Slipped strand DNA structures

Frontiers in Bioscience

Volumn 12, Issue 13, 2007, Pages 4788-4799

  Sinden, Richard R ^a   Pytlos Sinden, Malgorzata J ^a   Potaman, Vladimir N ^b  

^a Florida Institute of Technology   (United States)

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

Author keywords

Alternative DNA conformations; DNA repeats; DNA structure; Neurodegenerative diseases; Review; Slipped strand DNA; Triplet repeats; Unstable DNA repeats

Indexed keywords

DNA; DNA DIRECTED DNA POLYMERASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; REPETITIVE DNA;

BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; DNA REPAIR; DNA REPLICATION; GENOMIC INSTABILITY; NUCLEOTIDE REPEAT; PHYSIOLOGY; REVIEW;

DNA; DNA REPAIR; DNA REPAIR ENZYMES; DNA REPEAT EXPANSION; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; GENOMIC INSTABILITY; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 34547683666     PISSN: 27686701     EISSN: 27686698     Source Type: Journal    
DOI: 10.2741/2427     Document Type: Review

References (138)

1. L. W. Coggins, M. O'Prey, S. Akhter: Intrahelical pseudoknots and interhelical associations mediated by mispaired human minisatellite DNA sequences in vitro. Gene. 121, 279-285 (1992)
2. L. W. Coggins, M. O'Prey: DNA tertiary structures formed in vitro by misaligned hybridization of multiple tandem repeat sequences. Nucleic Acids Res. 17, 7417-7426 (1989) (Pubitemid 19242325)
3. M. Kato, K. Matsunaga, N. Shimizu: A novel unusual DNA structure formed in an inverted repeat sequence. Biochem Biophys Res Commun 246, 532-534 (1998) (Pubitemid 28412636)
4. M. Kato, S. Hokabe, S. Itakura, S. Minoshima, Y. L. Lyubchenko, T. D. Gurkov, H. Okawara, K. Nagayama, N. Shimizu: Interarm interaction of DNA cruciform forming at a short inverted repeat sequence. Biophys. J. 85, 402-408 (2003) (Pubitemid 36753643)
5. T. Ohta, S. Nettikadan, F. Tokumasu, H. Ideno, Y. Abe, M. Kuroda, H. Hayashi, K. Takeyasu: Atomic force microscopy proposes a novel model for stem-loop structure that binds a heat shock protein in the Staphylococcus aureus HSP70 operon. Biochem. Biophys. Res. Commun. 226, 730-734 (1996) (Pubitemid 26348540)
6. Y. L. Lyubchenko, L. S. Shlyakhtenko, M. Binus, C. Gaillard, F. Strauss: Visualization of hemiknot DNA structure with an atomic force microscope. Nucleic Acids Res. 30, 4902-4909 (2002) (Pubitemid 35414650)
7. C. E. Pearson, R. R. Sinden: Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci. Biochemistry 35, 5041-5053 (1996) (Pubitemid 26126721)
8. R. R. Sinden, V. N. Potaman, E. A. Oussatcheva, C. E. Pearson, Y. L. Lyubchenko, L. S. Shlyakhtenko: Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J. Biosci. 27, 53-65 (2002) (Pubitemid 34285619)
9. C. E. Pearson, R. R. Sinden. Slipped strand DNA, dynamic mutations, and human disease, in: R. D. Wells and S. T. Warren (Eds.), Genetic Instabilities and Hereditary Neurological Disorders, Academic Press, San Diego, pp. 585-621 (1998)
10. C. E. Pearson, M. Tam, Y. H. Wang, S. E. Montgomery, A. C. Dar, J. D. Cleary, K. Nichol: Slipped-strand DNAs formed by long (CAG) • (CTG) repeats: slipped-out repeats and slip-out junctions. Nucleic Acids Res. 30, 4534-4547 (2002) (Pubitemid 35277264)
11. M. Tam, M. S. Erin, M. Kekis, S. B. David, G. B. Price, C. E. Pearson: Slipped (CTG) • (CAG) repeats of the myotonic dystrophy locus: surface probing with anti-DNA antibodies. J. Mol. Biol. 332, 585-600 (2003) (Pubitemid 37075983)
12. P. D. Chastain, E. E. Eichler, S. Kang, D. L. Nelson, S. D. Levene, R. R. Sinden: Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry 34, 16125-16131 (1995)
13. P. D. Chastain, R. R. Sinden: CTG repeats associated with human genetic disease are inherently flexible. J Mol Biol 275, 405-411 (1998) (Pubitemid 28055060)
