Interaction of DAPI with individual strands of trinucleotide repeats: Effects on replication in vitro of the AAT·ATT triplet

European Journal of Biochemistry

Volumn 270, Issue 23, 2003, Pages 4755-4761

  Trotta, Edoardo ^a   Del Grosso, Nicoletta ^a   Erba, Maura ^b   Melino, Sonia ^b   Cicero, Daniel ^b,c,d   Paci, Maurizio ^b,c  

^a CNR   (Italy)

^b UNIVERSITY OF ROME TOR VERGATA   (Italy)

^c INFM   (Italy)

^d SISSA   (Italy)

Author keywords

DAPI; DNA structure; Hairpin; Klenow; Trinucleotide repeats

Indexed keywords

4',6 DIAMIDINO 2 PHENYLINDOLE; ADENINE; COMPLEMENTARY DNA; CYTOSINE; DNA DIRECTED DNA POLYMERASE BETA; GUANINE; LIGAND; PRIMER DNA; THYMINE;

AMINO ACID SEQUENCE; ARTICLE; CELL DIVISION; CHEMICAL STRUCTURE; COMPLEX FORMATION; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; DRUG BINDING; ELECTROPHORETIC MOBILITY; FLUORESCENCE; GEL ELECTROPHORESIS; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; TRINUCLEOTIDE REPEAT;

BASE SEQUENCE; DNA; DNA REPLICATION; FLUORESCENCE; INDOLES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; TEMPLATES, GENETIC; TRINUCLEOTIDE REPEATS;

EID: 0345256430     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2003.03877.x     Document Type: Article

References (38)

