Attenuation of loop-receptor interactions with pseudoknot formation

Nucleic Acids Research

Volumn 40, Issue 5, 2012, Pages 2168-2180

  Afonin, Kirill A ^a   Lin, Yen Ping ^a   Calkins, Erin R ^a   Jaeger, Luc ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GNRA RECEPTOR; RECEPTOR; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DISSOCIATION CONSTANT; GC RICH SEQUENCE; GEL MOBILITY SHIFT ASSAY; GENETIC TRANSCRIPTION; IN VITRO STUDY; MOLECULAR INTERACTION; MOLECULAR MODEL; NANOBIOTECHNOLOGY; PRIORITY JOURNAL; PSEUDOKNOT; RIBOSWITCH; RNA STRUCTURE; SYNTHETIC BIOLOGY; THERMODYNAMICS;

DIMERIZATION; MAGNESIUM; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; NUCLEOTIDE MOTIFS; POINT MUTATION; RIBOSWITCH; RNA; TRANSCRIPTION, GENETIC;

EID: 84863365893     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr926     Document Type: Article

References (64)

1. Tinoco, I. Jr and Bustamante, C. (1999) How RNA folds. J. Mol. Biol., 293, 271-281.
2. Noller, H. F. (2005) RNA structure: reading the ribosome. Science, 309, 1508-1514.
3. Geary, C., Chworos, A. and Jaeger, L. (2011) Promoting RNA helical stacking via A-minor junctions. Nucleic Acids Res., 39, 1066-1080.
4. Nissen, P., Ippolito, J. A., Ban, N., Moore, P. B. and Steitz, T. A. (2001) RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl. Acad. Sci., 98, 4899-4903.
5. Jaeger, L., Michel, F. and Westhof, E. (1994) Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol., 236, 1271-1276.
6. Costa, M. and Michel, F. (1995) Frequent use of the same tertiary motif by self-folding RNAs. EMBO J., 14, 1276-1285.
7. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Kundrot, C. E., Cech, T. R. and Doudna, J. A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678-1685.
8. Costa, M. and Michel, F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J., 16, 3289-3302.
9. Massire, C., Jaeger, L. and Westhof, E. (1997) Phylogenetic evidence for a new tertiary interaction in bacterial RNase P RNAs. RNA, 3, 553-556.
10. Abramovitz, D. L. and Pyle, A. M. (1997) Remarkable morphological variability of a common RNA folding motif: the GNRA tetraloop-receptor interaction. J. Mol. Biol., 266, 493-506.
11. Ban, N., Nissen, P., Hansen, J., Moore, P. B. and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2. 4 A resolution. Science, 289, 905-920.
12. Adams, P. L., Stahley, M. R., Gill, M. L., Kosek, A. B., Wang, J. and Strobel, S. A. (2004) Crystal structure of a group I intron splicing intermediate. RNA, 10, 1867-1887.
13. Torres-Larios, A., Swinger, K. K., Pan, T. and Mondragon, A. (2006) Structure of ribonuclease P-a universal ribozyme. Curr. Opin. Struct. Biol., 16, 327-335.
14. Ikawa, Y., Naito, D., Aono, N., Shiraishi, H. and Inoue, T. (1999) A conserved motif in group IC3 introns is a new class of GNRA receptor. Nucleic Acids Res., 27, 1859-1865.
15. Geary, C., Baudrey, S. and Jaeger, L. (2008) Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors. Nucleic Acids Res., 36, 1138-1152.
16. Michel, F. and Westhof, E. (1990) Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216, 585-610.
17. Lehnert, V., Jaeger, L., Michel, F. and Westhof, E. (1996) New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of the Tetrahymena thermophila ribozyme. Chem. Biol., 3, 993-1009.
18. Massire, C., Jaeger, L. and Westhof, E. (1998) Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol., 279, 773-793.
