Structural studies of CNG repeats

Nucleic Acids Research

Volumn 42, Issue 13, 2014, Pages 8189-8199

  Kiliszek, Agnieszka ^a   Rypniewski, Wojciech ^a  

^a POLISH ACADEMY OF SCIENCES   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; CAG REPEAT; CCG REPEAT; CGG REPEAT; CNG REPEAT; CRYSTAL STRUCTURE; CTG REPEAT; CUG REPEAT; DEGENERATIVE DISEASE; DNA FLANKING REGION; DNA HAIRPIN; DNA STRUCTURE; FRAGILE X ASSOCIATED TREMOR ATAXIA SYNDROME; FRAGILE X SYNDROME; GENETIC ASSOCIATION; GENETIC DISORDER; HUMAN; HYDROGEN BOND; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR PATHOLOGY; MOLECULAR STABILITY; MYOTONIC DYSTROPHY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PATHOGENESIS; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA CONFORMATION; RNA STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; STATIC ELECTRICITY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; THERMODYNAMICS; TOXICITY TESTING; TRINUCLEOTIDE REPEAT; TRINUCLEOTIDE REPEAT EXPANSION DISORDER; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS; TRINUCLEOTIDE REPEAT EXPANSION; TRINUCLEOTIDE REPEATS;

EID: 84905577624     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku536     Document Type: Article

References (84)

1. Kozlowski, P., de Mezer, M., and Krzyzosiak, W.J. Kozlowski, P., de Mezer, M., and Krzyzosiak, W.J. (2010) Trinucleotide repeats in human genome and exome. Nucleic Acids Res., 38, 4027-4039.
2. Lin, Y. and Wilson, J.H. Lin, Y. and Wilson, J.H. (2011) Transcription-induced DNA toxicity at trinucleotide repeats: double bubble is trouble. Cell Cycle, 10, 611-618.
3. Mirkin, S.M. Mirkin, S.M. (2007) Expandable DNA repeats and human disease. Nature, 447, 932-940.
4. Nelson, D.L., Orr, H.T., and Warren, S.T. Nelson, D.L., Orr, H.T., and Warren, S.T. (2013) The unstable repeats-three evolving faces of neurological disease. Neuron, 77, 825-843.
5. Polak, U., McIvor, E., Dent, S.Y., Wells, R.D., and Napierala, M. Polak, U., McIvor, E., Dent, S.Y., Wells, R.D., and Napierala, M. (2013) Expanded complexity of unstable repeat diseases. Biofactors, 39, 164-175.
6. O'Rourke, J.R. and Swanson, M.S.O'Rourke, J.R. and Swanson, M.S. (2009) Mechanisms of RNA-mediated disease. J. Biol. Chem., 284, 7419-7423.
7. Todd, P.K. and Paulson, H.L. Todd, P.K. and Paulson, H.L. (2010) RNA-mediated neurodegeneration in repeat expansion disorders. Ann. Neurol., 67, 291-300.
8. Echeverria, G.V. and Cooper, T.A. Echeverria, G.V. and Cooper, T.A. (2012) RNA-binding proteins in microsatellite expansion disorders: mediators of RNA toxicity. Brain Res., 1462, 100-111.
9. Wojciechowska, M. and Krzyzosiak, W.J. Wojciechowska, M. and Krzyzosiak, W.J. (2011) Cellular toxicity of expanded RNA repeats: focus on RNA foci. Hum. Mol. Genet., 20, 3811-3821.
10. Almeida, B., Fernandes, S., Abreu, I.A., and Macedo-Ribeiro, S. Almeida, B., Fernandes, S., Abreu, I.A., and Macedo-Ribeiro, S. (2013) Trinucleotide repeats: a structural perspective. Front. Neurol., 4, 76.
11. Budworth, H. and McMurray, C.T. Budworth, H. and McMurray, C.T. (2013) Bidirectional transcription of trinucleotide repeats: roles for excision repair. DNA Repair (Amst.), 12, 672-684.
12. Marti, E. and Estivill, X. Marti, E. and Estivill, X. (2013) Small non-coding RNAs add complexity to the RNA pathogenic mechanisms in trinucleotide repeat expansion diseases. Front. Mol. Neurosci., 6, 45.