1. Kapuscinski, J. (1995) DAPI: a DNA-specific fluorescent probe. Biotech Histochem 70, 220-233.
2. Parolin, C., Montecucco, A., Chiarocchi, G., Pedrali-Noy, G., Valisena, S., Palumbo, M. & Palù, G. (1990) The effect of the minor groove binding agent DAPI (4,6-diamidino-2-phenylindole) on DNA-directed enzymes: an attempt to explain inhibition of plasmid expression in Escherichia coli. FEMS Microbiol. Lett. 68, 341-346.
3. Straney, D.C. & Crothers, D.M. (1987) Effect of drug-DNA interactions upon transcription initiation at the lac promoter. Biochemistry 26, 1987-1995.
4. Chiang, S.-Y., Welch, J., Rauscher, F.J. & Beerman, T.A. (1994) Effects of minor groove binding drugs on the interaction of TATA box binding protein and TFIIA with DNA. Biochemistry 33, 7033-7040.
5. Storl, K., Storl, J., Zimmer, C.H. & Lown, J.W. (1993) Minor-groove binders are inhibitors of the catalytic activity of DNA gyrases. FEBS Lett. 317, 157-162.
6. Woynarowski, J.M., McHugh, M., Sigmund, R.D. & Beerman, T.A. (1989) Modulation of topoisomerase II catalytic activity by DNA minor groove binding agents distamycin, Hoechst 33258, and 4′,6-diamidine-2-phenylindole. Mol. Pharmacol. 35, 177-182.
7. McHugh, M.M., Woynarowski, R.D. & Beerman, T.A. (1989) Effect of minor groove binding drugs on mammalian topoisomerase I activity. Biochem. Pharmacol. 38, 2323-2328.
8. Parolin, C., Zanotti, G. & Palù, G. (1995) A model for the sequence-dependent DNA binding of 4′,6-diamidino-2-phenylindole (DAPI). Biochem. Biophys. Res. Commun. 208, 332-338.
9. Wilson, W.D., Tanious, F.A., Barton, H.J., Jones, R.L., Fox, K., Wydra, R.L. & Strekowski, L. (1990) DNA sequence dependent binding modes of 4′6-diamidino-2-phenylindole (DAPI). Biochemistry 29, 8452-8461.
10. 2 and its interaction with minor groove binding 4′,6-diamidino-2-phenylindole. J. Biol. Chem. 268, 3944-3951.
11. Trotta, E. & Paci, M. (1998) Solution structure of DAPI selectively bound in the minor groove of a DNA T·T mismatch-containing site: NMR and molecular dynamics studies. Nucleic Acids Res. 26, 4706-4713.
12. Wilson, W.D., Tanious, F.A., Barton, H.J., Strekowski, L. & Boykin, D.W. (1989) Binding of 4′,6-diamidino-2-phenylindole (DAPI) to GC and mixed sequences in DNA: intercalation of a classical groove-binding molecule. J. Am. Chem. Soc. 111, 5008-5010.
13. 1H NMR study. Nucleic Acids Res. 23, 1333-1340.
14. 2]: evidence for major groove binding of a DNA probe. J. Am. Chem. Soc. 115, 3441-3447.
15. 1H NMR Study. J. Biol. Chem. 271, 27608-27614.
16. Trotta, E., Del Grosso, N., Erba, M. & Paci, M. (2000) The ATT strand of AAT·ATT trinucleotide repeats adopts stable hairpin structures induced by minor-groove-binding ligands. Biochemistry 39, 6799-6808.
17. Gastier, J.M., Pulido, J.C., Sunden, S., Brody, T., Buetow, K.H., Murray, J.C., Weber, J.L., Hudson, T.J., Sheffield, V.C. & Duyk, G.M. (1995) Survey of trinucleotide repeats in the human genome: assessment of their utility as genetic markers. Hum. Mol. Genet. 4, 1829-1836.
18. Stallings, R.L. (1994) Distribution of trinucleotide microsatellites in different categories of mammalian genomic sequence: implications for human genetic diseases. Genomics 21, 116-121.
19. Lozano, G. & Levine, A.J. (1991) Tissue-specific expression of p53 in transgenic mice is regulated by intron sequences. Mol. Carcinogen. 4, 3-9.
20. Brinster, R.L., Allen, J.M., Behringer, R.R., Gelinas, R.E. & Palmiter, R.D. (1988) Introns increase transcriptional efficiency in transgenic mice. Proc. Natl Acad. Sci. USA 85, 836-840.
21. Ohshima, K., Kang, S., Larson, J.E. & Wells, R.D. (1996) TTA.TAA triplet repeats in plasmids form a non-H bonded structure. J. Biol. Chem. 271, 16784-16791.
22. 2+ concentration and mismatches on triplet-repeat expansion during DNA replication in vitro. Nucleic Acids Res. 27, 2235-2240.
23. Lyons-Darden, T. & Topal, M.D. (1999) Abasic sites induce triplet-repeat expansion during DNA replication in vitro. J. Biol. Chem. 274, 25975-25978.
24. Richards, R.I. & Holman, K., Yu, S. & Sutherland, G.R. (1993) Fragile X syndrome unstable element, p(CCG)n, and other simple tandem repeat sequences are binding sites for specific nuclear proteins. Hum. Mol. Genet. 2, 1429-1435.
25. Tanious, F.A., Veal, J.M., Buczak, H., Ratmeyer, L.S. & Wilson, W.D. (1992) DAPI (4′,6-diamidino-2-phenylindole) binds differently to DNA and RNA: minor-groove binding at AT sites and intercalation at AU Sites. Biochemistry 31, 3103-3122.
26. Eriksson, S., Kim, S.K., Chiarocchi, G., Kubista, M. & Norden, B. (1993) Binding of 4′,6-diamidino-2-phenylindole (DAPI) to AT regions of DNA: evidence for an allosteric conformational change. Biochemistry 32, 2987-2998.
27. Larsson, A., Akerman, B. & Jonsson, M. (1996) DAPI staining of DNA: effect of change in charge, flexibility, and contour length on orientational dynamics and mobility of the DNA during agarose gel electrophoresis. J. Phys. Chem. 100, 3252-3263.
28. Mitas, M. (1997) Trinucleotide repeats associated with human disease. Nucleic Acids Res. 25, 2243-2254.
29. Gacy, A.M., Goellner, G., Juranic, N., Macura, S. & McMurray, C.T. (1995) Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell 81, 533-540.
30. 15. Nucleic Acids Res. 23, 1050-1059.
31. Chen, X., Mariappan, S.V.S., Catasti, P., Ratliff, R., Moyzis, R.K., Laayoun, A., Smith, S.S., Bradbury, E.M. & Gupta, G. (1995) Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications. Proc. Natl Acad. Sci. USA 92, 5199-5203.
32. Samadashwily, G.M., Raca, G. & Mirkin, S.M. (1997) Trinucleotide repeats affect DNA replication in vivo. Nat. Genet. 17, 298-304.
33. Kang, S., Ohshima, K., Shimizu, M., Amirhaeri, S. & Wells, R.D. (1995) Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes. J. Biol. Chem. 270, 27014-27021.
34. Aboul-ela, F., Koh, D., Tinoco, I. & Martin, F.H. (1985) Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A,C,G,T). Nucleic Acids Res. 13, 4811-4824.
35. Werntges, H., Steger, G., Riesner, D. & Fritz, H.J. (1986) Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res. 14, 3773-3790.
36. Ikuta, S., Takagi, K., Wallace, R.B. & Itakura, K. (1987) Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base-pairs. Nucleic Acids Res. 15, 797-811.
37. Parsons, M.A., Sinden, R.R. & Izban, M.G. (1998) Transcriptional properties of RNA polymerase II within triplet repeat-containing DNA from the human myotonic dystrophy and fragile X loci. J. Biol. Chem. 273, 26998-27008.
38. Moore, H., Greenwell, P.W., Liu, C.-P., Arnheim, N. & Petes, T.D. (1999) Triplet repeats form secondary structures that escape DNA repair in yeast. Proc. Natl Acad. Sci. USA 96, 1504-1509.