14. A. Bacolla, R. Gellibolian, M. Shimizu, S. Amirhaeri, S. Kang, K. Ohshima, J. E. Larson, S. C. Harvey, B. D. Stollar, R. D. Wells: Flexible DNA - genetically unstable CTG•CAG and CGG•CCG from human hereditary neuromuscular disease genes. J. Biol. Chem. 272, 16783-16792 (1997) (Pubitemid 27289774)
15. C. E. Pearson, E. E. Eichler, D. Lorenzetti, S. F. Kramer, H. Y. Zoghbi, D. L. Nelson, R. R. Sinden: Interruptions in the triplet repeats of SCA1 and FRAXA reduce the propensity and complexity of slipped strand DNA (S-DNA) formation. Biochemistry 37, 2701-2708 (1998) (Pubitemid 28119348)
16. C. E. Pearson, Y. H. Wang, J. D. Griffith, R. R. Sinden: Structural analysis of slipped-strand DNA (S-DNA) formed in (CTG) n. (CAG) n repeats from the myotonic dystrophy locus. Nucleic Acids Res. 26, 816-823 (1998) (Pubitemid 28291282)
17. C. E. Pearson, R. R. Sinden: Trinucleotide repeat DNA structures: Dynamic mutations from dynamic DNA. Curr. Opin. Struct. Biol. 8, 321-330 (1998) (Pubitemid 28321359)
18. M. Mitas: Trinucleotide repeats associated with human disease. Nucleic Acids Res. 25, 2245-2253 (1997) (Pubitemid 27303679)
19. J. M. Darlow, D. F. Leach: Evidence for two preferred hairpin folding patterns in d (CGG) •. d (CCG) repeat tracts in vivo. J. Mol. Biol. 275, 17-23 (1998) (Pubitemid 28022383)
20. J. M. Darlow, D. R. F. Leach: Secondary structures in d (CGG) and d (CCG) repeat tracts. J. Mol. Biol. 275, 3-16 (1998) (Pubitemid 28022382)
21. J. Petruska, N. Arnheim, M. F. Goodman: Stability of intrastrand hairpin structures formed by the CAG/CTG class of DNA triplet repeats associated with neurological diseases. Nucleic Acids Res. 24, 1992-1998 (1996) (Pubitemid 26174538)
22. A. M. Gacy, C. T. McMurray: Influence of hairpins on template reannealing at trinucleotide repeat duplexes: a model for slipped DNA. Biochemistry 37, 9426-9434 (1998) (Pubitemid 28307698)
23. X. Gao, X. Huang, G. K. Smith, M. Zheng, H. Liu: 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, 8883-8884 (1995)
24. B. L. Heidenfelder, M. D. Topal: Effects of sequence on repeat expansion during DNA replication. Nucleic Acids Res. 31, 7159-7164 (2003) (Pubitemid 38008447)
25. R. Dere, M. Napierala, L. P. Ranum, R. D. Wells: Hairpin structure-forming propensity of the (CCTG. CAGG) tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2. J Biol. Chem. 279, 41715-41726 (2004) (Pubitemid 39313617)
26. I. S. Suen, J. N. Rhodes, M. Christy, B. McEwen, D. M. Gray, M. Mitas: Structural properties of Friedreich's ataxia d (GAA) repeats. Biochim. Biophys. Acta 1444, 14-24 (1999) (Pubitemid 29092847)
27. B. L. Heidenfelder, A. M. Makhov, M. D. Topal: Hairpin formation in Friedreich's ataxia triplet repeat expansion. J. Biol. Chem. 278, 2425-2431 (2003) (Pubitemid 36801317)
28. V. N. Potaman, E. A. Oussatcheva, Y. L. Lyubchenko, L. S. Shlyakhtenko, S. I. Bidichandani, T. Ashizawa, R. R. Sinden: Length-dependent structure formation in Friedreich ataxia (GAA) n• (TTC) n repeats at neutral pH. Nucleic Acids Res. 32, 1224-1231 (2004) (Pubitemid 38864678)
29. A. M. Albertini, M. Hofer, M. P. Calos, J. H. Miller: On the formation of spontaneous mutations: the importance of short sequence homologies in generation of large deletion. Cell 29, 319-328 (1982) (Pubitemid 12024829)
30. J. W. Drake, B. W. Glickman, L. S. Ripley: Updating the theory of mutation. Am. Scientist 71, 621-630 (1983)
31. L. S. Ripley: Frameshift mutation: Determinants of specificity. Annu. Rev. Genet. 24, 189-213 (1990) (Pubitemid 120011546)
32. R. R. Sinden, G. Zheng, R. G. Brankamp, K. N. Allen: On the deletion of inverted repeated DNA in Escherichia coli: Effects of length, thermal stability, and cruciform formation in vivo. Genetics 129, 991-1005 (1991)
33. T. Q. Trinh, R. R. Sinden: Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352, 544-547 (1991) (Pubitemid 21912381)