13. Sicot, G., Gourdon, G., and Gomes-Pereira, M. Sicot, G., Gourdon, G., and Gomes-Pereira, M. (2011) Myotonic dystrophy, when simple repeats reveal complex pathogenic entities: new findings and future challenges. Hum. Mol. Genet., 20, R116-R123.
14. Ladd, P.D., Smith, L.E., Rabaia, N.A., Moore, J.M., Georges, S.A., Hansen, R.S., Hagerman, R.J., Tassone, F., Tapscott, S.J., and Filippova, G.N. Ladd, P.D., Smith, L.E., Rabaia, N.A., Moore, J.M., Georges, S.A., Hansen, R.S., Hagerman, R.J., Tassone, F., Tapscott, S.J., and Filippova, G.N. (2007) An antisense transcript spanning the CGG repeat region of FMR1 is upregulated in premutation carriers but silenced in full mutation individuals. Hum. Mol. Genet., 16, 3174-3187.
15. Pearson, C.E. Pearson, C.E. (2011) Repeat associated non-ATG translation initiation: one DNA, two transcripts, seven reading frames, potentially nine toxic entities!. PLoS Genet., 7, e1002018.
16. Zu, T., Gibbens, B., Doty, N.S., Gomes-Pereira, M., Huguet, A., Stone, M.D., Margolis, J., Peterson, M., Markowski, T.W., and Ingram, M.A. et al. Zu, T., Gibbens, B., Doty, N.S., Gomes-Pereira, M., Huguet, A., Stone, M.D., Margolis, J., Peterson, M., Markowski, T.W., and Ingram, M.A. (2011) Non-ATG-initiated translation directed by microsatellite expansions. Proc. Natl. Acad. Sci. U.S.A., 108, 260-265.
17. Lawlor, K.T., O'Keefe, L.V., Samaraweera, S.E., van Eyk, C.L., McLeod, C.J., Maloney, C.A., Dang, T.H., Suter, C.M., and Richards, R.I. Lawlor, K.T., O'Keefe, L.V., Samaraweera, S.E., van Eyk, C.L., McLeod, C.J., Maloney, C.A., Dang, T.H., Suter, C.M., and Richards, R.I. (2011) Double-stranded RNA is pathogenic in Drosophila models of expanded repeat neurodegenerative diseases. Hum. Mol. Genet., 20, 3757-3768.
18. Yu, Z., Teng, X., and Bonini, N.M. Yu, Z., Teng, X., and Bonini, N.M. (2011) Triplet repeat-derived siRNAs enhance RNA-mediated toxicity in a Drosophila model for myotonic dystrophy. PLoS Genet., 7, e1001340.
19. Handa, V., Saha, T., and Usdin, K. Handa, V., Saha, T., and Usdin, K. (2003) The fragile X syndrome repeats form RNA hairpins that do not activate the interferon-inducible protein kinase, PKR, but are cut by Dicer. Nucleic Acids Res., 31, 6243-6248.
20. Krol, J., Fiszer, A., Mykowska, A., Sobczak, K., de Mezer, M., and Krzyzosiak, W.J. Krol, J., Fiszer, A., Mykowska, A., Sobczak, K., de Mezer, M., and Krzyzosiak, W.J. (2007) Ribonuclease dicer cleaves triplet repeat hairpins into shorter repeats that silence specific targets. Mol. Cell, 25, 575-586.
21. Malinina, L. Malinina, L. (2005) Possible involvement of the RNAi pathway in trinucleotide repeat expansion diseases. J. Biomol. Struct. Dyn., 23, 233-235.
22. Lin, Y., Leng, M., Wan, M., and Wilson, J.H. Lin, Y., Leng, M., Wan, M., and Wilson, J.H. (2010) Convergent transcription through a long CAG tract destabilizes repeats and induces apoptosis. Mol. Cell. Biol., 30, 4435-4451.
23. Groenen, P. and Wieringa, B. Groenen, P. and Wieringa, B. (1998) Expanding complexity in myotonic dystrophy. Bioessays, 20, 901-912.
