Abstract
Among the enormous quantity and diversity of enzymes found in nature, researchers have confirmed the existence of only seven distinct classes of biological catalysts that are made of RNA rather than protein. As currently understood, the natural functions of these ribozymes are limited to phosphoester transfer and phosphoester hydrolysis reactions that occur with RNA or DNA substrates (Kruger et al. 1982; Guerrier-Takadaet al. 1983; Peebles et al. 1986; Paddy et al. 1986; Buzayan et al. 1986; Sharmeen et al. 1988; Saville and Collins 1990; Zimmerly et al. 1995). Although ribozymes are exceedingly rare and their biochemical functions are limited, they serve as essential components of the metabolic machinery of all living systems. It has been proposed that nucleic acids preceded proteins in the evolutionary history of biocatalysis, and that these primitive ribozymes catalyzed many of the reactions performed by modern protein enzymes (Gilbert 1986; Benner et al. 1989; Hirao and Ellington 1995). Over the course of 4 billion years of evolution, it appears that nature has determined that proteins are a superior format for constructing enzymes; however, the true capacity of nucleic acids for catalytic function remains to be fully defined.
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References
Bartel DP, Szostak JW (1993) Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411–1418
Beaudry AA, Joyce GF (1992) Direct evolution of an RNA enzyme. Science 257: 635–641
Benner SA, Ellington AD, Tauer A (1989) Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci USA 86: 7054–7058
Breaker RR (1997a) In vitro selection of catalytic polynucleotides. Chem Rev 97: 371–390
Breaker RR (1997b) DNA aptamers and DNA enzymes. Curr Opin Chem Biol 1: 26–31
Breaker RR (1997c) DNA enzymes. Nature Biotechnol 15: 427–431
Breaker RR, Joyce GF (1994a) Emergence of a replicating species from an in vitro RNA evolution reaction. Proc Natl Acad Sci USA 91: 6093–6097
Breaker RR, Joyce GF (1994b) A DNA enzyme that cleaves RNA. Chem Biol 1: 223–229
Breaker RR, Joyce GF (1995) A DNA enzyme with Mg2tdependent RNA phosphoesterase activity. Chem Biol 2: 655–660
Burmeister J, von Kiedrowski G, Ellington AD (1997) Cofactor-assisted self-cleavage in DNA libraries with a 3’-5’-phosphoramidate bond. Angew Chem Int Ed 36: 1321–1324
Buzayan JM, Gerlach WL, Bruening G (1986) Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323: 349–353
Carmi N, Balkhi SR, Breaker RR (1998) Cleaving DNA with DNA. Proc Natl Acad Sci USA 95: 223–237
Carmi N, Shultz LA, Breaker RR (1996) In vitro selection of self-cleaving DNAs. Chem Biol 3: 1039–1046
Chapman KB, Szostak JW (1995) Isolation of a ribozyme with 5’-5’ ligase activity. Chem Biol 2: 325–333
Charlton J, Kirschenheuter GP, Smith D (1997a) Highly potent irreversible inhibitors of neutrophil elastase generated by selection from randomized DNA-valine phosphonate library. Biochemistry 36: 3018–3026
Charlton J, Sennello J, Smith D (1997b) In vivo imaging of inflammation using an aptamer inhibitor of human neutrophil elastase. Chem Biol 4: 809–816
Chowrira BM, Berzal-Herranz A, Burke JM (1993) Ionic requirements for RNA binding, cleavage, and ligation by the hairpin ribozyme. Biochemistry 32: 1088–1095
Cochran AG, Schultz PG (1990) Antibody-catalyzed porphyrin metallation. Science 249:781–783. Compton J (1991) Nature 350: 91–92
Conn MM, Prudent JR, Schultz PG (1996) Porphyrin metalation catalyzed by a small RNA molecule. J Am Chem Soc 118: 7012–7013
Couenoud B, Szostak JW (1995) A DNA metalloenzyme with DNA ligase activity. Nature 375: 611–614
Dahm SC, Uhlenbeck OC (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30: 9464–9469
Dai X, De Mesmaeker A, Joyce GF (1995) Cleavage of an amide bond by a ribozyme. Science 267: 237–240