19. Regulski, E. E., Moy, R. H., Weinberg, Z., Barrick, J. E., Yao, Z., Ruzzo, W. L. and Breaker, R. R. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Mol. Microbiol., 68, 918-932.
20. Sudarsan, N., Lee, E. R., Weinberg, Z., Moy, R. H., Kim, J. N., Link, K. H. and Breaker, R. R. (2008) Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science, 321, 411-413.
21. Cate, J. H., Gooding, A. R., Podell, E., Zhou, K., Golden, B. L., Szewczak, A. A., Kundrot, C. E., Cech, T. R. and Doudna, J. A. (1996) RNA tertiary structure mediation by adenosine platforms. Science, 273, 1696-1699.
22. Jaeger, L. and Leontis, N. B. (2000) TectoRNA: one-dimensional self-assembly through tertiary interactions. Angew. Chem. Int. Ed. Engl., 39, 2521-2524.
23. Jaeger, L., Westhof, E. and Leontis, N. B. (2001) TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res., 29, 455-463.
24. Jaeger, L. and Chworos, A. (2006) The architectonics of programmable RNA and DNA nanostructures. Curr. Opin. Struct. Biol., 16, 531-543.
25. Afonin, K. A. and Leontis, N. B. (2006) Generating new specific RNA interaction interfaces using C-loops. J. Am. Chem. Soc., 128, 16131-16137.
26. Nasalean, L., Baudrey, S., Leontis, N. B. and Jaeger, L. (2006) Controlling RNA self-assembly to form filaments. Nucleic Acids Res., 34, 1381-1392.
27. Ishikawa, J., Fujita, Y., Maeda, Y., Furuta, H. and Ikawa, Y. (2011) GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures. Methods, 54, 226-238.
28. Dawid, A., Cayrol, B. and Isambert, H. (2009) RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Phys. Biol., 6, 025007.
29. Gutierrez-Preciado, A., Henkin, T. M., Grundy, F. J., Yanofsky, C. and Merino, E. (2009) Biochemical features and functional implications of the RNA-based T-box regulatory mechanism. Microbiol. Mol. Biol. Rev., 73, 36-61.
30. Wachter, A. (2011) Riboswitch-mediated control of gene expression in eukaryotes. RNA Biol., 7, 67-76.
31. Breaker, R. R. (2010) Riboswitches and the RNA World. Cold Spring Harb. Perspect. Biol, November 24 (doi:10. 1101/cshperspect. a003566; epub ahead of print).
32. Hess, H. and Jaeger, L. (2010) Nanobiotechnology. Curr. Opin. Biotechnol., 21, 373-375.
33. Topp, S. and Gallivan, J. P. (2011) Emerging applications of riboswitches in chemical biology. ACS Chem. Biol., 5, 139-148.
34. de Las Heras, A., Carreno, C. A., Martinez-Garcia, E. and de Lorenzo, V. (2011) Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol. Rev., 34, 842-865.
35. Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
36. Davis, J. H., Foster, T. R., Tonelli, M. and Butcher, S. E. (2007) Role of metal ions in the tetraloop-receptor complex as analyzed by NMR. RNA, 13, 76-86.
37. Davis, J. H., Tonelli, M., Scott, L. G., Jaeger, L., Williamson, J. R. and Butcher, S. E. (2005) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex. J. Mol. Biol., 351, 371-382.
38. Wu, H. and Feigon, J. (2007) H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc. Natl Acad. Sci. USA, 104, 6655-6660.
39. Jin, H., Loria, J. P. and Moore, P. B. (2007) Solution Structure of an rRNA Substrate Bound to the Pseudouridylation Pocket of a Box H/ACA snoRNA. Mol. Cell., 26, 205-215.
40. Mathews, D. H., Sabina, J., Zuker, M. and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
41. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
42. Xayaphoummine, A., Bucher, T. and Isambert, H. (2005) Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res., 33, W605-W610.
