The expanding view of RNA and DNA function

Chemistry and Biology

Volumn 21, Issue 9, 2014, Pages 1059-1065

  Breaker, Ronald R ^a   Joyce, Gerald F ^b  

^a YALE UNIVERSITY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; DNA; RNA; DEOXYRIBOZYME; RIBOSWITCH; RIBOZYME;

CATALYSIS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DNA FUNCTION; DNA MODIFICATION; GENE EXPRESSION; HUMAN; LIGAND BINDING; NONHUMAN; NUCLEIC ACID STRUCTURE, METABOLISM AND FUNCTION; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; REVIEW; RIBOSWITCH; RNA ANALYSIS; RNA FUNCTION; RNA STRUCTURE; RNA TRANSCRIPTION; ALLOSTERISM; CHEMISTRY; CONFORMATION; METABOLISM;

ALLOSTERIC REGULATION; APTAMERS, NUCLEOTIDE; CATALYSIS; DNA; DNA, CATALYTIC; NUCLEIC ACID CONFORMATION; RIBOSWITCH; RNA; RNA, CATALYTIC;

EID: 84909580167     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2014.07.008     Document Type: Review

References (79)

1. Ameres, S.L., and Zamore, P.D. (2013). Diversifying microRNA sequence and function. Nat. Rev. Mol. Cell Biol. 14, 475-488.
2. Attwater, J., Wochner, A., and Holliger, P. (2013). In-ice evolution of RNA polymerase ribozyme activity. Nat. Chem. 5, 1011-1018.
3. Bartel, D.P., and Szostak, J.W. (1993). Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411-1418.
4. Beaudry, A., DeFoe, J., Zinnen, S., Burgin, A., and Beigelman, L. (2000). In vitro selection of a novel nuclease-resistant RNA phosphodiesterase. Chem. Biol. 7, 323-334.
5. Blount, K.F., and Breaker, R.R. (2006). Riboswitches as antibacterial drug targets. Nat. Biotechnol. 24, 1558-1564.
6. Breaker, R.R. (2011). Prospects for riboswitch discovery and analysis. Mol. Cell 43, 867-879.
7. Breaker, R.R., and Joyce, G.F. (1994). A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229.
8. 2+-dependent RNA phosphoesterase activity. Chem. Biol. 2, 655-660.
9. Cai, H., Santiago, F.S., Prado-Lourenco, L., Wang, B., Patrikakis, M., Davenport, M.P., Maghzal, G.J., Stocker, R., Parish, C.R., Chong, B.H., et al. (2012). DNAzyme targeting c-jun suppresses skin cancer growth. Sci. Transl. Med. 4, 139ra82.
10. Cavanagh, A.T., and Wassarman, K.M. (2014). 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond. Annu. Rev. Microbiol. Published online April 10, 2014. http://dx.doi.org/10.1146/annurev-micro-092611-150135.
11. Chalingné, R., and Heard, E. (2014). X-chromosome inactivation in development and cancer. FEBS Lett. 588, 2514-2522.
12. Chandra, M., and Silverman, S.K. (2008). DNA and RNA can be equally efficient catalysts for carbon-carbon bond formation. J. Am. Chem. Soc. 130, 2936-2937.
13. Chandra, M., Sachdeva, A., and Silverman, S.K. (2009). DNA-catalyzed sequence-specific hydrolysis of DNA. Nat. Chem. Biol. 5, 718-720.
14. Chen, A.G.Y., Sudarsan, N., and Breaker, R.R. (2011). Mechanism for gene control by a natural allosteric group I ribozyme. RNA 17 , 1967-1972.
15. Cho, E.A., Moloney, F.J., Cai, H., Au-Yeung, A., China, C., Scolyer, R.A., Yosufi, B., Raftery, M.J., Deng, J.Z., Morton, S.W., et al. (2013). Safety and tolerability of an intratumorally injected DNAzyme, Dz13, in patients with nodular basal-cell carcinoma: a phase 1 first-in-human trial (DISCOVER). Lancet 381, 1835-1843.
16. Crick, F.H.C. (1958). On protein synthesis. Symp. Soc. Exp. Biol. 12, 138-163.
17. Crick, F.H.C. (1966). The genetic code - yesterday, today, and tomorrow. Cold Spring Harb. Symp. Quant. Biol. 31, 1-9.
18. Crick, F.H.C. (1968). The origin of the genetic code. J. Mol. Biol. 38, 367-379.
19. Cuenoud, B., and Szostak, J.W. (1995). A DNA metalloenzyme with DNA ligase activity. Nature 375, 611-614.
20. Deigan, K.E., and Ferré-D'Amaré, A.R. (2011). Riboswitches: discovery of drugs that target bacterial gene-regulatory RNAs. Acc. Chem. Res. 44, 1329-1338.
21. Deiorio-Haggar, K., Anthony, J., and Meyer, M.M. (2013). RNA structures regulating ribosomal protein biosynthesis in bacilli. RNA Biol. 10, 1180-1184.