34. T. Q. Trinh, R. R. Sinden: The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli. Genetics 134, 409-422 (1993) (Pubitemid 23156938)
35. U. Dasgupta, K. Weston-Hafer, D. E. Berg: Local DNA sequence control of deletion formation in Escherichia coli plasmid pBR322. Genetics 115, 41-49 (1987)
36. K. Weston-Hafer, D. E. Berg: Palindromy and the location of deletion endpoints in Escherichia coli. Genetics 121, 651-658 (1989) (Pubitemid 19105483)
37. W. L. Williams, U. R. Muller: Effects of palindrome size and sequence on genetic stability in the bacteriophage MX174 genome. J. Mol. Biol. 196, 743-755 (1987)
38. K. Bebenek, T. A. Kunkel: Streisinger revisited: DNA synthesis errors mediated by substrate misalignments. Cold Spring Harb. Symp. Quant. Biol 65, 81-91 (2000) (Pubitemid 32611930)
39. T. A. Kunkel, A. Soni: Mutagenesis by transient misalignment. J. Biol Chem. 263, 14784-14789 (1988)
40. T. A. Kunkel: Misalignment-mediated DNA synthesis errors. Biochemistry 29, 8003-8011 (1990) (Pubitemid 20283280)
41. W. A. Rosche, L. S. Ripley, R. R. Sinden: Primer-template misalignments during leading strand DNA synthesis account for the most frequent spontaneous mutations in a quasipalindromic region in Escherichia coli. J. Mol. Biol. 284, 633-646 (1998) (Pubitemid 28550011)
42. C. Papanicolaou, L. S. Ripley: An in vitro approach to identifying specificity determinants of mutagenesis mediated by DNA misalignments. J. Mol Biol 221, 805-821 (1991) (Pubitemid 121003421)
43. L. S. Ripley: Frameshift mutation: Determinants of specificity. Annu. Rev. Genet. 24, 189-213 (1990) (Pubitemid 120011546)
44. V. van Noort, P. Worning, D. W. Ussery, W. A. Rosche, R. R. Sinden: Strand misalignments lead to quasipalindrome correction. Trends Genet. 19, 365-369 (2003) (Pubitemid 36794536)
45. R. R. Sinden, V. I. Hashem, W. A. Rosche: DNA-directed mutations: Leading and lagging strand specificity. Ann N Y Acad Sci 870, 173-189 (1999) (Pubitemid 29349342)
46. G. Streisinger, Y. Okada, J. Emrich, J. Newton, A. Tsugita, E. Terzaghi, M. Inouye: Frameshift mutations and the genetic code. Cold Spring Harb. Symp. Quant. Biol. 31, 77-84 (1966)
47. L. C. Kroutil, T. A. Kunkel: Deletion errors generated during replication of CAG repeats. Nucleic Acids Res. 27, 3481-3486 (1999) (Pubitemid 29414674)
48. M. Wierdl, M. Dominska, T. D. Petes: Microsatellite instability in yeast - dependence on the length of the microsatellite. Genetics 146, 769-779 (1997) (Pubitemid 27290966)
49. V. I. Hashem, W. A. Rosche, R. R. Sinden: Genetic assays for measuring rates of (CAG) • (CTG) repeat instability in Escherichia coli. Mutat. Res. 502, 25-37 (2002) (Pubitemid 34454995)
50. L. S. Ripley, A. Clark, J. G. deBoer: Spectrum of spontaneous frameshift mutations. Sequences of bacteriophage T4 rII gene frameshifts. J. Mol. Biol. 191, 601-613 (1986) (Pubitemid 17185962)
51. R. R. Sinden, M. J. Pytlos, V. N. Potaman. Mechanisms of DNA Repeat Expansion, in: M. Fry and K. Usdin (Eds.), Human Nucleotide Expansion Disorders, Springer, Berlin, pp. 3-53 (2006)
52. C. J. Cummings, H. Y. Zoghbi: Fourteen and counting: unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 9, 909-916 (2000) (Pubitemid 30216102)
53. P. Parniewski, P. Staczek: Molecular mechanisms of TRS instability. Adv. Exp. Med. Biol. 516., 1-25 (2002) (Pubitemid 36337734)
54. B. A. Lenzmeier, C. H. Freudenreich: Trinucleotide repeat instability: a hairpin curve at the crossroads of replication, recombination, and repair. Cytogenet. Genome Res. 100, 7-24 (2003) (Pubitemid 37467788)
55. J. D. Cleary, C. E. Pearson: The contribution of CIS-elements to disease-associated repeat instability: clinical and experimental evidence. Cytogenet. Genome Res. 100, 25-55 (2003) (Pubitemid 37467789)
