Sequence-specific covalent labelling of DNA

Biochemical Society Transactions

Volumn 39, Issue 2, 2011, Pages 623-628

  Gottfried, Anna ^a   Weinhold, Elmar ^a  

^a RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

DNA methyltransferase (DNA MTase); Hairpin polyamide; Nicking endonuclease (NEase); S adenosylmethionine analogue (AdoMet analogue); Triple helix forming oligonucleotide

Indexed keywords

DNA; DNA METHYLTRANSFERASE; DNA POLYMERASE; DOUBLE STRANDED DNA; ENDONUCLEASE; OLIGODEOXYNUCLEOTIDE; POLYAMIDE; SINGLE STRANDED DNA;

CARBOXY TERMINAL SEQUENCE; COVALENT BOND; DNA CROSS LINKING; DNA HAIRPIN; DNA REPLICATION; DNA SEQUENCE; GENE EXPRESSION; PRIORITY JOURNAL; REVIEW; TRIPLE HELIX;

BASE SEQUENCE; DNA; ENDONUCLEASES; HUMANS; HYDROGEN BONDING; INTERCALATING AGENTS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; STAINING AND LABELING; SUBSTRATE SPECIFICITY;

EID: 79953169545     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST0390623     Document Type: Review

References (50)

1. Kessler, C. (1995) Methods for nonradioactive labeling of nucleic acids. In Nonisotopic Probing, Blotting, and Sequencing (Kricka, L.J., ed.), pp. 41-109, Academic Press, San Diego
2. Caruthers, M.H., Barone, A.D., Beaucage, S.L., Dodds, D.R., Fisher, E.F., McBride, L.J., Matteucci, M., Stabinsky, Z. and Tang, J.-Y. (1987) Chemical synthesis of deoxyoligonucleotides by the phoshoramidite method. Methods Enzymol. 154, 287-313
3. Weisbrod, S.H. and Marx, A. (2008) Novel strategies for the site-specific covalent labelling of nucleic acids. Chem. Commun. 5675-5685
4. Heetebrij, R.J., Talman, E.G., van Velzen, M.A., van Gijlswijk, R.P.M., Snoeijers, S.S., Schalk, M., Wiegant, J., van de Rijke, F., Kerkhoven, R.M., Raap, A.K. et al. (2003) Platinum(II)-based coordination compounds as nucleic acid labeling reagents: synthesis, reactivity, and applications in hybridization assays. ChemBioChem 4, 573-583
5. Thuong, N.T. and Hélène, C. (1993) Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. Angew. Chem. Int. Ed. 32, 666-690
6. Escudé, C., Garestier, T. and Hélène, C. (1999) Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation. Proc. Natl. Acad. Sci. U.S.A. 96, 10603-10607
7. Roulon, T., Coulaud, D., Delain, E., Le Cam, E., Hélène, C. and Escudé, C. (2002) Padlock oligonucleotides as a tool for labeling superhelical DNA. Nucleic Acids Res. 30, e12
8. Géron-Landre, B., Roulon, T., Desbiolles, P. and Escudé, C. (2003) Sequence-specific fluorescent labeling of double-stranded DNA observed at the single molecule level. Nucleic Acids Res. 31, e125
9. Roulon, T., Hélène, C. and Escudé, C. (2002) Coupling of a targeting peptide to plasmid DNA using a new type of padlock nucleotide. Bioconjugate Chem. 13, 1134-1139
10. Pfannschmidt, C., Schaper, A., Heim, G., Jovin, T.M. and Langowski, J. (1996) Sequence-specific labeling of super-helical DNA by triple helix formation and psoralen crosslinking. Nucleic Acids Res. 24, 1702-1709 (Pubitemid 26137929)
11. Perrouault, L., Asseline, U., Rivalle, C., Thuong, N.T., Bisagni, E., Giovannangeli, C., Le Doan, T. and Hélène, C. (1990) Sequence-specific artificial photoinduced endonucleases based on triple helix-forming oligonucleotides. Nature 344, 358-360
12. Wemmer, D.E. and Dervan, P.B. (1997) Targeting the minor groove of DNA. Curr. Opin. Struct. Biol. 7, 355-361
13. Mrksich, M., Parks, M.E. and Dervan, P.B. (1994) Hairpin peptide motif. A new class of oligopeptides for sequence-specific recognition in the minor groove of double-helical DNA. J. Am. Chem. Soc. 116, 7983-7988