24. Brook, J.D., McCurrach, M.E., Harley, H.G., Buckler, A.J., Church, D., Aburatani, H., Hunter, K., Stanton, V.P., Thirion, J.P., and Hudson, T. et al. Brook, J.D., McCurrach, M.E., Harley, H.G., Buckler, A.J., Church, D., Aburatani, H., Hunter, K., Stanton, V.P., Thirion, J.P., and Hudson, T. (1992) Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3' end of a transcript encoding a protein kinase family member. Cell, 68, 799-808.
25. Ranum, L.P. and Cooper, T.A. Ranum, L.P. and Cooper, T.A. (2006) RNA-mediated neuromuscular disorders. Annu. Rev. Neurosci., 29, 259-277.
26. Napierala, M. and Krzyzosiak, W.J. Napierala, M. and Krzyzosiak, W.J. (1997) CUG repeats present in myotonin kinase RNA form metastable "slippery" hairpins. J. Biol. Chem., 272, 31079-31085.
27. Timchenko, L.T., Timchenko, N.A., Caskey, C.T., and Roberts, R. Timchenko, L.T., Timchenko, N.A., Caskey, C.T., and Roberts, R. (1996) Novel proteins with binding specificity for DNA CTG repeats and RNA CUG repeats: implications for myotonic dystrophy. Hum. Mol. Genet., 5, 115-121.
28. Miller, J.W., Urbinati, C.R., Teng-Umnuay, P., Stenberg, M.G., Byrne, B.J., Thornton, C.A., and Swanson, M.S. Miller, J.W., Urbinati, C.R., Teng-Umnuay, P., Stenberg, M.G., Byrne, B.J., Thornton, C.A., and Swanson, M.S. (2000) Recruitment of human muscleblind proteins to (CUG)(n) expansions associated with myotonic dystrophy. EMBO J., 19, 4439-4448.
29. Fardaei, M., Rogers, M.T., Thorpe, H.M., Larkin, K., Hamshere, M.G., Harper, P.S., and Brook, J.D. Fardaei, M., Rogers, M.T., Thorpe, H.M., Larkin, K., Hamshere, M.G., Harper, P.S., and Brook, J.D. (2002) Three proteins, MBNL, MBLL and MBXL, co-localize in vivo with nuclear foci of expanded-repeat transcripts in DM1 and DM2 cells. Hum. Mol. Genet., 11, 805-814.
30. Mankodi, A., Urbinati, C.R., Yuan, Q.P., Moxley, R.T., Sansone, V., Krym, M., Henderson, D., Schalling, M., Swanson, M.S., and Thornton, C.A. Mankodi, A., Urbinati, C.R., Yuan, Q.P., Moxley, R.T., Sansone, V., Krym, M., Henderson, D., Schalling, M., Swanson, M.S., and Thornton, C.A. (2001) Muscleblind localizes to nuclear foci of aberrant RNA in myotonic dystrophy types 1 and 2. Hum. Mol. Genet., 10, 2165-2170.
31. Timchenko, N.A., Wang, G.L., and Timchenko, L.T. Timchenko, N.A., Wang, G.L., and Timchenko, L.T. (2005) RNA CUG-binding protein 1 increases translation of 20-kDa isoform of CCAAT/enhancer-binding protein beta by interacting with the alpha and beta subunits of eukaryotic initiation translation factor 2.
32. La Spada, A.R. and Taylor, J.P. La Spada, A.R. and Taylor, J.P. (2010) Repeat expansion disease: progress and puzzles in disease pathogenesis. Nat. Rev. Genet., 11, 247-258.
33. Zoghbi, H.Y. and Orr, H.T. Zoghbi, H.Y. and Orr, H.T. (2009) Pathogenic mechanisms of a polyglutamine-mediated neurodegenerative disease, spinocerebellar ataxia type1. J. Biol. Chem., 284, 7425-7429.
34. Ho, T.H., Savkur, R.S., Poulos, M.G., Mancini, M.A., Swanson, M.S., and Cooper, T.A. Ho, T.H., Savkur, R.S., Poulos, M.G., Mancini, M.A., Swanson, M.S., and Cooper, T.A. (2005) Colocalization of muscleblind with RNA foci is separable from mis-regulation of alternative splicing in myotonic dystrophy. J. Cell Sci., 118, 2923-2933.