56. C. E. Pearson: Slipping while sleeping? Trinucleotide repeat expansions in germ cells. Trends Mol. Med. 9, 490-495 (2003) (Pubitemid 37464286)
57. L. Y. Brown, S. A. Brown: Alanine tracts: the expanding story of human illness and trinucleotide repeats. Trends Genet. 20, 51-58 (2004) (Pubitemid 38032820)
58. L. P. Ranum, J. W. Day: Myotonic dystrophy: RNA pathogenesis comes into focus. Am. J. Hum. Genet. 74, 793-804 (2004) (Pubitemid 38568955)
59. J. D. Cleary, C. E. Pearson: Replication fork dynamics and dynamic mutations: the fork-shift model of repeat instability. Trends Genet. 21, 272-280 (2005) (Pubitemid 40558932)
60. S. M. Mirkin: Molecular Models for Repeat Expansion. Chemtracts Biochem. Mol. Biol. 17, 639-662 (2004)
61. L.-J. C. Wong, T. Ashizawa, D. G. Monckton, C. T. Caskey, C. S. Richards: Somatic heterogeneity of the CTG repeat in myotonic dystrophy is age and size dependent. Am. J. Hum. Genet. 56, 114-122 (1995)
62. L. Martorell, D. G. Monckton, J. Gamez, K. J. Johnson, I. Gich, A. L. de Munain, M. Baiget: Progression of somatic CTG repeat length heterogeneity in the blood cells of myotonic dystrophy patients. Hum. Mol Genet. 7, 307-312 (1998) (Pubitemid 28048547)
63. I. V. Kovtun, C. T. McMurray: Trinucleotide expansion in haploid germ cells by gap repair. Nat. Genet. 27, 407-411 (2001) (Pubitemid 32268421)
64. C. T. McMurray, I. V. Kortun: Repair in haploid male germ cells occurs late in differentiation as chromatin is condensing. Chromosoma 111, 505-508 (2003) (Pubitemid 36705633)
65. M. Gomes-Pereira, M. T. Fortune, L. Ingram, J. P. McAbney, D. G. Monckton: Pms2 is a genetic enhancer of trinucleotide CAG•CTG repeat somatic mosaicism: implications for the mechanism of triplet repeat expansion. Hum Mol. Genet 13, 1815-1825 (2004) (Pubitemid 39173450)
66. V. N. Potaman, M. J. Pytlos, V. I. Hashem, J. J. Bissler, M. Leffak, R. R. Sinden. DNA structures and genetic instabilities associated with SCA10 (ATTCT) n• (AGAAT) n repeats suggest a DNA amplification model for repeat expansion, in: R. D. Wells and T. Ashizawa (Eds.), Genetic Instabilities and Neurological Diseases, Academic Press, pp. 447-460 (2006)
67. L. M. Pollard, R. Sharma, M. Gomez, S. Shah, M. B. Delatycki, L. Pianese, A. Monticelli, B. J. Keats, S. I. Bidichandani: Replication-mediated instability of the GAA triplet repeat mutation in Friedreich ataxia. Nucleic Acids Res. 32, 5962-5971 (2004) (Pubitemid 39619178)
68. R. Sharma, S. Bhatti, M. Gomez, R. M. Clark, C. Murray, T. Ashizawa, S. I. Bidichandani: The GAA triplet-repeat sequence in Friedreich ataxia shows a high level of somatic instability in vivo, with a significant predilection for large contractions. Hum. Mol Genet. 11, 2175-2187 (2002) (Pubitemid 34994006)
69. S. I. Bidichandani, S. M. Purandare, E. E. Taylor, G. Gumin, H. Machkhas, Y. Harati, R. A. Gibbs, T. Ashizawa, P. I. Patel: Somatic sequence variation at the Friedreich ataxia locus includes complete contraction of the expanded GAA triplet repeat, significant length variation in serially passaged lymphoblasts and enhanced mutagenesis in the flanking sequence. Hum Mol Genet 8, 2425-2436 (1999)
70. T. Matsuura, P. Fang, X. Lin, M. Khajavi, K. Tsuji, A. Rasmussen, R. P. Grewal, M. Achari, M. E. Alonso, S. M. Pulst, H. Y. Zoghbi, D. L. Nelson, B. B. Roa, T. Ashizawa: Somatic and germline instability of the ATTCT repeat in spinocerebellar ataxia type 10. Am. J. Hum. Genet. 74, 1216-1224 (2004) (Pubitemid 38669320)
71. T. Matsuura, T. Yamagata, D. L. Burgess, A. Rasmussen, R. P. Grewal, K. Watase, M. Khajavi, A. E. McCall, C. F. Davis, L. Zu, M. Achari, S. M. Pulst, E. Alonso, J. L. Noebels, D. L. Nelson, H. Y. Zoghbi, T. Ashizawa: Large expansion of the ATTCT pentanucleotide repeat in spinocerebellar ataxia type 10. Nat. Genet. 26, 191-194 (2000)
