A 96-well DNase I footprinting screen for drug-DNA interactions

Nucleic Acids Research

Volumn 35, Issue 12, 2007, Pages

  Ellis, Tom ^a   Evans, David A ^a   Martin, Christopher R H ^a   Hartley, John A ^a,b  

^a ASTRAZENECA   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BENZODIAZEPINE DERIVATIVE; DEOXYRIBONUCLEASE I; DNA TOPOISOMERASE (ATP HYDROLYSING); POLYAMIDE; POLYPYRROLE; PYRROLE DERIVATIVE; DNA BINDING PROTEIN; DNA TOPOISOMERASE II ALPHA; TUMOR ANTIGEN; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DNA BINDING; DNA DETERMINATION; DNA FOOTPRINTING; DNA SEQUENCE; DRUG DNA INTERACTION; DRUG STRUCTURE; GENE AMPLIFICATION; GENETIC CODE; PRIORITY JOURNAL; PROMOTER REGION; CHEMISTRY; DRUG SCREENING; EVALUATION; GENETICS; HUMAN; INFRARED RADIATION; INSTRUMENTATION; METHODOLOGY;

ANTIGENS, NEOPLASM; BENZODIAZEPINES; DEOXYRIBONUCLEASE I; DNA FOOTPRINTING; DNA TOPOISOMERASES, TYPE II, EUKARYOTIC; DNA-BINDING PROTEINS; DRUG EVALUATION, PRECLINICAL; HUMANS; INFRARED RAYS; PROMOTER REGIONS (GENETICS); PYRROLES;

EID: 34547623531     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm467     Document Type: Article

References (34)

