Trinucleotide repeat DNA structures: Dynamic mutations from dynamic DNA

Current Opinion in Structural Biology

Volumn 8, Issue 3, 1998, Pages 321-330

  Pearson, Christopher E ^a   Sinden, Richard R ^a  

^a TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; GENETIC STABILITY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW; TRINUCLEOTIDE REPEAT;

EID: 0032102835     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(98)80065-1     Document Type: Article

References (52)

1. Pearson CE, Sinden RR. Slipped strand DNA, dynamic mutations, and human disease. of special interest Wells RD, Warren ST. Genetic Instabilities and Hereditary Neurological Diseases. 1998;585-621 Academic Press, New York, This article contains a thorough review of triplet-repeat diseases, the DNA sequences involved, and expansion models. It is part of a comprehensive book describing the current state of this field.
2. Richards RI, Sutherland GR. Heritable unstable DNA sequences and human genetic disease. Cell. 70:1992;709-712.
3. Kohwi Y, Wang H, Kohwi-Shigematsu T. A single trinucleotide, 5'AGC3'/5'GCT3', of the triplet-repeat disease genes confers metal ion-induced non-B DNA structure. Nucleic Acids Res. 21:1993;5651-5655.
4. Chastain PD, Eichler EE, Kang S, Nelson DL, Levene SD, Sinden RR. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry. 34:1995;16125-16131.
5. 4 between A-tract curves abrogates overall DNA curvature to the same extent as interspersion of two consecutive T·T mismatches. This is a remarkable degree of flexibility for a very short repeat tract.
6. Levene SD, Zimm BH. Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science. 245:1989;396-399.
7. n repeats provides the bending and torsional moduli, persistence length, and helix repeat values. This paper presents the first demonstration of the flexibility of these triplet repeats.
8. Wang Y-H, Amirhaer S, Kang S, Wells RD, Griffith JD. Preferential nucleosome assembly at DNA triplet repeats from the myotonic dystrophy gene. Science. 265:1994;669-671.
9. Wang Y-H, Griffith JD. Expanded CTG triplet blocks from the myotonic dystrophy gene create the strongest known natural nucleosome positioning elements. Genomics. 25:1995;570-573.
10. Godde JS, Wolffe AP. Nucleosome assembly on CTG triplet repeats. J Biol Chem. 271:1996;15222-15229.
11. Wang Y-H, Gellibolian R, Shimizu M, Wells RD, Griffith J. Long CCG triplet repeat blocks exclude nucleosomes - a possible mechanism for the nature of fragile sites in chromosomes. J Mol Biol. 263:1996;511-516.
12. Godde JS, Kass SU, Hirst MC, Wolffe AP. Nucleosome assembly on methylated CGG triplet repeats in the fragile X mental retardation gene 1 promoter. J Biol Chem. 271:1996;24325-24328.
13. Shrader TE, Crothers DM. Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol. 216:1990;69-84.
14. Wang Y-H, Griffith J. Methylation of expanded CCG triplet repeat DNA from fragile X syndrome patients enhances nucleosome exclusion. J Biol Chem. 271:1996;22937-22940.
15. n oligonucleotides in solution and their possible relevance to fragile X and related human genetic diseases. Nucleic Acids Res. 23:1995;1876-1881.
16. anti base pairs. Biochemistry. 34:1995;12803-12811.
17. 15. Nucleic Acids Res. 23:1995;1050-1059.
18. 15 form hairpins. Nucleic Acids Res. 23:1995;4055-4057.
19. 15 adopts a hairpin conformation. Nucleic Acids Res. 23:1995;2706-2714.
20. Chen X, Mariappan SVS, Catasti P, Ratliff R, Moyzis RK, Laayoun A, Smith SS, Bradbury EM, Gupta G. Hairpins are formed by the single strands of the fragile X triplet repeats: Structure and biological implications. Proc Natl Acad Sci USA. 92:1995;5199-5203.
21. Zheng M, Huang X, Smith GK, Yang X, Gao X. Genetically unstable CXG repeats are structurally dynamic and have a high propensity for folding. An NMR and UV spectroscopic study. J Mol Biol. 264:1996;323-336.
22. n nucleotide repeats readily fold back to form unimolecular hairpin structures. J Biol Chem. 270:1995;28970-28977.
23. Petruska J, Arnheim N, Goodman MF. Stability of intrastrand hairpin structures formed by the CAG/CTG class of DNA triplet repeats associated with neurological diseases. Nucleic Acids Res. 24:1996;1992-1998.
24. n. Nucleic Acids Res. 24:1996;784-792.
25. Gao X, Huang X, Smith GK, Zheng M, Liu H. A new antiparallel duplex motif of DNA CCG repeats that is stabilized by extrahelical bases symetrically localized in the minor groove. J Am Chem Soc. 117:1995;8883-8884.
26. 15 intramolecular hairpin, which forms the 'e-motif'. The methods used in this paper are representative of those used in many similar analyses of this and other triplet repeats published during 1995 and 1996.
27. Mariappan SV, Garcia AE, Gupta G. Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy. Nucleic Acids Res. 24:1996;775-783.
28. Smith GK, Jie J, Fox GE, Gao X. DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes. Nucleic Acids Res. 23:1995;4303-4311.
29. Rabinovich D, Haran T, Eisenstein M, Shakked Z. Structures of the mismatched duplex d(GGGTGCCC) and one of its Watson-Crick analogues d(GGGCGCCC). J Mol Biol. 200:1988;151-161.