72. R. R. Sinden. DNA Structure and Function, Academic Press, San Diego, (1994).
73. D. N. Cooper, M. Krawczak. Human Gene Mutation, Bios Scientific Publishers, Oxford, U. K., (1993).
74. R. R. Sinden, R. D. Wells: DNA structure, mutations, and human genetic disease. Curr Opin Biotechnol 3, 612-622 (1992)
75. J. J. Bissler: DNA inverted repeats and human disease. Front Biosci 3., d408-d418 (1998)
76. L. S. Kaguni, D. A. Clayton: Template-directed pausing in in vitro DNA synthesis by DNA polymerase a from Drosophila melanogaster embryos. Proc. Natl. Acad. Sci. USA 79, 983-987 (1982) (Pubitemid 12114048)
77. D. T. Weaver, M. L. DePamphilis: Specific sequences in native DNA that arrest synthesis by DNA polymerase alpha. J. Biol Chem. 257, 2075-2086 (1982)
78. K. J. Hacker, B. M. Alberts: The rapid dissociation of the T4 DNA polymerase holoenzyme when stopped by a DNA hairpin helix. A model for polymerase release following the termination of each Okazaki fragment. J. Biol. Chem. 269, 24221-24228 (1994)
79. Z. Suo, K. A. Johnson: DNA secondary structure effects on DNA synthesis catalyzed by HIV-1 reverse transcriptase. J. Biol Chem. 273, 27259-27267 (1998) (Pubitemid 28500438)
80. D. A. Gordenin, K. S. Lobachev, N. P. Degtyareva, A. L. Malkova, E. Perkins, M. A. Resnick: Inverted DNA repeats: A source of eukaryotic genomic instability. Mol. Cell. Biol. 13, 5315-5322 (1993) (Pubitemid 23260635)
81. W. A. Rosche, T. Q. Trinh, R. R. Sinden: Leading strand specific spontaneous mutation corrects a quasipalindrome by an intermolecular strand switch mechanism. J. Mol. Biol. 269, 176-187 (1997) (Pubitemid 27248283)
82. M. Viswanathan, J. J. Lacirignola, R. L. Hurley, S. T. Lovett: A novel mutational hotspot in a natural quasipalindrome in Escherichia coli. J. Mol. Biol. 302, 553-564 (2000)
83. K. Yoshiyama, H. Maki: Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli: transcription-dependent mutagenesis involving templateswitching mechanisms. J Mol. Biol. 327, 7-18 (2003) (Pubitemid 36293299)
84. A. S. Kamath-Loeb, L. A. Loeb, E. Johansson, P. M. Burgers, M. Fry: Interactions between the Werner syndrome helicase and DNA polymerase delta specifically facilitate copying of tetraplex and hairpin structures of the d (CGG) n trinucleotide repeat sequence. J. Biol. Chem. 276, 16439-16446 (2001)
85. G. M. Samadashwily, G. Raca, S. M. Mirkin: Trinucleotide repeats affect DNA replication in vivo. Nature Genet. 17, 298-304 (1997) (Pubitemid 27475992)
86. M. M. Krasilnikova, S. M. Mirkin: Replication stalling at Friedreich's ataxia (GAA) n repeats in vivo. Mol. Cell. Biol. 24, 2286-2295 (2004) (Pubitemid 38325985)
87. R. Pelletier, M. M. Krasilnikova, G. M. Samadashwily, R. Lahue, S. M. Mirkin: Replication and expansion of trinucleotide repeats in yeast. Mol. Cell. Biol. 23, 1349-1357 (2003) (Pubitemid 36177043)
88. K. Usdin, K. J. Woodford: CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro. Nucleic Acids Res. 23, 4202-4209 (1995)
89. K. Usdin: NGG-triplet repeats form similar intrastrand structures: implications for the triplet expansion diseases. Nucleic Acids Res. 26, 4078-4085 (1998) (Pubitemid 28401364)
90. B. S. Rao, H. Manor, R. G. Martin: Pausing in simian virus 40 DNA replication by a sequence containing (dG-dA) 27• (dT-dC) 27. Nucleic Acids Res. 16, 8077-8094 (1988)