22. Ekland, E.H., and Bartel, D.P. (1996). RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382, 373-376.
23. Ellington, A.D., and Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
24. Feigon, J., Dieckmann, T., and Smith, F.W. (1996). Aptamer structures from A to zeta. Chem. Biol. 3, 611-617.
25. Fusz, S., Eisenführ, A., Srivatsan, S.G., Heckel, A., and Famulok, M. (2005). A ribozyme for the aldol reaction. Chem. Biol. 12, 941-950.
26. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., and Altman, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857.
27. Jiang, L., Suri, A.K., Fiala, R., and Patel, D.J. (1997). Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem. Biol. 4, 35-50.
28. Johnston, W.K., Unrau, P.J., Lawrence, M.S., Glasner, M.E., and Bartel, D.P. (2001). RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292, 1319-1325.
29. Joyce, G.F. (2004). Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73, 791-836.
30. Kortmann, J., and Narberhaus, F. (2012). Bacterial RNA thermometers: molecular zippers and switches. Nat. Rev. Microbiol. 10, 255-265.
31. Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E., and Cech, T.R. (1982). Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31, 147-157.
32. Lato, S.M., Boles, A.R., and Ellington, A.D. (1995). In vitro selection of RNA lectins: using combinatorial chemistry to interpret ribozyme evolution. Chem. Biol. 2, 291-303.
33. Lee, E.R., Baker, J.L., Weinberg, Z., Sudarsan, N., and Breaker, R.R. (2010). An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329, 845-848.
34. Lermer, L., Roupioz, Y., Ting, R., and Perrin, D.M. (2002). Toward an RNaseA mimic: a DNAzyme with imidazoles and cationic amines. J. Am. Chem. Soc. 124, 9960-9961.
35. Leva, S., Lichte, A., Burmeister, J., Muhn, P., Jahnke, B., Fesser, D., Erfurth, J., Burgstaller, P., and Klussmann, S. (2002). GnRH binding RNA and DNA Spiegelmers: a novel approach toward GnRH antagonism. Chem. Biol. 9, 351-359.
36. Levy, M., and Ellington, A.D. (2002). ATP-dependent allosteric DNA enzymes. Chem. Biol. 9, 417-426.
37. Li, Y., and Sen, D. (1996). A catalytic DNA for porphyrin metallation. Nat. Struct. Biol. 3, 743-747.
38. Li, Y., and Breaker, R.R. (1999). Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. USA 96, 2746-2751.
39. Lin, C.H., and Patel, D.J. (1997). Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP. Chem. Biol. 4, 817-832.
40. Lincoln, T.A., and Joyce, G.F. (2009). Self-sustained replication of an RNA enzyme. Science 323, 1229-1232.
41. Luteijn, M.J., and Ketting, R.F. (2013). PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat. Rev. Genet. 14, 523-534.
42. Marraffini, L.A., and Sontheimer, E.J. (2010). CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat. Rev. Genet. 11, 181-190.
43. Mayer, G., and Famulok, M. (2006). High-throughput-compatible assay for glmS riboswitch metabolite dependence. ChemBioChem 7, 602-604.
44. Mulhbacher, J., Brouillette, E., Allard, M., Fortier, L.-C., Malouin, F., and Lafontaine, D.A. (2010). Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLoS Pathog. 6, e1000865.
45. Murakami, H., Saito, H., and Suga, H. (2003). A versatile tRNA aminoacylation catalyst based on RNA. Chem. Biol. 10, 655-662.
46. Nahvi, A., Sudarsan, N., Ebert, M.S., Zou, X., Brown, K.L., and Breaker, R.R. (2002). Genetic control by a metabolite binding mRNA. Chem. Biol. 9, 1043-1049.
47. Nissen, P., Hansen, J., Ban, N., Moore, P.B., and Steitz, T.A. (2000). The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920-930.
48. Noller, H.F., Hoffarth, V., and Zimniak, L. (1992). Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256, 1416-1419.
49. Orgel, L.E. (1968). Evolution of the genetic apparatus. J. Mol. Biol. 38, 381-393.
50. Osborne, S.E., and Ellington, A.D. (1997). Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349-370.