30. Gacy AM, Goellner G, Juranic N, Macura S, McMurray CT. Trinucleotide repeats that expand in human disease form hairpin structures in vitro. Cell. 81:1995;533-540.
31. Sinden RR. DNA Structure and Function. 1994;Academic Press, San Diego.
32. Ohshima K, Kang S, Larson JE, Wells RD. Cloning, characterization, and properties of seven triplet repeat DNA sequences. J Biol Chem. 271:1996;16773-16783.
33. Fry M, Loeb LA. The fragile X syndrome d(CGG)n nucleotide repeats form a stable tetrahelical structure. Proc Natl Acad Sci USA. 91:1994;4950-4954.
34. Usdin K, Woodford KJ. CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro. Nucleic Acids Res. 23:1995;4202-4209.
35. Kettani A, Kumar RA, Patel DJ. Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat. J Mol Biol. 254:1995;638-656.
36. Pearson CE, Sinden RR. Alternative DNA structures within the trinucleotide repeats of the myotonic dystrophy and fragile X locus. Biochemistry. 35:1996;5041-5053.
37. Pearson CE, Ewel A, Acharya S, Fishel RA, Sinden RR. Human MSH2 binds to trinucleotide repeat DNA structures associated with neurodegenerative diseases. of special interest Hum Mol Genet. 6:1997;1117-1123 This paper presents the purification, characterization, and mechanism of binding to the human mismatch repair protein (hMSH2) to SI-DNA and S-DNA. SI-DNA (slipped intermediate DNA) contains heteroduplex triplet repeat regions in which the lengths of the repeat tracts in the complementary strands are different. Sister heteroduplexes migrate to different positions on a polyacrylamide gel. hMSH2 preferentially binds to SI-DNAs containing looped out CAG residues compared with CTG strands.
38. Lilley DMJ, Clegg RM. The structure of branched DNA species. Q Rev Biophys. 26:1993;131-175.
39. 255 S-DNAs.
40. Pearson CE, Eichler EE, Lorenzetti D, Kramer SF, Zoghbi HY, Nelson DL, Sinden RR. Interruptions in the triplet repeats of SCA1 and FRAXA reduce the propensity and complexity of slipped strand DNA (S-DNA) formation. of outstanding interest Biochemistry. 37:1998;2701-2708 This paper demonstrates the fact that sequence interruptions within triplet repeat tracts reduce both the percentage and the complexity of the S-DNA formed following denaturation and renaturation. A model is proposed for this effect that correlates with the effect of repeat interruptions upon the stability of repeats in humans.
41. Kang S, Jaworski A, Ohshima K, Wells RD. Expansion and deletion of CTG triplet repeats from human disease genes are determined by the direction of replication in E. coli. Nat Genet. 10:1995;213-218.
42. Maurer DJ, O'Callaghan BL, Livingston DM. Orientation dependence of trinucleotide CAG repeat instability in Saccharomyces cerevisiae. Mol Cell Biol. 16:1996;6617-6622.
43. Freudenreich CH, Stavenhagen JB, Zakian VA. Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol Cell Biol. 17:1997;2090-2098.
44. Miret JJ, Pessoabrandao L, Lahue RS. Instability of CAG and CTG trinucleotide repeats in Saccharomyces cerevisiae. Mol Cell Biol. 17:1997;3382-3387.
45. Rosche WA, Jaworski A, Kang S, Kramer SF, Larson JE, Giedroc DP, Wells RD, Sinden RR. Single-stranded DNA binding protein enhances the stability of CTG triplet repeats in Escherichia coli. J Bacteriol. 178:1996;5042-5044.
46. n triplet repeats from human hereditary diseases. Proc Natl Acad Sci USA. 92:1995;11019-11023.
47. Schweitzer JK, Livingston DM. Destabilization of CAG trinucleotide repeat tracts by mismatch repair mutations in yeast. Hum Mol Genet. 6:1997;349-355.
48. Samadashwily GM, Raca G, Mirkin SM. Trinucleotide repeats affect DNA replication in vivo. of special interest Nat Genet. 17:1997;298-304 This paper reveals stalling of the replication fork within the repeat tract in Escherichia coli. Pausing is dependent upon repeat length and orientation with respect to the origin of plasmid replication. This paper is representative of many showing an in vivo biological effect of triplet repeats, and the authors suggest that the formation of an unusual DNA structure is responsible. To date, however, these papers have not presented biochemical data consistent with the formation of any alternative triplet repeat DNA structure in vivo. This is likely to be an important area for future research.
49. Ohshima K, Wells RD. Hairpin formation during DNA synthesis primer realignment in vitro in triplet repeat sequences from human hereditary disease genes. J Biol Chem. 272:1997;16798-16806.
50. Bidichandani SI, Ashizawa T, Patel PI. The GAA triplet-repeat expansion in Friedreich ataxia interferes with transcription and may be associated with an unusual DNA structure. Am J Hum Genet. 62:1998;111-121.
51. Gacy AM, Goellner GM, Spiro C, Chen X, Gupta G, Bradbury EM, Dyer RB, Mikesell MJ, Yao JZ, et al. GAA instability in Friedreichs-ataxia shares a common, DNA-directed and intra-allelic mechanism with other trinucleotide diseases. Mol Cell. 1:1998;583-593.
52. Darlow JM, Leach DRF. Evidence for two preferred hairpin folding patterns in d(CGG)·d(CCG) repeat tracts in vivo. J Mol Biol. 275:1998;17-23.