91. N. Baran, A. Lapidot, H. Manor: Formation of DNA triplexes accounts for arrests of DNA synthesis at d (TC) n and d (GA) n tracts. Proc. Natl. Acad. Sci. USA 88, 507-511 (1991) (Pubitemid 21915494)
92. A. S. Krasilnikov, I. G. Panyutin, G. M. Samadashwily, R. Cox, Y. S. Lazurkin, S. M. Mirkin: Mechanisms of triplexcaused polymerization arrest. Nucleic Acids Res. 25, 1339-1346 (1997)
93. V. N. Potaman, J. J. Bissler: Overcoming a barrier for DNA polymerization in triplex-forming sequences. Nucleic Acids Res. 27, e5 (1999)
94. A. Dayn, G. M. Samadashwily, S. M. Mirkin: Intramolecular DNA triplexes: Unusual sequence requirements and influence on DNA polymerization. Proc. Natl. Acad. Sci. USA 89, 11406-11410 (1992)
95. J. C. Hanvey, M. Shimizu, R. D. Wells: Intramolecular DNA triplexes in supercoiled plasmids. Proc. Natl. Acad. Sci. USA 85, 6292-6296 (1988)
96. K. Ohshima, S. Kang, J. E. Larson, R. D. Wells: TTA. TAA triplet repeats in plasmids form a non-H bonded structure. J. Biol. Chem. 271, 16784-16791 (1996) (Pubitemid 26239044)
97. S. I. Bidichandani, T. Ashizawa, P. I. Patel: 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, 111-121 (1998) (Pubitemid 28093840)
98. N. Sakamoto, P. D. Chastain, P. Parniewski, K. Ohshima, M. Pandolfo, J. D. Griffith, R. D. Wells: Sticky DNA: selfassociation properties of long GAA•TTC repeats in R•R•Y triplex structures from Friedreich's ataxia. Mol. Cell 3, 465-475 (1999) (Pubitemid 29292603)
99. C. Spiro, R. Pelletier, M. L. Rolfsmeier, M. J. Dixon, R. S. Lahue, G. Gupta, M. S. Park, X. Chen, S. V. Mariappan, C. T. McMurray: Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Mol Cell 4, 1079-1085 (1999) (Pubitemid 30054913)
100. A. A. Vetcher, M. Napierala, R. R. Iyer, P. D. Chastain, J. D. Griffith, R. D. Wells: Sticky DNA, a long GAA. GAA. TTC triplex that is formed intramolecularly, in the sequence of intron 1 of the frataxin gene. J Biol. Chem. 277, 39217-39227 (2002) (Pubitemid 35190891)
101. K. Ohshima, L. Montermini, R. D. Wells, M. Pandolfo: Inhibitory effects of expanded GAA•TTC triplet repeats from intron I of the Friedreich ataxia gene on transcription and replication in vivo. J. Biol. Chem. 273, 14588-14595 (1998) (Pubitemid 28319183)
102. E. Grabczyk, K. Usdin: The GAA•TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner. Nucleic Acids Res. 28, 2815-2822 (2000) (Pubitemid 30488540)
103. V. N. Potaman, J. J. Bissler, V. I. Hashem, E. A. Oussatcheva, L. Lu, L. S. Shlyakhtenko, Y. L. Lyubchenko, T. Matsuura, T. Ashizawa, M. Leffak, C. J. Benham, R. R. Sinden: Unpaired structures in SCA10 (ATTCT) n• (AGAAT) n repeats. J. Mol. Biol. 326, 1095-1111 (2003) (Pubitemid 36263385)
104. M. J. Hartenstine, M. F. Goodman, J. Petruska: Base stacking and even/odd behavior of hairpin loops in DNA triplet repeat slippage and expansion with DNA polymerase. J. Biol. Chem. 275, 18382-18390 (2000) (Pubitemid 30414795)
105. J. Petruska, M. J. Hartenstine, M. F. Goodman: Analysis of strand slippage in DNA polymerase expansions of CAG/CTG triplet repeats associated with neurodegenerative disease. J. Biol. Chem. 273, 5204-5210 (1998) (Pubitemid 28108683)
106. B. L. Ruggiero, M. D. Topal: Triplet repeat expansion generated by DNA slippage is suppressed by human flap endonuclease 1. J. Biol. Chem. 279, 23088-23097 (2004) (Pubitemid 38685613)