14. Trauger, J.W., Baird, E.E. and Dervan, P.B. (1996) Recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (Pubitemid 26262061)
15. White, S., Szewczyk, J.W., Turner, J.M., Baird, E.E. and Dervan, P.B. (1998) Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands. Nature 391, 468-471 (Pubitemid 28086542)
16. Chenoweth, D.M. and Dervan, P.B. (2009) Allosteric modulation of DNA by small molecules. Proc. Natl. Acad. Sci. U.S.A. 106, 13175-13179
17. Fechter, E.J., Olenyuk, B. and Dervan, P.B. (2005) Sequence-specific fluorescence detection of DNA by polyamide-Thiazole Orange conjugates. J. Am. Chem. Soc. 127, 16685-16691
18. Rucker, V.C., Foister, S., Melander, C. and Dervan, P.B. (2003) Sequence specific fluorescence detection of double strand DNA. J. Am. Chem. Soc. 125, 1195-1202
19. Maeshima, K., Janssen, S. and Laemmli, U.K. (2001) Specific targeting of insect and vertebrate telomeres with pyrrole and imidazole polyamides. EMBO J. 20, 3218-3228 (Pubitemid 32612009)
20. Bando, T., Iida, H., Saito, I. and Sugiyama, H. (2001) Sequence-specific DNA interstrand cross-linking by imidazole-pyrrole CPI conjugate. J. Am. Chem. Soc. 123, 5158-5159
21. Bando, T., Narita, A., Saito, I. and Sugiyama, H. (2003) Highly efficient sequence-specific DNA interstrand cross-linking by pyrrole/imidazole CPI conjugates. J. Am. Chem. Soc. 125, 3471-3485
22. Xiao, M., Phong, A., Ha, C., Chan, T.-F., Cai, D., Leung, L., Wan, E., Kistler, A., DeRisi, J.L., Selvin, P.R. and Kwok, P.-Y. (2007) Rapid DNA mapping by fluorescent single molecule detection. Nucleic Acids Res. 35, e16
23. Jo, K., Dhingra, D.M., Odijk, T., de Pablo, J.J., Graham, M.D., Runnheim, R., Forrest, D. and Schwartz, D.C. (2007) A single-molecule barcoding system using nanoslits for DNA analysis. Proc. Natl. Acad. Sci. U.S.A. 104, 2673-2678
24. Kuhn, H. and Frank-Kamenetskii, M.D. (2008) Labeling of unique sequences in double-stranded DNA at sites of vicinal nicks generated by nicking endonucleases. Nucleic Acids Res. 36, e40
25. Klimašauskas, S. and Weinhold, E. (2007) A new tool for biotechnology: AdoMet-dependent methyltransferases. Trends Biotechnol. 25, 99-104 (Pubitemid 46273755)
26. Dryden, D.T.F. (1999) Bacterial DNA methyltransferases. In S-Adenosylmethionine-Dependent Methyltransferases: Structures and Functions (Cheng, X. and Blumenthal, R.M., eds), pp. 283-340, World Scientific, Singapore
27. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2005) REBASE: a database for DNA restriction and modification enzymes, genes and genomes. Nucleic Acids Res. 38, D234-D236
28. Pignot, M., Siethoff, C., Linscheid, M. and Weinhold, E. (1998) Coupling of a nucleoside with DNA by a methyltransferase. Angew. Chem. Int. Ed. 37, 2888-2891
29. Pljevaljčić, G., Pignot, M. and Weinhold, E. (2003) Design of a new fluorescent cofactor for DNA methyltransferase and sequence-specific labeling of DNA. J. Am. Chem. Soc. 125, 3486-3492
30. Pljevaljcic, G., Schmidt, F., Peschlow, A. and Weinhold, E. (2004) Sequence-specific DNA labeling using methyltransferases. Methods Mol. Biol. 283, 145-161
31. Pljevaljčić, G., Schmidt, F., Scheidig, A.J., Lurz, R. and Weinhold, E. (2007) Quantitative labeling of long plasmid DNA with nanometer precision. ChemBioChem 8, 1516-1519 (Pubitemid 47436909)
32. Pljevaljčić, G., Schmidt, F. and Weinhold, E. (2004) Sequence-specific methyltransferase-induced labeling of DNA (SMILing DNA). ChemBioChem 5, 265-269 (Pubitemid 39257118)
