Mismatch cleavage by single-strand specific nucleases

Nucleic Acids Research

Volumn 32, Issue 8, 2004, Pages 2632-2641

  Till, Bradley J ^a   Burtner, Chris ^b   Comai, Luca ^b   Henikoff, Steven ^a,c  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIVALENT CATION; HETERODUPLEX; NUCLEASE; PLANT EXTRACT; SINGLE STRANDED DNA; CELL EXTRACT; DEOXYRIBONUCLEASE; NUCLEASE S1;

ARTICLE; ASPERGILLUS; ASSAY; BASE MISPAIRING; CELERY; CLINICAL PROTOCOL; CONTROLLED STUDY; DNA CLEAVAGE; DNA TEMPLATE; ENZYME BINDING; ENZYME POLYMORPHISM; ENZYME PURIFICATION; GENE AMPLIFICATION; GENE MUTATION; MUNG BEAN; NONHUMAN; PH; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE; CLASSIFICATION; ENZYMOLOGY; FUNGUS; HETERODUPLEX ANALYSIS; METABOLISM; PHYLOGENY; PLANT;

APIUM GRAVEOLENS VAR. DULCE; ASPERGILLUS; PHASEOLUS (ANGIOSPERM); VIGNA RADIATA VAR. RADIATA;

ASPERGILLUS NUCLEASE S1; BASE PAIR MISMATCH; CELL EXTRACTS; ENDODEOXYRIBONUCLEASES; FUNGI; HETERODUPLEX ANALYSIS; NUCLEIC ACID HETERODUPLEXES; PHYLOGENY; PLANTS;

EID: 3042525130     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh599     Document Type: Article

References (35)