107. K. H. Schmidt, C. M. Abbott, D. R. Leach: Two opposing effects of mismatch repair on CTG repeat instability in Escherichia coli. Mol. Microbiol. 35, 463-471 (2000) (Pubitemid 30055243)
108. S. Schumacher, R. P. P. Fuchs, M. Bichara: Expansion of CTG repeats from human disease genes is dependent upon replication mechanisms in Escherichia coli - The effect of long patch mismatch repair revisited. J. Mol. Biol. 279, 1101-1110 (1998) (Pubitemid 28302387)
109. P. Parniewski, A. Jaworski, R. D. Wells, R. P. Bowater: Length of CTG•CAG repeats determines the influence of mismatch repair on genetic instability. J. Mol Biol. 299, 865-874 (2000)
110. S. Kang, A. Jaworski, K. Ohshima, R. D. Wells: Expansion and deletion of CTG triplet repeats from human disease genes are determined by the direction of replication in E. coli. Nat. Genet. 10, 213-218 (1995)
111. C. H. Freudenreich, J. B. Stavenhagen, V. A. Zakian: Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol. Cell. Biol. 17, 2090-2098 (1997) (Pubitemid 27133294)
112. C. H. Freudenreich, S. M. Kantrow, V. A. Zakian: Expansion and length-dependent fragility of CTG repeats in yeast. Science 279, 853-856 (1998) (Pubitemid 28106277)
113. J. J. Miret, L. Pessoabrandao, R. S. Lahue: Instability of CAG and CTG trinucleotide repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 3382-3387 (1997) (Pubitemid 27215053)
114. J. J. Miret, L. Pessoa-Brandao, R. S. Lahue: Orientationdependent and sequence-specific expansions of CTG/CAG trinucleotide repeats in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 95, 12438-12443 (1998) (Pubitemid 28483783)
115. D. J. Maurer, B. L. O'Callaghan, D. M. Livingston: Orientation dependence of trinucleotide CAG repeat instability in Saccharomyces cerevisiae. Mol. Cell. Biol. 16, 6617-6622 (1996) (Pubitemid 26389719)
116. G. B. Panigrahi, J. D. Cleary, C. E. Pearson: In vitro (CTG) • (CAG) expansions and deletions by human cell extracts. J. Biol. Chem. 277, 13926-13934 (2002) (Pubitemid 34967999)
117. J. D. Cleary, K. Nichol, Y. H. Wang, C. E. Pearson: Evidence of cis-acting factors in replication-mediated trinucleotide repeat instability in primate cells. Nat. Genet. 31, 37-46 (2002)
118. E. A. Oussatcheva, V. I. Hashem, Y. Zou, R. R. Sinden, V. N. Potaman: Involvement of the nucleotide excision repair protein UvrA in instability of (CAG) • (CTG) repeat sequences in E. coli. J. Biol. Chem. 276, 30878-30884 (2001)
119. P. Parniewski, A. Bacolla, A. Jaworski, R. D. Wells: Nucleotide excision repair affects the stability of long transcribed (CTG) • (CAG) tracts in an orientationdependent manner in Escherichia coli. Nucleic Acids Res. 27, 616-623 (1999) (Pubitemid 29210031)
120. C. E. Pearson, A. Ewel, S. Acharya, R. A. Fishel, R. R. Sinden: Human MSH2 binds to trinucleotide repeat DNA structures associated with neurodegenerative diseases. Hum. Mol. Genet. 6, 1117-1123 (1997) (Pubitemid 27308398)
121. B. A. Owen, Z. Yang, M. Lai, M. Gajek, J. D. Badger, J. J. Hayes, W. Edelmann, R. Kucherlapati, T. M. Wilson, C. T. McMurray: (CAG) (n)-hairpin DNA binds to Msh2-Msh3 and changes properties of mismatch recognition. Nat. Struct. Mol Biol., (2005)
