Sequence-specific interactions of minor groove binders with restriction fragments of cDNAs for H Tau 40 protein and MAP kinase 2. A qualitative and quantitative footprinting study

Journal of Molecular Recognition

Volumn 12, Issue 2, 1999, Pages 121-130

  Kittler, L ^a   Baguley, B C ^b   Lober G ^a   Waring, M J ^c  

^a FRITZ LIPMANN INSTITUTE   (Germany)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

CDNAs of tau protein and MAP kinase 2; DNA sequence reading ligands; Gene targetting; Qualitative and quantitative footprinting

Indexed keywords

BASE PAIRING; CDNA LIBRARY; CONGOCIDINE; DISTAMYCIN A; DNA FOOTPRINTING; GLYCINE; MITOGEN ACTIVATED PROTEIN KINASE; MOLECULAR GENETICS; MOLECULAR INTERACTION; OLIGONUCLEOTIDE; QUANTITATIVE ANALYSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

CISPLATIN; DENSITOMETRY; DISTAMYCINS; DNA FOOTPRINTING; DNA RESTRICTION ENZYMES; DNA, COMPLEMENTARY; LIGANDS; MEMBRANE PROTEINS; MITOGEN-ACTIVATED PROTEIN KINASE 1; NETROPSIN; NUCLEIC ACID CONFORMATION; PYRIDINES; QUINOLINIUM COMPOUNDS;

EID: 0033103803     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1099-1352(199903/04)12:2<121::AID-JMR450>3.0.CO;2-Z     Document Type: Article

References (52)