1. Desai,N.A. and Shankar,V. (2003) Single-strand-specific nucleases. FEMS Microbiol. Rev., 26, 457-491.
2. Shenk,T.E., Rhodes,C., Rigby,P.W. and Berg,P. (1975) Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40. Proc. Natl Acad. Sci. USA, 72, 989-993.
3. Wiegand,R.C., Godson,N. and Radding,C.M. (1975) Specificity of the S1 nuclease from Aspergillus oryzae. J. Biol. Chem., 250, 8848-8855.
4. Berk,A.J. (1989) Characterization of RNA molecules by S1 nuclease analysis. Methods Enzymol., 180, 334-347.
5. Colbert,T., Till,B.J., Tompa,R., Reynolds,S., Steine,M.N., Yeung,A.T., McCallum,C.M., Comai,L. and Henikoff,S. (2001) High-throughput screening for induced point mutations. Plant Physiol., 126, 480-484.
6. Vogt,V.M. (1973) Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. Eur. J. Biochem., 33, 192-200.
7. Fujimoto,M., Kuninaka,A. and Yoshino,H. (1974) Purification of a nuclease from Penicillium citrinum. Agric. Biol. Chem., 38, 777-783.
8. Vogt,V.M. (1980) Purification and properties of S1 nuclease from Aspergillus. Methods Enzymol., 65, 248-255.
9. Laskowski,M.,Sr (1980) Purification and properties of the mung bean nuclease. Methods Enzymol., 65, 263-276.
10. Yang,B., Wen,X., Kodali,N.S., Oleykowski,C.A., Miller,C.G., Kulinski,J., Besack,D., Yeung,J.A., Kowalski,D. and Yeung,A.T. (2000) Purification, cloning and characterization of the CEL I nuclease. Biochemistry, 39, 3533-3541.
11. Henikoff,S. (1984) Unidirectional digestion with Exonuclease III creates targeted breakpoints for DNA sequencing. Gene, 28, 351-359.
12. Volbeda,A., Lahm,A., Sakiyama,F. and Suck,D. (1991) Crystal structure of Penicillium citrinum P1 nuclease at 2.8Å resolution. EMBO J., 10, 1607-1618.
13. Dodgson,J.B. and Wells,R.D. (1977) Action of single-strand specific nucleases on model DNA heteroduplexes of defined size and sequence. Biochemistry, 16, 2374-2379.
14. Silber,J.R. and Loeb,L.A. (1981) S1 nuclease does not cleave DNA at single-base mismatches. Biochim. Biophys. Acta, 656, 256-264.
15. Oleykowski,C.A., Bronson Mullins,C.R., Godwin,A.K. and Yeung,A.T. (1998) Mutation detection using a novel plant endonuclease. Nucleic Acids Res., 26, 4597-4602.
16. Howard,J.T., Ward,J., Watson,J.N. and Roux,K.H. (1999) Heteroduplex cleavage analysis using S1 nuclease. Biotechniques, 27, 18-19.
17. Sokurenko,E.V., Tchesnokova,V., Yeung,A.T., Oleykowski,C.A., Trintchina,E., Hughes,K.T., Rashid,R.A., Brint,J.M., Moseley,S.L. and Lory,S. (2001) Detection of simple mutations and polymorphisms in large genomic regions. Nucleic Acids Res., 29, e111.
18. Taylor,G.R. and Deeble,J. (1999) Enzymatic methods for mutation scanning. Genet. Anal., 14, 181-186.
19. Henikoff,S. and Comai,L. (2003) Single-nucleotide mutations for plant functional genomics. Annu. Rev. Plant Biol., 54, 375-401.
20. Ahmad,A., Holloman,W.K. and Holliday,R. (1975) Nuclease that preferentially inactivates DNA containing mismatched bases. Nature, 258, 54-56.
21. Pukkila,P.J. (1978) The recognition of mismatched base pairs in DNA by DNase I from Ustilago maydis. Mol. Gen. Genet., 161, 245-250.
22. Bartok,K., Fraser,M.J. and Fareed,G.C. (1974) Detection of sequence heterology by use of the N. crassa nucleases. Biochem. Biophys. Res. Commun., 60, 507-514.
23. Oleykowski,C.A., Bronson Mullins,C.R., Chang,D.W. and Yeung,A.T. (1999) Incision at nucleotide insertions/deletions and base pair mismatches by the SP nuclease of spinach. Biochemistry, 38, 2200-2205.
24. Till,B.J., Reynolds,S.H., Greene,E.A., Codomo,C.A., Enns,L.C., Johnson,J.E., Burtner,C., Odden,A.R., Young,K., Taylor,N.E., Henikoff,J.G., Comai,L. and Henikoff,S. (2003) Large-scale discovery of induced point mutations with high throughput TILLING. Genome Res., 13, 524-530.
25. Comai,L., Young,K., Till,B.J., Reynolds,S.H., Greene,E.A., Codomo,C.A., Enns,L.C., Johnson,J.E., Burtner,C., Odden,A.R. and Henikoff,S. (2004) Efficient discovery of DNA polymorphisms in natural populations by ecotilling. Plant J., 37, 778-786.
26. Wienholds,E., van Eeden,F.J., Kosters,M., Mudde,J., Plasterk,R.H. and Cuppen,E. (2003) Efficient target-selected mutagenesis in zebrafish. Genome Res., 13, 2700-2707.
27. Smits,B.M. G., Mudde,J., Plasterk,R.H. A. and Cuppen,E. (2004) Target-selected matagenesis of the rat. Genomics, 83, 332-334.
28. Till,B.J., Colbert,T., Tompa,R., Enns,L.C., Codomo,C.A., Johnson,J.E., Reynolds,S.H., Henikoff,J.G., Greene,E.A., Stein,M.N., Comai,L. and Henikoff,S. (2003) High-throughput TILLING for functional genomics. In Grotewald,E. (ed.), Plant Functional Genomics: Methods and Protocols. Humana Press, Clifton, NJ, pp. 205-220.
29. Chakrabarti,R. and Schutt,C.E. (2002) Novel sulfoxides facilitate GC-rich template amplification. Biotechniques, 32, 866-874.
30. Perez-Amador,M.A., Abler,M.L., De Rocher,E.J., Thompson,D.M., van Hoof,A., LeBrasseur,N.D., Lers,A. and Green,P.J. (2000) Identification of BFN1, a bifunctional nuclease induced during leaf and stem senescence in Arabidopsis. Plant Physiol., 122, 169-180.
31. Greene,E.A., Codomo,C.A., Taylor,N.E., Henikoff,J.G., Till,B.J., Reynolds,S.H., Enns,L.C., Burtner,C., Johnson,J.E., Odden,A.R., Comai,L. and Henikoff,S. (2003) Spectrum of chemically induced mutations from a large-scale reverse-genetic screen in Arabidopsis. Genetics, 164, 731-740.
32. Kroeker,W.D., Kowalski,D. and Laskowski,M.,Sr (1976) Mung bean nuclease I. Terminally directed hydrolysis of native DNA. Biochemistry, 15, 4463-4467.
33. Esteban,J.A., Salas,M. and Blanco,L. (1992) Activation of S1 nuclease at neutral pH. Nucleic Acids Res., 20, 4932.
34. Kowalski,D. and Sanford,J.P. (1982) Action of mung bean nuclease on supercoiled PM2 DNA. J. Biol. Chem., 257, 7820-7825.
35. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.