Chemical mapping of cytosines enzymatically flipped out of the DNA helix

Nucleic Acids Research

Volumn 36, Issue 10, 2008, Pages

  Daujotyte, Dalia ^a,b   Liutkevičiute, Zita ^a   Tamulaitis, Gintautas ^a   Klimašauskas, Saulius ^a  

^a VILNIUS UNIVERSITY   (Lithuania)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROACETALDEHYDE; CYTOSINE; DNA METHYLTRANSFERASE ALUL; DNA METHYLTRANSFERASE HHAL; DNA METHYLTRANSFERASE SSSL; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE ECL18KL; RESTRICTION ENDONUCLEASE PSPGL; SITE SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE SPECIFIC); ACETALDEHYDE; DNA; DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA MODIFICATION METHYLASE ALUI; DNA MODIFICATION METHYLASE HHAI; DNA MODIFICATION METHYLASE SSSI; DRUG DERIVATIVE; ENDODEOXYRIBONUCLEASE BSTNI; ENDODEOXYRIBONUCLEASE ECL18KI; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; CHEMICAL MODIFICATION; CONFORMATIONAL TRANSITION; DNA HELIX; DNA PROTEIN COMPLEX; NUCLEIC ACID BASE SUBSTITUTION; PEPTIDE MAPPING; PRIORITY JOURNAL; X RAY CRYSTALLOGRAPHY; BIOCHEMISTRY; CHEMISTRY; EVALUATION; METABOLISM; METHODOLOGY;

ACETALDEHYDE; BIOCHEMISTRY; CYTOSINE; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA RESTRICTION ENZYMES; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC);

EID: 45549086919     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn200     Document Type: Article

References (41)