1. Galas,D.J. and Schmitz,A. (1978) DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170.
2. Bailly,C., Kluza,J., Martin,C., Ellis,T. and Waring,M.J. (2005) DNase I footprinting of small molecule binding sites on DNA. Methods Mol. Biol., 288, 319-342.
3. Fox,K-R. (1997) DNase I footprinting. Methods Mol. Biol., 90 1-22.
4. Rippe,R.A., Brenner,D.A. and Tugores,A. (2001) Techniques to measure nucleic acid-protein binding and specificity. Nuclear extract preparations, DNase I footprinting, and mobility shift assays. Methods Mol. Biol., 160, 459-479.
5. Brenowitz,M., Senear,D.F., Shea,M.A. and Ackers,G.K. (1986) Quantitative DNase footprint titration: A method for studying protein-DNA interactions. Methods Enzymol., 130, 132-181.
6. Petri,V. and Brenowitz,M. (1997) Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches. Curr. Opin. Biotechnol., 8, 36-44.
7. Trauger,J.W. and Dervan,P.B. (2001) Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes. Methods Enzymol., 340, 450-466.
8. Fox,K.R. and Waring,M.J. (2001) High-resolution footprinting studies of drug-DNA complexes using chemical and enzymatic probes. Methods Enzymol., 340, 412-430.
9. Sandaltzopoulos,R. and Becker,P.B. (1994) Solid phase DNase I footprinting: Quick and versatile. Nucleic Acids Res., 22, 1511-1512.
10. Sandaltzopoulos,R., Ansorge,W., Becker,P.B. and Voss,H. (1994) Nonradioactive, solid-phase DNase I footprints analyzed on an A.L.F. DNA sequencer. Biotechniques, 17, 474, 476, 478.
11. Machida,M., Kamio,H. and Sorensen,D. (1997) Long-range and highly sensitive DNase I footprinting by an automated infrared DNA sequencer. Biotechniques, 23, 300-303.
12. Yindeeyoungyeon,W. and Schelm,M.A. (2000) Footprinting with an automated capillary DNA sequencer. Biotechniques, 29, 1034-1036, 1038, 1040-1031.
13. Wilson,D.O., Johnson,P. and McCord,B.R. (2001) Nonradiochemical DNase I footprinting by capillary electrophoresis. Electrophoresis, 22 1979-1986.
14. Wang,K., Gan,L., Boysen,C. and Hood,L. (1995) A microtiter plate-based high-throughput DNA purification method. Anal. Biochem., 226 85-90.
15. Bencini,D.A., O'Donovan,G.A. and Wild,J.R. (1984) Rapid chemical degradation sequencing. Biotechniques, 2, 4-5.
16. PDL - The Perl Data Language. http://pdl.perl.org.
17. Tolner,B., Hartley,J.A. and Hochhauser,D. (2001) Transcriptional regulation of topoisomerase II alpha at confluence and pharmacological modulation of expression by bis-benzimidazole drugs. Mol. Pharmacol. 59, 699-706.
18. Isaacs,R.J., Harris,A.L. and Hickson,I.D. (1996) Regulation of the human topoisomerase IIalpha gene promoter in confluence-arrested cells. J. Biol. Chem., 271, 16741-16747.
19. Wells,G., Martin,C.R., Howard,P.W., Sands,Z.A., Laughton,C.A., Tiberghien,A., Woo,C.K., Masterson,L.A., Stephenson,M.J. et al. (2006) Design, synthesis, and biophysical and biological evaluation of a series of pyrrolobenzodiazepine-poly(N-methylpyrrole) conjugates. J. Med. Chem., 49, 5442-5461.
20. Steffens,D.L., Jang,G.Y., Sutter,S.L., Brumbaugh,J.A., Middendorf,L.R., Muhlegger,K., Mardis,E.R., Weinstock,L.A. and Wilson,R.K. (1995) An infrared fluorescent dATP for labeling DNA. Genome Res., 5, 393-399.
21. Middendorf,L.R., Bruce,J.C., Bruce,R.C., Eckles,R.D., Grone,D.L., Roemer,S.C., Sloniker,G.D., Steffens,D.L., Sutter,S.L. et al. (1992) Continuous, on-line DNA sequencing using a versatile infrared laser scanner electrophoresis apparatus. Electrophoresis, 13 487-494.
22. Humphries,S.E., Gudnason,V., Whittall,R. and Day,I.N. (1997) Single-strand conformation polymorphism analysis with high throughput modifications, and its use in mutation detection in familial hypercholesterolemia. International Federation of Clinical Chemistry Scientific Division: Committee on Molecular Biology Techniques. Clin. Chem., 43, 427-435.
23. Takamoto,K., Chance,M.R, and Brenowitz,M. (2004) Semi-automated, single-band peak-fitting analysis of hydroxyl radical nucleic acid footprint autoradiograms for the quantitative analysis of transitions. Nucleic Acids Res., 32, 119.
24. Shadle,S.E., Allen,D.F., Guo,H., Pogozelski,W.K., Bashkin,J.S. and Tullius,T.D. (1997) Quantitative analysis of electrophoresis data: Novel curve fitting methodology and its application to the determination of a protein-DNA binding constant. Nucleic Acids Res., 25, 850-860.
25. Das,R., Laederach,A., Pearlman,S.M., Herschlag,D. and Altman,R.B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA, 11, 344-354.
26. Crow,S.D., Bailly,C., Garbay-Jaureguiberry,C., Roques,B., Shaw,B.R. and Waring,M.J. (2002) DNA sequence recognition by the antitumor drug ditercalinium. Biochemistry, 41, 8672-8682.
27. Martin,C., Ellis,T., McGurk,C.J., Jenkins,T.C., Hartley,J.A., Waring,M.J. and Thurston,D.E. (2005) Sequence-selective interaction of the minor-groove interstrand cross-linking agent SJG-136 with naked and cellular DNA: Footprinting and enzyme inhibition studies. Biochemistry, 44, 4135-4147.
28. Trauger,J.W., Baird,E.E., Mrksich,M. and Dervan,P.B. (1996) Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs. J. Am. Chem. Soc. 118, 6160-6166.
29. Dabrowiak,J.C. and Goodisman,J. (1989) In Kallenbach,N. R. (ed), Chemistry and Physics of DNA-Ligand Interactions, Adenine Press, New York, pp. 143-174.
30. Kawai,J., Shinagawa,A., Shibata,K., Yoshino,M., Itoh,M., Ishii,Y., Arakawa,T., Hara,A., Fukinishi,Y. et al. (2001) Functional annotation of a full-length mouse cDNA collection. Nature, 409 685-690.
31. Myburg,A.A., Remington,D.L., O'Malley,D.M., Sederoff,R.R and Whetten,R.W (2001) High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer. Biotechniques, 30, 348-352, 354, 356-347.
32. Sano,M., Ohyama,A., Takase,K., Yamamoto,M. and Machida,M. (2001) Electrophoretic mobility shift scanning using an automated infrared DNA sequencer. Biotechniques, 31, 1056-1058, 1060, 1062.
33. Dai,S.M., Chen,H.H., Chang,C., Riggs,A.D. and Flanagan,S.D. (2000) Ligation-mediated PCR for quantitative in vivo footprinting. Nature Biotechnol., 18, 1108-1111.
34. McIndoe,R.A., Hood,L. and Bumgarner,R.E. (1996) An analysis of the dynamic range and linearity of an infrared DNA sequencer. Electrophoresis, 17, 652-658.