Kinetic analysis of sequence-specific alkylation of DNA by pyrimidine oligodeoxyribonucleotide-directed triple-helix formation

Bioconjugate Chemistry

Volumn 8, Issue 3, 1997, Pages 354-364

  Taylor, Matthew J ^a   Dervan, Peter B ^a  

^a California Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; DNA; ENZYMATIC HYDROLYSIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IONIC LIQUIDS; OLIGONUCLEOTIDES; POSITIVE IONS; RATE CONSTANTS;

BASE PAIRS; DUPLEX DNA; ELECTROPHILES; GEL MOBILITY; GUANINE BASIS; HELICAL COMPLEXES; KINETIC ANALYSIS; RATE CONSTANT K; SECOND-ORDER RATE CONSTANTS; TRIPLE-HELIX FORMATION;

ALKYLATION;

EID: 0031149643     PISSN: 10431802     EISSN: None     Source Type: Journal    
DOI: 10.1021/bc970035x     Document Type: Article

References (36)

1. (a) Hertzberg, R. P., and Dervan, P. B. (1982) Cleavage of Double-Helical DNA by (Methidiumpropyl-EDTA)iron(II). J. Am. Chem. Soc. 104, 313.
2. (b) Hertzberg, R. P., and Dervan, P. B. (1984) Cleavage of DNA with Methidiumpropyl-EDTA-Iron(II): Reaction Conditions and Product Analyses. Biochemistry 23, 3934.
3. (c) Schultz, P. G., Taylor, J. S., and Dervan, P. B. (1982) Design and Synthesis of a Sequence-Specific DNA Cleaving Molecule. (Distamycin-EDTA)iron(II). J. Am. Chem. Soc. 104, 6861.
4. (d) Mack, D. P., Iverson, B. L., and Dervan, P. B. (1988) Design and Chemical Synthesis of a Sequence-Specific DNA-Cleaving Protein. J. Am. Chem. Soc. 110, 7572.
5. (e) Mack, D. P., and Dervan, P. B. (1990) Nickel-Mediated Sequence-Specific Oxidative Cleavage of DNA by a Designed Metalloprotein. J. Am. Chem. Soc. 112, 4604.
6. (f) Bruice, T. W., Wise, J. G., Rosser, D. S. E., and Sigman, D. S. (1991) Conversion of Lambda Phage Cro into an Operator-Specific Nuclease. J. Am. Chem. Soc. 113, 5446.
7. (a) Baker, B. F., and Dervan, P. B. (1985) Sequence-Specific Cleavage of Double-Helical DNA. N-Bromoacetyldistamycin. J. Am. Chem. Soc. 107, 8266.
8. (b) Baker, B. F., and Dervan, P. B. (1989) Sequence-Specific Cleavage of DNA by N-Bromoacetyldistamycin - Product and Kinetic Analysis. J. Am. Chem. Soc. 111, 2700.
9. (c) Boger, D. L., and Mesini, P. (1995) DNA Alkylation Properties of CC-1065 and Duocarmycin Analogs Incorporating the 2,3,10,10a-Tetrahydrocyclopropa-[d]benzo[f]quinol-5-one Alkylation Subunit - Identification of Subtle Structural Features that Contribute to the Regioselectivity of the Adenine N3 Alkylation Reaction. J. Am. Chem. Soc. 117, 11647.
10. (a) Moser, H. E., and Dervan, P. B. (1987) Sequence-Specific Cleavage of Double Helical DNA by Triple Helix Formation. Science 238, 645.
11. (b) Povsic, T. J., and Dervan, P. B. (1989) Triple Helix Formation by Oligonucleotides on DNA Extended to the Physiological pH Range. J. Am. Chem. Soc. 111, 3059.
12. (c) Strobel, S. A., and Dervan, P. B. (1991) Single-Site Enzymatic Cleavage of Yeast Genomic DNA Mediated by Triple Helix Formation. Nature 350, 172.
13. (a) LeDoan, T., Perrouault, L., Praseuth, D., Habhoub, N., Decout, J.-L., Thuong, N. T., Lhomme, J., and Helene, C. (1987) Sequence-Specific Recognition, Photocrosslinking, and Cleavage of the DNA Double Helix by an Oligo-[α]-Thymidylate Covalently Linked to an Azidoproflavine Derivative. Nucleic Acids Res. 15, 7749.
14. (b) Perrouault, L., Asseline, U., Rivalle, C., Thoung, N. T., Bisagni, E., Giovannangeli, C., Le Doan, T., and Helene, C. (1990) Sequence-Specific Artificial Photoinduced Endonucleases Based on Triple Helix-Forming Oligonucleotides. Nature 344, 358.
15. (c) Thuong, N. T., and Helene, C. (1993) Sequence-Specific Recognition and Modification of Double-Helical DNA by Oligonucleotides. Angew. Chem., Int. Ed. Engl. 32, 666.