35. de Mezer, M., Wojciechowska, M., Napierala, M., Sobczak, K., and Krzyzosiak, W.J. de Mezer, M., Wojciechowska, M., Napierala, M., Sobczak, K., and Krzyzosiak, W.J. (2011) Mutant CAG repeats of Huntingtin transcript fold into hairpins, form nuclear foci and are targets for RNA interference. Nucleic Acids Res., 39, 3852-3863.
36. Yuan, Y., Compton, S.A., Sobczak, K., Stenberg, M.G., Thornton, C.A., Griffith, J.D., and Swanson, M.S. Yuan, Y., Compton, S.A., Sobczak, K., Stenberg, M.G., Thornton, C.A., Griffith, J.D., and Swanson, M.S. (2007) Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs. Nucleic Acids Res., 35, 5474-5486.
37. Mykowska, A., Sobczak, K., Wojciechowska, M., Kozlowski, P., and Krzyzosiak, W.J. Mykowska, A., Sobczak, K., Wojciechowska, M., Kozlowski, P., and Krzyzosiak, W.J. (2011) CAG repeats mimic CUG repeats in the misregulation of alternative splicing. Nucleic Acids Res., 39, 8938-8951.
38. Daughters, R.S., Tuttle, D.L., Gao, W., Ikeda, Y., Moseley, M.L., Ebner, T.J., Swanson, M.S., and Ranum, L.P. Daughters, R.S., Tuttle, D.L., Gao, W., Ikeda, Y., Moseley, M.L., Ebner, T.J., Swanson, M.S., and Ranum, L.P. (2009) RNA gain-of-function in spinocerebellar ataxia type 8. PLoS Genet., 5, e1000600.
39. Li, L.B., Yu, Z., Teng, X., and Bonini, N.M. Li, L.B., Yu, Z., Teng, X., and Bonini, N.M. (2008) RNA toxicity is a component of ataxin-3 degeneration in Drosophila. Nature, 453, 1107-1111.
40. Orr, H.T. and Zoghbi, H.Y. Orr, H.T. and Zoghbi, H.Y. (2007) Trinucleotide repeat disorders. Annu. Rev. Neurosci., 30, 575-621.
41. Fu, Y.H., Kuhl, D.P., Pizzuti, A., Pieretti, M., Sutcliffe, J.S., Richards, S., Verkerk, A.J., Holden, J.J., Fenwick, R.G. Jr, and Warren, S.T. et al. Fu, Y.H., Kuhl, D.P., Pizzuti, A., Pieretti, M., Sutcliffe, J.S., Richards, S., Verkerk, A.J., Holden, J.J., Fenwick, R.G. Jr, and Warren, S.T. (1991) Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell, 67, 1047-1058.
42. Dombrowski, C., Levesque, S., Morel, M.L., Rouillard, P., Morgan, K., and Rousseau, F. Dombrowski, C., Levesque, S., Morel, M.L., Rouillard, P., Morgan, K., and Rousseau, F. (2002) Premutation and intermediate-size FMR1 alleles in 10572 males from the general population: loss of an AGG interruption is a late event in the generation of fragile X syndrome alleles. Hum. Mol. Genet., 11, 371-378.
43. Napierala, M., Michalowski, D., de Mezer, M., and Krzyzosiak, W.J. Napierala, M., Michalowski, D., de Mezer, M., and Krzyzosiak, W.J. (2005) Facile FMR1 mRNA structure regulation by interruptions in CGG repeats. Nucleic Acids Res., 33, 451-463.
44. Zhong, N., Ju, W., Pietrofesa, J., Wang, D., Dobkin, C., and Brown, W.T. Zhong, N., Ju, W., Pietrofesa, J., Wang, D., Dobkin, C., and Brown, W.T. (1996) Fragile X "gray zone" alleles: AGG patterns, expansion risks, and associated haplotypes. Am. J. Med. Genet., 64, 261-265.
45. Hagerman, R.J., Leehey, M., Heinrichs, W., Tassone, F., Wilson, R., Hills, J., Grigsby, J., Gage, B., and Hagerman, P.J. Hagerman, R.J., Leehey, M., Heinrichs, W., Tassone, F., Wilson, R., Hills, J., Grigsby, J., Gage, B., and Hagerman, P.J. (2001) Intention tremor, parkinsonism, and generalized brain atrophy in male carriers of fragile X. Neurology, 57, 127-130.