122. V. C. Wheeler, L. A. Lebel, V. Vrbanac, A. Teed, H. te Riele, M. E. MacDonald: Mismatch repair gene Msh2 modifies the timing of early disease in Hdh (Q111) striatum. Hum. Mol Genet. 12, 273-281 (2003) (Pubitemid 36204424)
123. K. Manley, T. L. Shirley, L. Flaherty, A. Messer: Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice. Nat. Genet. 23, 471-473 (1999)
124. C. Savouret, C. Garcia-Cordier, J. Megret, H. te Riele, C. Junien, G. Gourdon: MSH2-dependent germinal CTG repeat expansions are produced continuously in spermatogonia from DM1 transgenic mice. Mol. Cell Biol. 24, 629-637 (2004) (Pubitemid 38057915)
125. C. Savouret, E. Brisson, J. Essers, R. Kanaar, A. Pastink, H. te Riele, C. Junien, G. Gourdon: CTG repeat instability and size variation timing in DNA repair-deficient mice. EMBO J. 22, 2264-2273 (2003) (Pubitemid 36565549)
126. W. J. van Den Broek, M. R. Nelen, D. G. Wansink, M. M. Coerwinkel, te Riele H., P. J. Groenen, B. Wieringa: Somatic expansion behaviour of the (CTG) (n) repeat in myotonic dystrophy knock-in mice is differentially affected by Msh3 and Msh6 mismatch-repair proteins. Hum. Mol Genet. 11, 191-198 (2002) (Pubitemid 34157011)
127. K. Watase, K. J. Venken, Y. Sun, H. T. Orr, H. Y. Zoghbi: Regional differences of somatic CAG repeat instability do not account for selective neuronal vulnerability in a knockin mouse model of SCA1. Hum. Mol Genet. 12, 2789-2795 (2003) (Pubitemid 37407115)
128. G. B. Panigrahi, R. Lau, S. E. Montgomery, M. R. Leonard, C. E. Pearson: Slipped (CTG) • (CAG) repeats can be correctly repaired, escape repair or undergo errorprone repair. Nat. Struct. Mol Biol 12, 654-662 (2005) (Pubitemid 43086270)
129. Y. Liu, H. I. Kao, R. A. Bambara: Flap endonuclease 1: a central component of DNA metabolism. Annu. Rev. Biochem. 73., 589-615 (2004) (Pubitemid 39050381)
130. S. Lee, M. S. Park: Human FEN-1 can process the 5'-flap DNA of CTG/CAG triplet repeat derived from human genetic diseases by length and sequence dependent manner. Exp. Mol. Med. 34, 313-317 (2002) (Pubitemid 35221669)
131. L. A. Henricksen, J. Veeraraghavan, D. R. Chafin, R. A. Bambara: DNA ligase I competes with FEN1 to expand repetitive DNA sequences in vitro. J. Biol Chem. 277, 22361-22369 (2002) (Pubitemid 34967204)
132. D. A. Gordenin, T. A. Kunkel, M. A. Resnick: Repeat expansion-all in a flap? Nature Genet. 16, 116-118 (1997)
133. J. Veeraraghavan, M. L. Rossi, R. A. Bambara: Analysis of DNA replication intermediates suggests mechanisms of repeat sequence expansion. J. Biol Chem. 278, 42854-42866 (2003) (Pubitemid 37345895)
134. S. H. Kim, M. J. Pytlos, R. R. Sinden: Replication restart: a pathway for (CTG). (CAG) repeat deletion in Escherichia coli. Mutat. Res. 595, 5-22 (2006) (Pubitemid 43277844)
135. V. I. Hashem, W. A. Rosche, R. R. Sinden: Genetic recombination destabilizes (CTG) n (CAG) n repeats in E. coli. Mutat. Res. 554, 95-109 (2004)
136. S. Kang, K. Ohshima, M. Shimizu, S. Amirhaeri, R. D. Wells: 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 (1995)
137. R. R. Sinden: Biological implications of the DNA structures associated with disease-causing triplet repeats. Am. J. Hum. Genet. 64, 346-353 (1999) (Pubitemid 129500516)
138. P. Cluzel, A. Lebrun, C. Heller, R. Lavery, J. L. Viovy, D. Chatenay, F. Caron: DNA: an extensible molecule. Science. 271, 792-794 (1996) (Pubitemid 26058929)