1. Klimasauskas,S., Kumar,S., Roberts,R.J. and Cheng,X. (1994) Hha1 methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
2. Reinisch,K.M., Chen,L., Verdine,G.L. and Lipscomb,W.N. (1995) The crystal structure of HaeIII methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing. Cell, 82, 143-153.
3. Goedecke,K., Pignot,M., Goody,R.S., Scheidig,A.J. and Weinhold,E. (2001) Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat. Struct. Biol., 8, 121-125.
4. Roberts,R.J. and Cheng,X. (1998) Base flipping. Annu. Rev. Biochem. 67, 181-198.
5. Cheng,X. and Roberts,R.J. (2001) AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res., 29 3784-3795.
6. Stivers,J.T. and Jiang,J.S. (2003) A mechanistic perspective on the chemistry of DNA repair glycosylases. Chem. Rev., 103, 2729-2759.
7. Lim,H.M., Lee,H.J., Roy,S. and Adhya,S. (2001) A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding. Proc. Natl Acad. Sci. USA, 98, 14849-14852.
8. Nair,D.T., Johnson,R.E., Prakash,L., Prakash,S. and Aggarwal,A.K. (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science, 309, 2219-2222.
9. Bochtler,M., Szczepanowski,R.H., Tamulaitis,G., Grazulis,S., Czapinska,H., Manakova,E. and Siksnys,V. (2006) Nucleotide flips determine the specificity of the Ecl18kl restriction endonuclease. EMBO J., 25, 2219-2229.
10. Tamulaitis,G., Zaremba,M., Szczepanowski,R.H., Bochtler,M. and Siksnys,V. (2007) Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steaidy-state fluorescence. Nucleic Acids Res., 35, 4792-4799.
11. Holz,B., Klimasauskas,S., Serva,S. and Weinhold,E. (1998) 2-Amino purine as a fluorescence probe for DNA base flipping by methyltransferases. Nucleic Acids Res., 26, 1076-1083.
12. Allan,B.W., Beechem,J.M., Lindstrom,W.M. and Reich,N., (1998) Direct real time observation of base flipping by the EcoRI DNA methyltransferase. J. Biol. Chem., 273, 2368-2373.
13. Neely,R.K., Daujotyte,D., Grazulis,S., Magennis,S.W., Dryden,D.T., Klimasauskas,S. and Jones,A.C. (2005) Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res., 33, 6953-6960.
14. Zhou,Y. and Ts'o,P.O.P. (1996) Solid-phase synthesis of oligo-2-pyrimidinone-2′-deoxyribonucleotides and oligo-2-pyrimidinone-2′-deoxyriboside methylphosphonates. Nucleic Acids Res., 24, 2652-2659.
15. Tinsley,R.A. and Walter,N.G. (2006) Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA, 12, 522-529.
16. Lin,K.-Y., Jones,R.J. and Matteucci,M. (1995) Tricyclic 2′-deoxycytidine analogs: Syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J. Am. Chem. Soc., 117, 3873-3874.
17. Godde,F., Toulme,J.-J. and Moreau,S. (2000) 4-amino-1H-benzo[g]quinazoline-2-one: A fluorescent analog of cytosine to probe protonation sites in triplex forming oligonucleotides. Nucleic Acids Res., 28, 2977-2985.
18. Serva,S., Weinhold,E., Roberts,R.J. and Klimasauskas,S. (1998) Chemical display of thymine residues flipped out by DNA methyltransferases. Nucleic Acids Res., 26, 3473-3479.
19. Bischerour,J. and Chalmers,R. (2007) Base-flipping dynamics in a DNA hairpin processing reaction. Nucleic Acids Res., 35, 2584-2595.
20. Kusmierek,J.T. and Singer, B. (1982) Chloroacetaldehyde-treated ribo- and deoxyribopolynucleotides. 1. Reaction products. Biochemistry, 21. 5717-5722.
21. Kusmierek,J.T. and Singer,B. (1982) Chloroacetaldehyde-treated ribo- and deoxyribopolynucleotides. 2. Errors in transcription by different polymerases resulting from ethenocytosine and its hydrated intermediate. Biochemistry, 21, 5723-5728.
22. Kohwi-Shigematsu,K. and Kohwi,Y. (1992) Detection of non-B-DNA structures at supercoiled DNA and chromatin with haloacetaldehyde and diethyl pyrocarbonate. In Lilley,D.M.J. and Dahlberg,J.E. (eds), Methods Enzymol. Academic Press, San Diego, Vol. 212, pp. 155-180.
23. Carpenter,M., Divvela,P., Pingoud,V., Bujnicki,J. and Bhagwat,A.S. (2006) Sequence-dependent enhancement of hydrolytic deamination of cytosines in DNA by the restriction enzyme PspGI. Nucleic Acids Res. 34, 3762-3770.
24. Daujotyte,D., Vilkaitis,G., Manelyte,L., Skalicky,J., Szyperski,T. and Klimasauskas,S. (2003) Solubility engineering of the HhaI methyltransferase. Protein Eng., 16, 295-301.
25. Sokolowska,M., Kaus-Drobek,M., Czapinska,H., Tamulaitis,G., Szczepanowski,R.H., Urbanke,C., Siksnys,V. and Bochtler,M. (2007) Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J. Mol. Biol., 369, 722-734.
26. Sambrook,J. and Russell,D.W. (2001) Molecular Cloning. 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
27. O'Gara,M., Roberts,R.J. and Cheng,X. (1996) A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase. J. Mol. Biol., 263, 597-606.
28. Daujotyte,D., Serva,S., Vilkaitis,G., Merkiene,E., Venclovas,C. and Klimasauskas,S. (2004) HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine. Structure, 12, 1047-1055.
29. Klimasauskas,S. and Roberts,R.J. (1995) M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res., 23, 1398-1395.
30. Klimasauskas,S., Szyperski,T., Serva,S. and Wüthrich,K. (1998) Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution. EMBO J., 17, 317-324.
31. Vilkaitis,G., Dong,A., Weinhold,E., Cheng,X. and Klimasauskas,S. (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem., 275, 38722-38730.
32. Roberts,R.J., Vincze,T., Posfai,J. and Macelis,D. (2007) REBASE-enzymes and genes for DNA restriction and DNA modification. Nucleic Acids Res., 35, D269-D270.
33. Kumar,S., Cheng,X., Pflugrath,J.W. and Roberts,R.J. (1992) Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex. Biochemistry, 31, 8648-8653.
34. Yang,A.S., Shen,J.C., Zingg,J.M., Mi,S. and Jones,P.A. (1995) HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. Nucleic Acids Res., 23, 1380-1387.
35. Shen,J.C., Zingg,J.M., Yang,A.S., Schmutte,C. and Jones,P.A. (1995) A mutant HpaII methyltransferase functions as a mutator enzyme. Nucleic Acids Res., 23, 4275-4282.
36. Pingoud,V., Conzelmann,C., Kinzebach,S., Sudina,A., Metelev,V., Kubareva,E., Bujnicki,J.M., Lurz,R., Luder,G., Xu,S.Y. et al. (2003) PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: Structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J. Mol. Biol., 329, 913-929.
37. Pestov,D.G., Dayn,A., Siyanova,E.Y., George,D.L. and Mirkin,S.M. (1991) H-DNA and Z-DNA in the mouse c-Ki-ras promoter. Nucleic Acids Res. 19, 6527-6532.
38. Kladde,M.P., Kohwi,Y., Kohwi-Shigematsu,T. and Gorski,J. (1994) The non-B-DNA structure of d(CA/TG)n differs from that of Z-DNA. Proc. Natl Acad. Sci. USA, 91, 1898-1902.
39. O'Gara,M., Horton,J.R., Roberts,R.J. and Cheng,X. (1998) Structures of HhaI methyltransferase complexed. with substrates containing mismatches at the target base. Nat. Struct. Biol., 5, 872-877.
40. McLean,M.J., Larson,J.E., Wohlrab,F. and Wells,R.D. (1987) Reaction conditions affect the specificity of bromoacetaldehyde as a probe for DNA cruciforms and B-Z junctions. Nucleic Acids Res., 15, 6917-6935.
41. Dayn,A., Malkhosyan,S., Duzhy,D., Lyamichev,V., Panchenko,Y. and Mirkin,S. (1991) Formation of (dA-dT)n cruciforms in Escherichia coli cells under different environmental conditions. J. Bacteriol., 173, 2658-2664.