43. Leontis, N. B. and Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
44. Afonin, K. A., Bindewald, E., Yaghoubian, A. J., Voss, N., Jacovetty, E., Shapiro, B. A. and Jaeger, L. (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol., 5, 676-682.
45. Paillart, J. C., Skripkin, E., Ehresmann, B., Ehresmann, C. and Marquet, R. (1996) A loop-loop 'kissing' complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proc. Natl Acad. Sci. USA, 93, 5572-5577.
46. Afonin, K. A., Cieply, D. J. and Leontis, N. B. (2008) Specific RNA self-assembly with minimal paranemic motifs. J. Am. Chem. Soc., 130, 93-102.
47. Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T. and Turner, D. H. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA, 83, 9373-9377.
48. Mahen, E. M., Harger, J. W., Calderon, E. M. and Fedor, M. J. (2005) Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast. Mol. Cell., 19, 27-37.
49. Mahen, E. M., Watson, P. Y., Cottrell, J. W. and Fedor, M. J. (2010) mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol., 8, e1000307.
50. Smith, K. D., Lipchock, S. V., Ames, T. D., Wang, J., Breaker, R. R. and Strobel, S. A. (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat. Struct. Mol. Biol., 16, 1218-1223.
51. Kulshina, N., Baird, N. J. and Ferre-D'Amare, A. R. (2009) Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat. Struct. Mol. Biol., 16, 1212-1217.
52. Toor, N., Keating, K. S., Fedorova, O., Rajashankar, K., Wang, J. and Pyle, A. M. (2010) Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA, 16, 57-69.
53. Baird, N. J., Kulshina, N. and Ferre-D'Amare, A. R. (2010) Riboswitch function: flipping the switch or tuning the dimmer? RNA Biol., 7, 328-332.
54. Prathiba, J. and Malathi, R. (2008) Group I introns and GNRA tetraloops: remnants of 'The RNA world'? Mol. Biol. Rep., 35, 239-249.
55. Sheehy, J. P., Davis, A. R. and Znosko, B. M. (2010) Thermodynamic characterization of naturally occurring RNA tetraloops. RNA, 16, 417-429.
56. Macke, T. J., Ecker, D. J., Gutell, R. R., Gautheret, D., Case, D. A. and Sampath, R. (2001) RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res., 29, 4724-4735.
57. Gardner, P. P., Daub, J., Tate, J., Moore, B. L., Osuch, I. H., Griffiths-Jones, S., Finn, R. D., Nawrocki, E. P., Kolbe, D. L., Eddy, S. R. et al. (2011) Rfam: wikipedia, clans and the 'decimal' release. Nucleic Acids Res., 39, D141-D145.
58. Mitra, S., Laederach, A., Golden, B. L., Altman, R. B. and Brenowitz, M. (2011) RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. RNA, 17, 1589-1603.
59. Jaeger, L. and Calkins, E. R. (2011) Downward causation by information control in micro-organisms. Interface Focus, September 29 (doi:10. 1098/rsfs. 2011. 0045; epub ahead of print).
60. Plotkin, J. B. and Kudla, G. (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet., 12, 32-42.
61. Severcan, I., Geary, C., Chworos, A., Voss, N., Jacovetty, E. and Jaeger, L. (2010) A polyhedron made of tRNAs. Nat. Chem., 2, 772-779.
62. Chworos, A., Severcan, I., Koyfman, A. Y., Weinkam, P., Oroudjev, E., Hansma, H. G. and Jaeger, L. (2004) Building programmable jigsaw puzzles with RNA. Science, 306, 2068-2072.
63. Bindewald, E., Kluth, T. and Shapiro, B. A. (2010) CyloFold: secondary structure prediction including pseudoknots. Nucleic Acids Res., 38, W368-W372.
64. Jaeger, L., Verzemnieks, E. J. and Geary, C. (2009) The UA-handle: a versatile submotif in stable RNA architectures. Nucleic Acids Res., 37, 215-230.