAMBDA; CONTROLLED STUDY; DNA RNA HYBRIDIZATION; DNA STRAND; ELECTROPHORETIC MOBILITY; HETERODUPLEX ANALYSIS; HYDROLYSIS; IN VITRO STUDY; NUCLEIC ACID BASE SUBSTITUTION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RESTRICTION MAPPING; RNA CLEAVAGE;

BACTERIOPHAGE LAMBDA; BASE SEQUENCE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; DNA CLEAVAGE; DNA, VIRAL; KINETICS; OLIGONUCLEOTIDES; RNA; SUBSTRATE SPECIFICITY;

EID: 78650502368     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq702     Document Type: Article

References (31)

1. Smith, H.O. and Wilcox, K.W. (1970) A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J. Mol. Biol., 51, 379-391.
2. Danna, K. and Nathans, D. (1971) Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc. Natl Acad. Sci. USA, 68, 2913-2917.
3. Cohen, S.N., Chang, A.C., Boyer, H.W. and Helling, R.B. (1973) Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. USA, 70, 3240-3244.
4. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236.
5. Orlowski, J. and Bujnicki, J.M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569.
6. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S., Dryden, D.T., Dybvig, K. et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res., 31, 1805-1812.
7. Sokolowska, M., Czapinska, H. and Bochtler, M. (2009) Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res., 37, 3799-3810.
8. Galburt, E.A. and Stoddard, B.L. (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry, 41, 13851-13860.
9. Rimseliene, R., Maneliene, Z., Lubys, A. and Janulaitis, A. (2003) Engineering of restriction endonucleases: using methylation activity of the bifunctional endonuclease Eco57I to select the mutant with a novel sequence specificity. J. Mol. Biol., 327, 383-391.
10. Morgan, R.D. and Luyten, Y.A. (2009) Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity. Nucleic Acids Res., 37, 5222-5233.
11. Connolly, B.A., Eckstein, F. and Pingoud, A. (1984) The stereochemical course of the restriction endonuclease EcoRI-catalyzed reaction. J. Biol. Chem., 259, 10760-10763. (Pubitemid 14031199)
12. Mizuuchi, K., Nobbs, T.J., Halford, S.E., Adzuma, K. and Qin, J. (1999) A new method for determining the stereochemistry of DNA cleavage reactions: application to the SfiI and HpaII restriction endonucleases and to the MuA transposase. Biochemistry, 38, 4640-4648.
13. Gromova, E.S., Kubareva, E.A., Vinogradova, M.N., Oretskaya, T.S. and Shabarova, Z.A. (1991) Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII. J. Mol. Recognit., 4, 133-141.
14. Langhans, M.T. and Palladino, M.J. (2009) Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes. Curr. Issues Mol. Biol., 11, 1-12.
15. Molloy, P.L. and Symons, R.H. (1980) Cleavage of DNA.RNA hybrids by type II restriction enzymes. Nucleic Acids Res., 8, 2939-2946.
16. Ohtsuka, E., Ishino, Y., Ibaraki, K. and Ikehara, M. (1984) Recognition by restriction endonuclease EcoRI of deoxyoctanucleotides containing modified sugar moieties. Eur. J. Biochem., 139, 447-450.
17. Nazarenko, I.A., Gorbunov Iu, A. and Malygin, E.G. (1987) [Cleavage of synthetic RNA-DNA hybrids with restriction endonucleases BamH1 and Sau3A]. Bioorg. Khim., 13, 928-933.
18. Dock-Bregeon, A.C., Chevrier, B., Podjarny, A., Moras, D., deBear, J.S., Gough, G.R., Gilham, P.T. and Johnson, J.E. (1988) High resolution structure of the RNA duplex [U(U-A)6A]2. Nature, 335, 375-378.
19. 0-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. Biochemistry, 32, 3221-3237.
20. Pingoud, A. and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res., 29, 3705-3727.
21. Salazar, M., Fedoroff, O.Y., Miller, J.M., Ribeiro, N.S. and Reid, B.R. (1993) The DNA strand in DNA.RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry, 32, 4207-4215.
22. Nowotny, M., Gaidamakov, S.A., Crouch, R.J. and Yang, W. (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell, 121, 1005-1016.
23. Nowotny, M., Gaidamakov, S.A., Ghirlando, R., Cerritelli, S.M., Crouch, R.J. and Yang, W. (2007) Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol. Cell, 28, 264-276.
24. Lu, X.J., Shakked, Z. and Olson, W.K. (2000) A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol., 300, 819-840.
25. Marathe, A., Karandur, D. and Bansal, M. (2009) Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. BMC Struct. Biol., 9, 24.
26. Nandakumar, J., Ho, C.K., Lima, C.D. and Shuman, S. (2004) RNA substrate specificity and structure-guided mutational analysis of bacteriophage T4 RNA ligase 2. J. Biol. Chem., 279, 31337-31347.
27. Murray, I.A., Hawkins, A.R., Keyte, J.W. and Shaw, W.V. (1988) Nucleotide sequence analysis and overexpression of the gene encoding a type III chloramphenicol acetyltransferase. Biochem. J., 252, 173-179.
28. Bath, A.J., Milsom, S.E., Gormley, N.A. and Halford, S.E. (2002) Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem., 277, 4024-4033.
29. Huang, L.H., Farnet, C.M., Ehrlich, K.C. and Ehrlich, M. (1982) Digestion of highly modified bacteriophage DNA by restriction endonucleases. Nucleic Acids Res., 10, 1579-1591.
30. 0 homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter. Nucleic Acids Res., 32, e14.
31. Bullard, D.R. and Bowater, R.P. (2006) Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4. Biochem. J., 398, 135-144.