Abstract
Many of the anticancer chemotherapeutic agents in current clinical use are known to interact strongly with DNA (e.g., Adriamycin, cis-platinum, melphalan, mitomycin C, and mitoxantrone). Although the exact mechanism of action remains unresolved in most cases, the apparent role of DNA has prompted, over several decades, a wide range of studies of these drug-DNA interactions. The major objective of such studies has been to determine the structure of the drug-DNA complex, with the objective being to use this information in the design of new derivatives.
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References
Phillips, D. R., White, R. J., Trist, H., Cullinane, C., Dean, D., and Crothers, D. M. (1990) New insight into drug-DNA interactions at individual drug binding sites probed by RNA polymerase during active transcription of the DNA. Anti-Cancer Drug Design 5, 21–29.
Leupin, W. (1990) Experimental proofs of a drug’s DNA specificity, in Molecular Basis of Specijkity in Nucleic Acid-Drug Interactions (Pullman, B. and Jortner, J., eds.) Kluwer Academic, Dordrecht, pp. 579–603.
Van Dyke, M. W. and Dervan, P. B. (1983) Methidium-EDTA·Fe(I1) and DNase I footprinting report different small molecule binding site sizes on DNA. Nucleic Acids Res. 11, 5555–5567.
Dervan, P. (1986) Design of sequence-specific DNA binding molecules. Science 232, 464–471.
Tullius, T. D. (1988) DNA footprinting with hydroxyl radical. Nature 332, 663,664.
Dabrowiak, J. C. and Goodisman, J. (1989) Quantitative footprinting analysis of drug-DNA interactions, in Chemistry and Physics of DNA-Ligand Interactions (Kallenbach, N. R., ed.) Adenine, New York, pp. 143–174.
Phillips, D. R. and Crothers, D. M. (1986) Kinetics and sequence specificity of drug-DNA interactions: an in vitro transcription assay. Biochemistry 25, 7355–7362
Trist, H. and Phillips, D. R. (1989) In vitro transcription analysis of the role of flanking sequences on the DNA sequence specificity of Adriamycin. Nucleic Acids Res. 17, 3673–3688.
White, R. J. and Phillips, D. R. (1989) Bidirectional transcription footprinting of DNA binding ligands. Biochemistry 28, 6259–6269.
White, R. J. and Phillips, D. R. (1989) Sequence-dependent termination of bacteriophage T7 transcription in vitro by DNA binding drugs. Biochemistry 28, 4277–4283.
Cullinane, C. and Phillips, D. R. (1990) Induction of stable transcriptional blockage sites by Adriamycin: GpC specificity of apparent Adriamycin-DNA adducts and dependence on iron (III) ions. Biochemistry 29, 5638–5646.
Straney, D. C. and Crothers, D. M. (1985) Intermediates in transcription initiation from the E. coli lac UV5 promoter. Cell 43, 449–459.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Biology. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Phillips, D.R., White, R. J., Dean, D., and Crothers, D. M (1990) Monte-Carlo simulation of multisite echinomycin-DNA interactions detected by in vitro transcription analysis. Biochemistry 29, 4812–4819.
Wu, H. and Crothers, D. M. (1984) The locus of sequence-directed and protein-induced DNA binding. Nature 308, 509–513.
Silverstone, A. E., Arditti, R. R., and Magasnik, B. (1970) Catabolite-insensitive revertants of lac promoter mutants. Proc. Natl. Acad. Sci. USA 66, 773–779.
Schaeffer, F., Kolb, A., and But, H. (1982) Point mutations change the thermal denaturation profile of a short DNA fragment containing the lactose control elements. Comparison between experiment and theory. EMBO J. 1, 99–105.
Cullinane, C. and Phillips, D. R. (1993) Nucleic Acids Res. 21, 1857–1862.
Stefano, J. E. and Gralla, J. (1979) Lac UV5 transcription in vitro. Rate limitation subsequent to formation of an RNA polymerase-DNA complex. Biochemistry 18, 1063–1067.
Melton, D. A., Kreig, P. A., Rebagliati, M. R., Maniatis, T., Zinn, K., and Green, M. R. (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 12, 7035–7056.
Caprousis, A. J., Stefano, J. E., and Gralla, J. D. (1982) 5′-Nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters. J. Mol. Biol. 157, 619–633.
Dabrowiak, J. C., Skorobogaty, A., Rich, N., Vary, C. P. H., and Vournakis, J. N. (1986) Computer assisted microdensitometric analysis of footprinting autoradio-graphic data. Nucleic Acids Res. 14, 489–499.
Phillips, D. R., Moate, P. J., and Boston, R. C. (1994) A modelling procedure for the analysis of dynamic drug-DNA interactions probed during active transcription of the DNA. Anti-Cancer Drug Des. 9, in press.
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© 1995 Humana Press Inc.
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Phillips, D.R., Crothers, D.M. (1995). An In Vitro Transcription Assay for Probing Drug-DNA Interactions During Active Transcription of DNA. In: Tymms, M.J. (eds) In Vitro Transcription and Translation Protocols. Methods in Molecular Biology, vol 37. Humana Press. https://doi.org/10.1385/0-89603-288-4:89
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DOI: https://doi.org/10.1385/0-89603-288-4:89
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