46. Jacquemont, S., Hagerman, R.J., Leehey, M., Grigsby, J., Zhang, L., Brunberg, J.A., Greco, C., Des Portes, V., Jardini, T., and Levine, R. et al. Jacquemont, S., Hagerman, R.J., Leehey, M., Grigsby, J., Zhang, L., Brunberg, J.A., Greco, C., Des Portes, V., Jardini, T., and Levine, R. (2003) Fragile X premutation tremor/ataxia syndrome: molecular, clinical, and neuroimaging correlates. Am. J. Hum. Genet., 72, 869-878.
47. Sherman, S.L. Sherman, S.L. (2000) Premature ovarian failure among fragile X premutation carriers: parent-of-origin effect?. Am. J. Hum. Genet., 67, 11-13.
48. Glass, I.A. Glass, I.A. (1991) X linked mental retardation. J. Med. Genet., 28, 361-371.
49. Zhang, B.R., Tian, J., Yan, Y.P., Yin, X.Z., Zhao, G.H., Wu, Z.Y., Gu, W.H., Xia, K., and Tang, B.S. Zhang, B.R., Tian, J., Yan, Y.P., Yin, X.Z., Zhao, G.H., Wu, Z.Y., Gu, W.H., Xia, K., and Tang, B.S. (2012) CCG polymorphisms in the huntingtin gene have no effect on the pathogenesis of patients with Huntington's disease in mainland Chinese families. J. Neurol. Sci., 312, 92-96.
50. Braida, C., Stefanatos, R.K., Adam, B., Mahajan, N., Smeets, H.J., Niel, F., Goizet, C., Arveiler, B., Koenig, M., and Lagier-Tourenne, C. et al. Braida, C., Stefanatos, R.K., Adam, B., Mahajan, N., Smeets, H.J., Niel, F., Goizet, C., Arveiler, B., Koenig, M., and Lagier-Tourenne, C. (2010) Variant CCG and GGC repeats within the CTG expansion dramatically modify mutational dynamics and likely contribute toward unusual symptoms in some myotonic dystrophy type 1 patients. Hum. Mol. Genet., 19, 1399-1412.
51. Gu, Y., Shen, Y., Gibbs, R.A., and Nelson, D.L. Gu, Y., Shen, Y., Gibbs, R.A., and Nelson, D.L. (1996) Identification of FMR2, a novel gene associated with the FRAXE CCG repeat and CpG island. Nat. Genet., 13, 109-113.
52. Galka-Marciniak, P., Urbanek, M.O., and Krzyzosiak, W.J. Galka-Marciniak, P., Urbanek, M.O., and Krzyzosiak, W.J. (2012) Triplet repeats in transcripts: structural insights into RNA toxicity. Biol. Chem., 393, 1299-1315.
53. Krzyzosiak, W.J., Sobczak, K., Wojciechowska, M., Fiszer, A., Mykowska, A., and Kozlowski, P. Krzyzosiak, W.J., Sobczak, K., Wojciechowska, M., Fiszer, A., Mykowska, A., and Kozlowski, P. (2012) Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target. Nucleic Acids Res., 40, 11-26.
54. Sobczak, K., deMezer, M., Michlewski, G., Krol, J., and Krzyzosiak, W.J. Sobczak, K., de Mezer, M., Michlewski, G., Krol, J., and Krzyzosiak, W.J. (2003) RNA structure of trinucleotide repeats associated with human neurological diseases. Nucleic Acids Res., 31, 5469-5482.
55. Sobczak, K., Michlewski, G., de Mezer, M., Kierzek, E., Krol, J., Olejniczak, M., Kierzek, R., and Krzyzosiak, W.J. Sobczak, K., Michlewski, G., de Mezer, M., Kierzek, E., Krol, J., Olejniczak, M., Kierzek, R., and Krzyzosiak, W.J. (2010) Structural diversity of triplet repeat RNAs. J. Biol. Chem., 285, 12755-12764.