51. Paul, N., and Joyce, G.F. (2002). A self-replicating ligase ribozyme. Proc. Natl. Acad. Sci. USA 99, 12733-12740.
52. Pinheiro, V.B., Taylor, A.I., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J.C., Wengel, J., Peak-Chew, S.Y., McLaughlin, S.H., et al. (2012). Synthetic genetic polymers capable of heredity and evolution. Science 336, 341-344.
53. Robertson, D.L., and Joyce, G.F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467-468.
54. Robertson, M.P., and Joyce, G.F. (2014). Highly efficient self-replicating RNA enzymes. Chem. Biol. 21, 238-245.
55. Saito, H., Kourouklis, D., and Suga, H. (2001). An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J. 20, 1797-1806.
56. Santoro, S.W., and Joyce, G.F. (1997). A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94, 4262-4266.
57. Santoro, S.W., Joyce, G.F., Sakthivel, K., Gramatikova, S., and Barbas, C.F., 3rd. (2000). RNA cleavage by a DNA enzyme with extended chemical functionality. J. Am. Chem. Soc. 122, 2433-2439.
58. Seelig, B., and Jäschke, A. (1999). A small catalytic RNA motif with Diels-Alderase activity. Chem. Biol. 6, 167-176.
59. Sengle, G., Eisenführ, A., Arora, P.S., Nowick, J.S., and Famulok, M. (2001). Novel RNA catalysts for the Michael reaction. Chem. Biol. 8, 459-473.
60. Sheppard, T.L., Ordoukhanian, P., and Joyce, G.F. (2000). A DNA enzyme with N-glycosylase activity. Proc. Natl. Acad. Sci. USA 97, 7802-7807.
61. Soukup, G.A., and Breaker, R.R. (1999). Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. USA 96, 3584-3589.
62. Sreedhara, A., Li, Y., and Breaker, R.R. (2004). Ligating DNA with DNA. J. Am. Chem. Soc. 126, 3454-3460.
63. Srinivasan, J., Cload, S.T., Hamaguchi, N., Kurz, J., Keene, S., Kurz, M., Boomer, R.M., Blanchard, J., Epstein, D., Wilson, C., and Diener, J.L. (2004). ADP-specific sensors enable universal assay of protein kinase activity. Chem. Biol. 11, 499-508.
64. Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G.M., and Breaker, R.R. (2005). Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem. Biol. 12, 1325-1335.
65. Sun, L., Cui, Z., Gottlieb, R.L., and Zhang, B. (2002). A selected ribozyme catalyzing diverse dipeptide synthesis. Chem. Biol. 9, 619-628.
66. Tang, J., and Breaker, R.R. (1997). Rational design of allosteric ribozymes. Chem. Biol. 4, 453-459.
67. Tarasow, T.M., Tarasow, S.L., and Eaton, B.E. (1997). RNA-catalysed carbon-carbon bond formation. Nature 389, 54-57.
68. Tuerk, C., and Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.
69. Ulitsky, I., and Bartel, D.P. (2013). lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26-46.
70. Walsh, S.M., Sachdeva, A., and Silverman, S.K. (2013). DNA catalysts with tyrosine kinase activity. J. Am. Chem. Soc. 135, 14928-14931.
71. Warner, K.D., Homan, P., Weeks, K.M., Smith, A.G., Abell, C., and Ferré-D'Amaré, A.R. (2014). Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically. Chem. Biol. 21, 591-595.
72. Waters, L.S., and Storz, G. (2009). Regulatory RNAs in bacteria. Cell 136, 615-628.
73. Wiegand, T.W., Janssen, R.C., and Eaton, B.E. (1997). Selection of RNA amide synthases. Chem. Biol. 4, 675-683.
74. Wilson, D.S., and Szostak, J.W. (1999). In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611-647.
75. Wochner, A., Attwater, J., Coulson, A., and Holliger, P. (2011). Ribozyme-catalyzed transcription of an active ribozyme. Science 332, 209-212.
76. Woese, C. (1967). The Genetic Code: The Molecular Basis for Genetic Expression. (New York: Harper & Row), pp. 179-195.
77. Yu, H., Zhang, S., and Chaput, J.C. (2012). Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor. Nat. Chem. 4, 183-187.
78. Zhang, B., and Cech, T.R. (1997). Peptide bond formation by in vitro selected ribozymes. Nature 390, 96-100.
79. Zhang, B., and Cech, T.R. (1998). Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. Chem. Biol. 5, 539-553.