In vitro expansion of DNA triplet repeats with bulge binders and different DNA polymerases

FEBS Journal

Volumn 275, Issue 18, 2008, Pages 4510-4521

  Ouyang, Di ^a   Yi, Long ^a   Liu, Liangliang ^a   Mu, Hong Tao ^a   Xi, Zhen ^a  

^a NANKAI UNIVERSITY   (China)

Author keywords

Bulge binder; DNA polymerase; DNA slippage; Drug DNA interaction; Repeat sequences

Indexed keywords

DNA POLYMERASE; ENEDIYNE; REPETITIVE DNA; ZINOSTATIN CHROMOPHORE;

ARTICLE; CHEMICAL STRUCTURE; CIRCULAR DICHROISM; DNA STRUCTURE; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS; THERMOSTABILITY; ULTRAVIOLET RADIATION;

DNA; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; GLUCOSAMINE; KINETICS; NUCLEIC ACID CONFORMATION; SPIRO COMPOUNDS; TEMPLATES, GENETIC; TRINUCLEOTIDE REPEAT EXPANSION;

EID: 50849087361     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2008.06593.x     Document Type: Article

References (46)

1. Toth G, Gaspari Z Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10, 967 981.
2. Nag DK, Suri M Stenson EK (2004) Both CAG repeats and inverted DNA repeats stimulate spontaneous unequal sister-chromatid exchange in Saccharomyces cerevisiae. Nucleic Acids Res 32, 5677 5684.
3. Wells RD, Dere R, Hebert ML, Napierala M Son LS (2005) Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Res 33, 3785 3798.
4. Wells RD Warren ST (eds 1998) Genetic Instabilities and Hereditary Neurological Diseases. Academic Press, San Diego, CA.
5. Cummings CJ Zoghbi HY (2000) Trinucleotide repeats: mechanisms and pathophysiology. Annu Rev Genomics Hum Genet 1, 281 328.
6. Ashizawa T Zoghbi HY (1997) Diseases with trinucleotide repeat expansion. In Current Neurology, Vol. 17 (Appel SH, ed.), pp. 79 135. IOS Press, Amsterdam.
7. Kunkel TA (1993) Slippery DNA and diseases. Nature 365, 207 208.
8. Kashi Y, King D Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13, 74 78.
9. Napierala M, Bacolla A Wells RD (2005) Increased negative superhelical density in vivo enhances the genetic instability of triplet repeat sequences. J Biol Chem 280, 37366 37376.
10. Parniewski P, Jaworski A, Wells RD Bowater RP (2000) Length of CTG·CAG repeats determines the influence of mismatch repair on genetic instability. J Mol Biol 299, 865 874.
11. Wells RD (1996) Molecular basis of genetic instability of triplet repeats. J Biol Chem 271, 2875 2878.
12. Perutz MF (1996) Glutamine repeats and inherited neurodegenerative disease: molecular aspects. Curr Opin Struct Biol 6, 848 858.
13. Harvey SC (1997) Slipped structures in DNA triplet repeat sequences: entropic contributions to genetic instabilities. Biochemistry 36, 3047 3049.
14. Kappen LS, Lin Y, Jones GB Goldberg IH (2007) Probing DNA bulges with designed helical spirocyclic molecules. Biochemistry 46, 561 567.
15. Xi Z, Jones GB, Qabaja G, Wright J, Johnson FS Goldberg IH (1999) Synthesis and DNA binding of spirocyclic model compounds related to the neocarzinostatin chromophore. Org Lett 1, 1375 1377.
16. Xi Z, Hwang GS, Goldberg IH, Harris JL, Pennington WT, Fouad FS, Qabaja G, Wright JM Jones GB (2002) Targeting DNA bulged microenvironments with synthetic agents: lessons from a natural product. Chem Biol 9, 925 931.
17. Zhang N, Lin Y, Xiao Z, Jones GB Goldberg IH (2007) Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA. Biochemistry 46, 4793 4803.
18. Lin Y, Jones GB, Hwang GS, Kappen L Goldberg IH (2005) Convenient synthesis of ncs-chromophore metabolite isosteres: binding agents for bulged DNA microenvironments. Org Lett 7, 71 74.
19. Trotta E, Grosso ND, Erba M, Melino S, Cicero D Paci M (2003) Interaction of DAPI with individual strands of trinucleotide repeats. Effects on replication in vitro of the AATATT triplet. Eur J Biochem 270, 4755 4761.
20. Xi Z, Ouyang D Mu HT (2006) Stimulation on DNA triplet repeat strand slippage synthesis by the designed spirocycles. Bioorg Med Chem Lett 16, 1180 1184.