16. (a) Fedorova, O. S., Knorre, D. G., Podust, L. M., and Zarytova, V. F. (1988) Complementary Addressed Modification of Double-Stranded DNA within a Ternary Complex. FEBS Lett. 228, 273.
17. (b) Vlassov, V. V., Gaidamakov, S. A., Zarytova, V. F., Knorre, D. G., Levina, A. S., Nikonova, A. A., Podust, L. M., and Fedorova, O. S. (1988) Sequence-Specific Chemical Modification of Double-Stranded DNA with Alkylating Oligodeoxyribonucleotide Derivatives. Gene 72, 313.
18. (c) Povsic, T. J., and Dervan, P. B. (1990) Sequence-Specific Alkylation of Double-Helical DNA by Oligonucleotide-Directed Triple-Helix Formation. J. Am. Chem. Soc. 112, 9428.
19. (d) Shaw, J-P., Milligan, J. F., Krawczyk, S. H., and Matteucci, M. (1991) Specific, High Efficiency, Triple-Helix-Mediated Cross-Linking to Duplex DNA. J. Am. Chem. Soc. 113, 7765.
20. (e) Young, S. L., Krawczyk, S. H., Matteucci, M. D., and Toole, J. J. (1991) Triple Helix Formation Inhibits Transcription Elongation In Vitro. Proc. Natl. Acad. Sci. U.S.A. 88, 10023.
21. (a) Povsic, T. J., Strobel, S. A., and Dervan, P. B. (1992) Sequence-Specific Double-Strand Alkylation and Cleavage of DNA Mediated by Triple-Helix Formation. J. Am. Chem. Soc. 114, 5934.
22. (b) Kutyavin, I. V., Gamper, H. B., Gall, A. A., and Meyer, R. B. (1993) Efficient, Specific Interstrand Cross-Linking of Double-Stranded DNA by a Chlorambucil-Modified, Triplex-Forming Oligonucleotide. J. Am. Chem. Soc. 115, 9303.
23. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
24. Iverson, B. L., and Dervan, P. B. (1993) Adenine-Specific DNA Chemical Sequencing Reaction. Methods Enzymol. 218, 222.
25. Gait, M. J. (1984) Oligonucleotide Synthesis: A Practical Approach; IRL Press, Oxford, U.K., and references cited therein.
26. (a) de Groot, N., Lapidot, Y., Panet, A., and Wolman, Y. (1966) The Synthesis of N-Acetylphenylalanyl-sRNA. Biochem. Biophys. Res. Commun. 25, 17.
27. (b) Pelligrini, M., Oen, H., and Cantor, C. R. (1972) Covalent Attachment of a Peptidyl-Transfer RNA Analog to the 50S Subunit of Escherichia coli Ribosomes. Proc. Natl. Acad. Sci. U.S.A. 69, 837.
28. Dreyer, G. B., and Dervan, P. B. (1985) Sequence-Specific Cleavage of Single-Stranded DNA: Oligodeoxynucleotide-EDTA·Fe(II). Proc. Natl. Acad. Sci. U.S.A. 82, 968.
29. Zurlo, J., Curphey, T. J., Hiley, R., and Longnecker, D. S. (1982) Identification of 7-Carboxymethylguanine in DNA from Pancreatic Acinar Cells Exposed to Azaserine. Cancer Res. 42, 1286.
30. Maxam, A. M., and Gilbert, W. (1980) Sequencing End-Labeled DNA with Base-Specific Chemical Cleavages. Methods Enzymol. 65, 499.
31. Cameron, V., and Uhlenbeck, O. C. (1977) 3′-Phosphatase Activity in T4 Polynucleotide Kinase. Biochemistry 16, 5120.
32. Razzell, W. E., and Khorana, H. G. (1959) Studies on Polynucleotides: IV. Enzyme Degradation. The Stepwise Action of Venom Phosphodiesterase on Deoxyribo-Oligonucleotides. J. Biol. Chem. 234, 2114.
33. Hemminki, K., Peltonen, K., and Vodicka, P. (1989) Depurination from DNA of 7-(2-Aminoethyl)-Guanine and Ring-Opened 7-Methylguanines. Chem.-Biol. Interact. 70, 289.
34. Bevington, P. R., and Robinson, D. K. (1990) Data Reduction and Error Analysis for the Physical Sciences, 2nd ed., McGraw-Hill, New York.
35. Frost, A. A., and Pearson, R. G. (1961) Kinetics and Mechanism, 2nd ed., pp 40-46, Wiley, New York.
36. Page, M. I., and Jencks, W. P. (1971) Entropic Contributions to Rate Accelerations in Enzymic and Intramolecular Reactions and the Chelate Effect. Proc. Natl. Acad. Sci. U.S.A. 68, 1678.