1. Abu-Daya, A., Brown, P. M. and Fox, K. R. (1995). DNA sequence preferences of several AT-selective minor groove binding ligands. Nucl. Acids Res. 23, 3385-3392.
2. Bailly, C. and Henichart, J. P. (1991). DNA-recognition by intercalator-minor-groove binder hybrid molecules. Biocon. Chem. 2, 379-393.
3. Bailly, C. and Waring, M. J. (1995). Transferring the purine 2-amino group from guanines to adenines in DNA changes the sequence-specific binding of antibiotics. Nucleic Acids Res. 23, 885-892.
4. Bailly, C., Marchand, Ch., Nguyen, C. H., Bisagni, E., Garestier, T., Hélène, C. and Waring, M. J. (1995). Localized chemical reactivity in double-stranded DNA associated with the intercalative binding of benzo[e]pyridonidol and benzo[g]-pyridoindol triple-helix-stabilizing ligands. Eur. J. Biochem. 232, 66-76.
5. Baringa, M. (1995). Missing Alzheimer's gene found. Science 269, 9917-9918
6. Bell, A., Kittler, L., Löber, G. and Zimmer, C. (1996). Influence of minor groove binders on the eukaryotic topoisomerase II cleavage reaction with 41 base pair model oligonucleotides. Invest. New Drugs 13, 271-284.
7. Bell, A., Kittler, L., Löber, G. and Zimmer, C. (1997). DNA binding properties of minor groove binders and their influence on the topoisomerase II cleavage reaction. J. Mol. Recognit. 10, 245-255.
8. Burckhardt, G., Votavova, H., Sponar, J., Luck, G. and Zimmer, Ch. (1985). Two binding modes of netropsin are involved in the complex formation with poly(dA-dT)·poly(dA-dT) and other alternating DNA duplex polymers. J. Biomol. Struct. Dyn. 2, 721-736.
9. Chan, P. P. and Glazer, P. M. (1997). Triplex DNA: fundamentals, advances, and potential applications for gene therapy. J. Mol. Med. 75, 267-282.
10. Chen, S. M., Leupin, W., Rance, M. and Chazini, W. J. (1992). Two-dimensional NMR studies of d(GGTTATGCGGT)-d(ACCGCATTAACC) complexed with the minor groove binding drug SN-6999. Biochemistry 31, 4406-4413.
11. Cheng, A. J. and van Dyke, M. W. (1994). Oligodeoxynucleotide length and sequence effects on intermolecular, purine-purine-pyrimidine triple-helix formation. Nucl. Acids Res. 22, 4742-4747.
12. Curcio, L. D., Bouffard, D. Y. and Scanlon, K. J. (1997). Oligonucleotides as modulators of cancer gene expression. Pharmac. Ther. 74, 317-332.
13. Delacourte, A. (1994). Pathalogical tau proteins of Alzheimer's disease as a biological marker of neurofibrillary degeneration. Biomed. Pharmacother. 48, 287-295.
14. Epping, B. (1996). Der Wahnsinn hat Falten. Bild der Wissenschaft 24-29.
15. Forrow, S. M., Lee, M., Souhami, R. L. and Hartley, J. A. (1995). The effect of AT and GC sequence specific minor groove-binding agents on restriction endonuclease activity. Chem. Biol. Interact. 96, 125-142.
16. Förtsch, I., Baguley, B. and Zimmer, Ch. (1998). Structure-dependent effects of minor groove binders on the DNA triple helix motif poly(dA)2-poly(dT): influence of antitumoractive nonintercalative bisquaternary ammonium heterocycles. Anti-Cancer Drug Des. 13, 417-429.
17. 6G]AATTCGCG)-SN6999 complex. Biochemistry 32, 9639-9648.
18. Goedert, M. (1995). Molecular dissection of the neurofibrillary lesions of Alzheimer's disease. Arzneim. Forschung/Drug Res., 45, 403-409.
19. Gottesfeld, J. M., Neely, L., Tranger, J. W., Baired, E. E. and Dervan, P. B. (1997). Regulation of gene expression by small molecules. Nature 387, 202-205.
20. Grokhovsky, S. L. and Zubarev, V. E. (1991). Sequence-specific cleavage of double-stranded DNA caused by X-ray ionization of the platinum atom in Pt-bis-netropsin-DNA complex. Nucleic Acids Res. 19, 257-264.
21. Guo, D., Gupta, R. and Lown, J. W. (1993). DNA sequence-selective binding of head-to-tail linked bis-lexitropsins: relation of phasing to cytotoxic potency. Anti-Cancer Drug Des. 8, 369-397.
22. Kielkopf, C. L., Bairel, E. E., Dervan, P. B. and Rees, D. C. (1998). Structural basis for G·C recognition in the DNA minor groove. Nature Struct. Biol. 5, 104-108.
23. Kissinger, K. L., Dabrowiak, J. C. and Lown, J.C. (1990). Molecular recognition between oligopeptides and nucleic acids: DNA binding specificity of a series of bis-netropsin analogues deduced from footprinting analysis. Chem. Res. Toxicol. 3, 162-168.
24. Kittler, L. and Löber, G. (1995). Sequence specificity of DNA-psoralen photoproduct formation in supercoiled plasmid DNA (pUC19). J. Photochem. Photobiol. B. Biol. 27, 161-166.
25. Kittler, L., Wähnert, U., Baguley, B. C., Bailly, C., Waring, M. J. and Löber, G. (1996a). Sequence-specific binding of antitumour bisquaternary ammonium heterocycles to DNA and inhibition of polymerase activity in vitro. Anti-Cancer Drug Des. 11, 101-115.
26. Kittler, L., Bell, A., Baguley, B. C. and Löber, G. (1996b). Inhibition of restriction endonucleases by DNA sequence-reading ligands. Biochem. Mol. Biol. Int. 40, 263-272.