21. Jones GB, Lin YQ, Xiao ZW, Kappen L Goldberg IH (2007) Molecular probes of DNA bulges: functional assay and spectroscopic analysis. Bioorg Med Chem 15, 784 790.
22. Xiao Z, Kappen LS Goldberg IH (2006) Development of new simple molecular probes of DNA bulged structures. Bioorg Med Chem Lett 16, 2895 2899.
23. Hwang GS, Jones GB Goldberg IH (2004) Stereochemical control of small molecule binding to bulged DNA: comparison of structures of spirocyclic enantiomer-bulged DNA complexes. Biochemistry 43, 641 650.
24. Kappen LS Goldberg IH (1993) DNA conformation-induced activation of an enediyne for site-specific cleavage. Science 261, 1319 1321.
25. Yang CF, Stassinopoulos A Goldberg IH (1995) Specific binding of the biradical analog of neocarzinostatin chromophore to bulged DNA: implications for thiol-independent cleavage. Biochemistry 34, 2267 2275.
26. Gao X, Stassinopolous A, Ji J, Kwon Y, Bare S Goldberg IH (2002) Induced formation of a DNA bulge structure by a molecular wedge ligand-postactivated neocarzinostatin chromophore. Biochemistry 41, 5131 5143.
27. Xi Z Goldberg IH (1999) Comprehensive Natural Products Chemistry, Vol. 7 (Barton DHR Nakanishi K, eds), pp. 553 592. Elsevier Science, Oxford.
28. Kappen L, Xi Z, Jones GB Goldberg IH (2003) Stimulation of DNA strand slippage synthesis by a bulge binding synthetic agent. Biochemistry 42, 2166 2173.
29. Liu L, Yi L, Yang X, Yu Z, Xi Z Wen X (2008) Synthesis and spectroscopic characterization of binaphthol aminosugars for stimulation of DNA strand slippage synthesis. Tetrahedron, 64, 5885 5890.
30. Kornberg A (1980) DNA Replication (Bartlett AC, ed.), pp. 415 440. W. H. Freeman, San Francisco, CA.
31. Kang S, Ohshima K, Shimizu M, Amirhaeri S Wells RD (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.
32. Tuntiwechapikul W Salazar M (2002) Mechanism of in vitro expansion of long DNA repeats: effect of temperature, repeat length, repeat sequence, and DNA polymerase. Biochemistry 41, 854 860.
33. Fasman GD (1996) Circular Dichroism and the Conformational Analysis of Biomolecules. Plenum Press, New York, NY.
34. Johnson WC (2000) Circular Dichroism: Principles and Applications (Berova N, Nakanishi K Woody RW, eds p. 738. Wiley, New York, NY.
35. Štefl R, Trantírek L, Vorlíčková M, Koča J, Sklenář V Kypr J (2001) A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC). J Mol Biol 307, 513 524.
36. Schlotterer C Tautz D (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Res 20, 211 215.
37. 2+ concentration and mismatches on triplet-repeat expansion during DNA replication in vitro. Nucleic Acids Res 27, 2235 2240.
38. Pearson CE Sinden RR (1998) Slipped strand DNA, dynamic mutations, and human disease. In Genetic Instabilities and Hereditary Neurological Diseases (Wells RD Warren ST, eds), pp. 585 626. Academic Press, New York, NY.
39. Ohshima K, Kang S, Larson JE Wells RD (1996) TTA·TAA triplet repeats in plasmids form a non-H bonded structure. J Biol Chem 271, 16784 16791.
40. Trotta E, Grosso ND, Erba M Paci M (2000) The ATT stand of AAT·ATT trinucleotide repeats adopts stable hairpin structures induced by minor groove binding ligands. Biochemistry 39, 6799 6808.
41. Tam M, Montgomery ES, Kekis M, Stollar DB, Price GB Pearson CE (2003) Slipped (CTG)·(CAG) repeats of the myotonic dystrophy locus: surface probing with anti-DNA antibodies. J Mol Biol 332, 585 600.
42. Pearson CE, Tam M, Wang YH, Montgomery SE, Dar AC, Cleary JD Nichol K (2002) Slipped-strand DNAs formed by long (CAG)·(CTG) repeats: slipped-out repeats and slip-out junctions. Nucleic Acids Res 30, 4534 4547.
43. Kang S, Jaworski A, Ohshima K Wells RD (1995) Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in E. coli. Nat Genet 10, 213 218.
44. Taylor JP, Hardy J Fischback KH (2002) Toxic proteins in neurodegenerative disease. Science 296, 1991 1995.
45. Brown LY Brown SA (2004) Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet 20, 51 58.
46. Maniatis T, Fritsch EF Sambrook J (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.