33. Schmidt, F.H.-G., Hüben, M., Gider, B., Renault, F., Teulade-Fichou, M.-P. and Weinhold, E. (2008) Sequence-specific methyltransferase-induced labelling (SMILing) of plasmid DNA for studying cell transfection. Bioorg. Med. Chem. 16, 40-48
34. Wilkinson, S., Diechtierow, M., Estabrook, A.E., Schmidt, F., Hüben, M., Weinhold, E. and Reich, N.O. (2008) Molecular scale architecture: engineered three- and four-way junctions. Bioconjugate Chem. 19, 470-475 (Pubitemid 351294918)
35. Braun, G., Diechtierow, M., Wilkinson, S., Schmidt, F., Hüben, M., Weinhold, E. and Reich, N.O. (2008) Enzyme-directed positioning of nanoparticles on large DNA templates. Bioconjugate Chem. 19, 476-479 (Pubitemid 351294919)
36. Comstock, L.R. and Rajski, S.R. (2005) Conversion of DNA methyltransferases into azidonucleosyl transferases via synthetic cofactors. Nucleic Acids Res. 33, 1644-1652 (Pubitemid 41418392)
37. Weller, R. and Rajski, S.R. (2005) DNA methyltransferase-moderated click chemistry. Org. Lett. 7, 2141-2144
38. Comstock, L.R. and Rajski, S.R. (2005) Methyltransferase-directed DNA strand scission. J. Am. Chem. Soc. 127, 14136-14137
39. Schlenk, F. and Dainko, J.L. (1975) The S-n-propyl analogue of S-adenosylmethionine. Biochim. Biophys. Acta 385, 312-323
40. Dalhoff, C., Lukinavičius, G., Klimašauskas, S. and Weinhold, E. (2006) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nat. Chem. Biol. 2, 31-32
41. Dalhoff, C., Lukinavičius, G., Klimašauskas, S. and Weinhold, E. (2006) Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases. Nat. Protoc. 1, 1879-1886
42. Lukinavičius, G., Lapiene, V., Staševskij, Z., Dalhoff, C., Weinhold, E. and Klimašauskas, S. (2007) Targeted labeling of DNA by methyltransferase-directed transfer of activated groups (mTAG). J. Am. Chem. Soc. 129, 2758-2759
43. Neely, R.K., Dedecker, P., Hotta, J., Urbanavičiūte, G., Klimašauskas, S. and Hofkens, J. (2010) DNA fluorocode: a single molecule, optical map of DNA with nanometre resolution. Chem. Sci. 1, 453-460
44. Stecher, H., Tengg, M., Ueberbacher, B.J., Remler, P., Schwab, H., Griengl, H. and Gruber-Khadjawi, M. (2009) Biocatalytic Friedel-Crafts alkylation using non-natural cofactors. Angew. Chem. Int. Ed. 48, 9546-9548
45. Lee, B.W.K., Sun, H.G., Zang, T., Kim, B.J., Alfaro, J.F. and Zhou, Z.S. (2010) Enzyme-catalyzed transfer of a ketone group from an S-adenosylmethionine analogue: a tool for the functional analysis of methyltransferases. J. Am. Chem. Soc. 132, 3642-3643
46. Motorin, Y., Burhenne, J., Teimer, R., Koynov, R., Willnow, S., Weinhold, E. and Helm, M. (2010) Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling. Nucleic Acids Res., doi:10.1093/nar/gkq825
47. Peters, W., Willnow, S., Duisken, M., Kleine, H., Macherey, T., Duncan, K.E., Litchfield, D.W., Lüscher, B. and Weinhold, E. (2010) Enzymatic site-specific functionalization of protein methyltransferase substrates with alkynes for click labelling. Angew. Chem. Int. Ed. 49, 5170-5173
48. Xu, G.-L. and Bestor, T.H. (1997) Cytosine methylation targeted to pre-determined sequences. Nat. Genet. 17, 376-378
49. Kiss, A. and Weinhold, E. (2008) Functional reassembly of split enzymes on-site: a novel approach for highly sequence-specific targeted DNA methylation. ChemBioChem 9, 351-353
50. Van Der Gun, B.T.F., Maluszynska-Hoffman, M., Kiss, A., Arendzen, A.J., Ruiters, M.H.J., McLaughlin, P.M.J., Weinhold, E. and Rots, M.G. (2010) Targeted DNA methylation by a DNA methyltransferase coupled to a triple helix forming oligonucleotide to down-regulate the epithelial cell adhesion molecule. Bioconjugate Chem. 21, 1239-1245