27. Kopka, M. L. and Larsen, T. A. (1992). Netropsin and lexitropsins. The search for sequence-specific minor-groove-binding ligands. In Nucleic Acid Targeted Drug Design. (ed. by C. L. Propst and T. J. Perun) pp. 304-374. Marcel Dekker, New York.
28. Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. and Dickerson, R. E. (1985). The molecular origin of DNA-drug specificity in netropsin and distamycin. Proc. Natl Acid. Sci USA 82, 1376-1380.
29. Kopka, M. L., Goodsell, D. S., Han, G. W., Chin, T. K., Lown, J. W. and Dickerson, R. E. (1997). Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G. Structure 5, 1033-1046.
30. Lavery, R. and Pullmann, B. (1985). The dependence of the surface electrostatic potential of B-DNA on environmental factors. J. Biomol. Struct. Dyn. 2, 1021-1031.
31. Lepre, C. A. and Lippard, S. J. (1990). Interaction of platinum antitumor compounds. In Nucleic Acids and Molecular Biology, Vol. 4 (ed. by F. Eckstein and D. M. J. Lilley), pp. 9-38, Springer, Heidelberg.
32. Lown, J. W. (1992). Lexitropsins in antiviral drug development. Antiviral Res. 17, 179-196.
33. Lown, J. W. (1994). DNA recognition by lexitropsins, minor groove binding agents. J. Mol. Recognit. 7, 79-88.
34. Luck, G., Störl, J., Baguley, B., Zimmer, C. (1992). DNA binding of the nonintercalative ligands SN-6132, SN-61431 and SN-6113: minor variations of the ligand structure may cause changes in the base pair preference. J. Biomol. Struct. Dyn. 10, 551-564.
35. Marchand, C., Bailly, C., Nguyen, C. H., Bisagni, E., Garestier, T., Hélène, C. and Waring, M. J. (1996). Stabilization of triple helix DNA by a benzopyridoquinoxaline intercalator. Biochemistry 35, 5022-5032.
36. Nikolaev, V. A., Grokhovsky, S. L., Surovaya, A. N., Leinsoo, T. A., Sidorova, N. Yu., Zasedatelev, A. S., Zhuze, A. L., Strahan, G. A., Shafer, R. H. and Gursky, G. V. (1996). Design sequence-specific DNA binding ligands that use a two-stranded peptide motif for DNA sequence recognition. J. Biomol. Struct. Dyn. 14, 31-46.
37. Pelton, J. G. and Wemmer, D. E. (1989). Structural characterization of a 2:1 distamycin A-d(GCAAATTGGC) complex by two-dimensional NMR. Proc. Natl Acad. Sci USA 86, 5723-5727.
38. Renzeperis, D., Marky, L. A., Dwyer, T. J., Geierstanger, B. H., Pelton, J. G. and Wemmer, D. E. (1995). Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry 34, 2937-2945.
39. Sayers, E. W. and Waring, M. J. (1993). Footprinting titration studies on the binding of echinomycin to DNA incapable of forming Hoogsteen base pairs. Biochemistry 32, 9094-9107.
40. Selkoe, E. W. (1994). Normal and abnormal biology of the β-amyloid precursor protein. A. Rev. Neurol. Sci. 17, 489-517.
41. Slickers, P., Hillebrand, M., Kittler, L., Löber, G. and Sühnel, J. (1998). Molecular modelling and footprinting studies of DNA minor groove binders: bisquaternary ammonium heterocyclic compounds. Anti-Cancer Drug Des. 13, 463-488.
42. Stull, R. A. and Szoka, F. C. (1995). Antigene, ribozyme and aptamer nucleic acids drugs: progress and prospects. Pharm. Res. 12, 465-483.
43. Surovaya, A. N., Burckhard, G., Grokhovsky, S. L., Birch-Hirschfeld, E., Gursky, G. V. and Zimmer, Ch (1997). Hairpin polyamids that use parallel and antiparallel side-by-side peptide motifs in binding to DNA. J. Biomol. Struct. Dyn. 14, 595-606.
44. Swalley, S. E., Baired, E. E. and Dervan, P. B. (1997). Discrimination of 5'-GGGG-3', 5'-GCGC-3', and 5'-GGCC-3' sequences in the minor groove of DNA by eight-ring hairpin polyamids. J. Am. Chem. Soc. 119, 6953-6961.
45. Thuong, N. T. and Hélène, C. (1995). Sequenzspezifische Erkennung und Modifikation von Doppelhelix-DNA durch Oligonucleotide. Angew. Chem. Int. Ed. 32, 666-690.
46. Waring, M. J. (1993). Echinomycin and related quinoxaline antibiotics. In Molecular Aspects of Anticancer Drug-DNA Interactions Vol. I (ed. by S. Neidle and M. J. Waring), pp. 213-242, Macmillan, London.
47. Waring, M. J. and Bailly, C. (1994a). DNA recognition by intercalators and hybrid molecules. J. Mol. Recognit. 7, 109-122.
48. Waring, M. J. and Bailly, C. (1994b). The purine 2-amino group as a critical recognition element for binding of small molecules to DNA. Gene 149, 69-79.
49. Wemmer, D. (1998). Reading DNA. Nature Struct. Biol. 5, 169-171.
50. Workman, P., D'Incalci, M., Berdel, W. E., Egorin, M. J., Hélène, E., Hickman, J. A., Jarman, M., Schwartsmann, G. and Sikora, K. (1992). New approaches in cancer pharmacology: Drug design and development. Eur. J. Cancer 28A, 1190-1200.
51. Zasedatelev, A. S., Borodulin, V. B., Grokhovsky, A. M., Nikitin, A. M., Salmanova, D. V., Zhuze, A. L., Gursky, G. V. and Shafer, R. H. (1995). Mono-, di-and trimeric binding of a bis-netropsin to DNA. FEBS Lett. 375, 304-306.
52. Zimmer, C. and Wähnert, U. (1986). Nonintercalating DNA-binding ligands: specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material. Progr. Biophys. Mol. Biol. 47, 31-112