56. Michlewski, G. and Krzyzosiak, W.J. Michlewski, G. and Krzyzosiak, W.J. (2004) Molecular architecture of CAG repeats in human disease related transcripts. J. Mol. Biol., 340, 665-679.
57. Sobczak, K. and Krzyzosiak, W.J. Sobczak, K. and Krzyzosiak, W.J. (2004) Imperfect CAG repeats form diverse structures in SCA1 transcripts. J. Biol. Chem., 279, 41563-41572.
58. Sobczak, K. and Krzyzosiak, W.J. Sobczak, K. and Krzyzosiak, W.J. (2005) CAG repeats containing CAA interruptions form branched hairpin structures in spinocerebellar ataxia type 2 transcripts. J. Biol. Chem., 280, 3898-3910.
59. Wells, R.D., Dere, R., Hebert, M.L., Napierala, M., and Son, L.S. Wells, R.D., Dere, R., Hebert, M.L., Napierala, M., and Son, L.S. (2005) Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucleic Acids Res., 33, 3785-3798.
60. Mitas, M. Mitas, M. (1997) Trinucleotide repeats associated with human disease. Nucleic Acids Res., 25, 2245-2254.
61. Liu, G., Chen, X., Bissler, J.J., Sinden, R.R., and Leffak, M. Liu, G., Chen, X., Bissler, J.J., Sinden, R.R., and Leffak, M. (2010) Replication-dependent instability at (CTG) x (CAG) repeat hairpins in human cells. Nat. Chem. Biol., 6, 652-659.
62. Mooers, B.H., Logue, J.S., and Berglund, J.A. Mooers, B.H., Logue, J.S., and Berglund, J.A. (2005) The structural basis of myotonic dystrophy from the crystal structure of CUG repeats. Proc. Natl. Acad. Sci. U.S.A., 102, 16626-16631.
63. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. (2009) Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy. Nucleic Acids Res., 37, 4149-4156.
64. Auffinger, P. and Hashem, Y. Auffinger, P. and Hashem, Y. (2007) SwS: a solvation web service for nucleic acids. Bioinformatics, 23, 1035-1037.
65. Popenda, M., Blazewicz, M., Szachniuk, M., and Adamiak, R.W. Popenda, M., Blazewicz, M., Szachniuk, M., and Adamiak, R.W. (2008) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res., 36, D386-D391.
66. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A., and Leontis, N.B. Sarver, M., Zirbel, C.L., Stombaugh, J., Mokdad, A., and Leontis, N.B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol., 56, 215-252.
67. Kumar, A., Park, H., Fang, P., Parkesh, R., Guo, M., Nettles, K.W., and Disney, M.D. Kumar, A., Park, H., Fang, P., Parkesh, R., Guo, M., Nettles, K.W., and Disney, M.D. (2011) Myotonic dystrophy type 1 RNA crystal structures reveal heterogeneous 1 × 1 nucleotide UU internal loop conformations. Biochemistry, 50, 9928-9935.
68. Tamjar, J., Katorcha, E., Popov, A., and Malinina, L. Tamjar, J., Katorcha, E., Popov, A., and Malinina, L. (2012) Structural dynamics of double-helical RNAs composed of CUG/CUG- and CUG/CGG-repeats. J. Biomol. Struct. Dyn., 30, 505-523.
69. Coonrod, L.A., Lohman, J.R., and Berglund, J.A. Coonrod, L.A., Lohman, J.R., and Berglund, J.A. (2012) Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Biochemistry, 51, 8330-8337.
70. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. (2010) Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases. Nucleic Acids Res., 38, 8370-8376.
71. Yildirim, I., Park, H., Disney, M.D., and Schatz, G.C. Yildirim, I., Park, H., Disney, M.D., and Schatz, G.C. (2013) A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations. J. Am. Chem. Soc., 135, 3528-3538.
72. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. (2011) Crystal structures of CGG RNA repeats with implications for fragile X-associated tremor ataxia syndrome. Nucleic Acids Res., 39, 7308-7315.
73. Kumar, A., Fang, P., Park, H., Guo, M., Nettles, K.W., and Disney, M.D. Kumar, A., Fang, P., Park, H., Guo, M., Nettles, K.W., and Disney, M.D. (2011) A crystal structure of a model of the repeating r(CGG) transcript found in fragile X syndrome. Chembiochem, 12, 2140-2142.
74. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. Kiliszek, A., Kierzek, R., Krzyzosiak, W.J., and Rypniewski, W. (2012) Crystallographic characterization of CCG repeats. Nucleic Acids Res., 40, 8155-8162.
75. Riedel, K., Herbst, C., Hafner, S., Leppert, J., Ohlenschlager, O., Swanson, M.S., Gorlach, M., and Ramachandran, R. Riedel, K., Herbst, C., Hafner, S., Leppert, J., Ohlenschlager, O., Swanson, M.S., Gorlach, M., and Ramachandran, R. (2006) Constraints on the structure of (CUG)97 RNA from magic-angle-spinning solid-state NMR spectroscopy. Angew. Chem. Int. Ed. Engl., 45, 5620-5623.
76. Parkesh, R., Fountain, M., and Disney, M.D. Parkesh, R., Fountain, M., and Disney, M.D. (2011) NMR spectroscopy and molecular dynamics simulation of r(CCGCUGCGG)(2) reveal a dynamic UU internal loop found in myotonic dystrophy type 1. Biochemistry, 50, 599-601.
77. Zumwalt, M., Ludwig, A., Hagerman, P.J., and Dieckmann, T. Zumwalt, M., Ludwig, A., Hagerman, P.J., and Dieckmann, T. (2007) Secondary structure and dynamics of the r(CGG) repeat in the mRNA of the fragile X mental retardation 1 (FMR1) gene. RNA Biol., 4, 93-100.
78. Zheng, M., Huang, X., Smith, G.K., Yang, X., and Gao, X. Zheng, M., Huang, X., Smith, G.K., Yang, X., and Gao, X. (1996) Genetically unstable CXG repeats are structurally dynamic and have a high propensity for folding. An NMR and UV spectroscopic study. J. Mol. Biol., 264, 323-336.
79. Broda, M., Kierzek, E., Gdaniec, Z., Kulinski, T., and Kierzek, R. Broda, M., Kierzek, E., Gdaniec, Z., Kulinski, T., and Kierzek, R. (2005) Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure. Biochemistry, 44, 10873-10882.
80. Teplova, M. and Patel, D.J. Teplova, M. and Patel, D.J. (2008) Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-likeMBNL1. Nat. Struct. Mol. Biol., 15, 1343-1351.
81. Hu, J., Gagnon, K.T., Liu, J., Watts, J.K., Syeda-Nawaz, J., Bennett, C.F., Swayze, E.E., Randolph, J., Chattopadhyaya, J., and Corey, D.R. Hu, J., Gagnon, K.T., Liu, J., Watts, J.K., Syeda-Nawaz, J., Bennett, C.F., Swayze, E.E., Randolph, J., Chattopadhyaya, J., and Corey, D.R. (2011) Allele-selective inhibition of ataxin-3 (ATX3) expression by antisense oligomers and duplex RNAs. Biol. Chem., 392, 315-325.
82. Ofori, L.O., Hoskins, J., Nakamori, M., Thornton, C.A., and Miller, B.L. Ofori, L.O., Hoskins, J., Nakamori, M., Thornton, C.A., and Miller, B.L. (2012) From dynamic combinatorial 'hit' to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy. Nucleic Acids Res., 40, 6380-6390.
83. Jahromi, A.H., Nguyen, L., Fu, Y., Miller, K.A., Baranger, A.M., and Zimmerman, S.C. Jahromi, A.H., Nguyen, L., Fu, Y., Miller, K.A., Baranger, A.M., and Zimmerman, S.C. (2013) A novel CUG(exp).MBNL1 inhibitor with therapeutic potential for myotonic dystrophy type 1. ACS Chemi Biol. 8: 1037-1043.
84. Wong, C.H., Fu, Y., Ramisetty, S.R., Baranger, A.M., and Zimmerman, S.C. Wong, C.H., Fu, Y., Ramisetty, S.R., Baranger, A.M., and Zimmerman, S.C. (2011) Selective inhibition of MBNL1-CCUG interaction by small molecules toward potential therapeutic agents for myotonic dystrophy type 2 (DM2). Nucleic Acids Res., 39, 8881-8890.