Dai X, De Mesmaeker A, Joyce GF (1996) Amide cleavage by a ribozyme:correction. Science 272: 18–19
Eaton BE (1997) The joys of in vitro selection:chemically dressing oligonucleotides to satiate protein targets. Curr Opin Chem Biol 1: 10–16
Ekland EH, Bartel DP (1996) RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382: 373–376
Ekland EH, Szostak JW, Bartel DP (1995) Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269: 364–370
Faulhammer D, Famulok M (1997) Characterization and divalent metal-ion dependence of in vitro selected deoxyribozymes which cleave DNA/RNA chimeric oligonucleotides. J Mol Biol 269:188–202
Frauendorf C, Jaschke A (1998) Catalysis of organic reactions by RNA. Angew Chem Int Ed 37: 1378–1381
Geyer CR, Sen D (1997) Evidence for the metal-cofactor independence of an RNA phosphodiestercleaving DNA enzyme. Chem Biol 4: 579–593
Gilbert W (1986) The RNA world. Nature 319: 618
Guatelli JC, Whitefield KM, Kwoh DY, Barringer KJ, Richman DD, Gingeras TR (1990) Isothermal, in vitro amplification of nucleic acids by a multienzyme reaction modeled after retroviral replication. Proc Natl Acad Sci USA 87: 1874–1878
Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849–857
Hager AJ, Szostak JW (1997) Isolation of novel ribozymes that ligate AMP-activated RNA substrates. Chem Biol 4: 607–617
Hager JA, Pollard JD, Szostak JW (1996) Ribozymes: aiming at RNA replication and protein synthesis. Chem Biol 3: 717–725
Hampel A, Cowan JA (1997) A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage. Chem Biol 4: 513–517
Hirao I, Ellington AD (1995) Recreating the RNA world. Curr Biol 5: 1017–1022
Huang F, Yarus M (1997a) 5’-RNA self-capping from guanosine diphosphate. Biochemistry 36: 6557–6563
Huang F, Yarus M (1997b) Versatile 5’ phosphoryl coupling of small and large molecules to an RNA. Proc Natl Acad Sci USA 94: 8965–8969
Huang F, Yarus M (1997e) A calcium-metalloribozyme with autodecapping and pyrophosphatase activities. Biochemistry 36: 14107–14119
Illangasekare M, Sanchez G, Nickles T, Yarus M (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267: 643–647
Jayasena VK, Gold L (1997) In vitro selection of self-cleaving RNAs with a low pH optimum. Proc Nat] Acad Sci USA 94: 10612–10617
Jenne A, Famulok M (1998) A novel ribozyme with ester transferase activity. Chem Biol 5: 23–34
Joyce GF (1992) Selective amplification techniques for optimization of ribozyme function. In: Antisense RNA and DNA, TR Cech ed., Wiley-Liss, New York, pp 353–372
Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31: 147–157
Kuimelis RG, McLaughlin RW (1995) Hammerhead ribozyme mediated cleavage of a substrate analogue containing an internucleotidic bridging 5’-phosphorothioate: implications for the cleavage mechanism and the catalytic role of the metal cofactor. J Am Chem Soc 117: 11019–11020
Letsinger RL, Wu T (1995) Use of a stilbenecarboxamide bridge in stabilizing, monitoring, and photochemically altering folded conformations of oligonucleotides. J Am Chem Soc 117: 7323–7328
Li Y, Sen D (1996) A catalytic DNA for porphyrin metallation. Nat Struct Biol 3: 743–747
Li Y, Sen D (1998) The modus operandi of a DNA enzyme: enhancement of substrate basicity. Chem Biol 5: 1–12
Lin Y, Qiu Q, Gill SC, Jayasena SD (1994) Modified RNA sequence pools for in vitro selection. Nucleic Acids Res 22: 5229–5234
Lohse PA, Szostak JW (1996), Ribozyme-catalysed amino-acid transfer reactions. Nature 381: 442–444
Lorsch JR, Szostak JW (1994) In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 371: 31–36
Macaya RF, Waldron JA, Beutel BA, Gao H, Joesten ME, Yang M, Patel R, Bertelsen AH, Cook AF (1995) Structural and functional characterization of potent antithrombic oligonucleotides possessing both quadruplez and duplex motifs. Biochemistry 34: 4478–4492
Nelson JS, Giver L, Ellington AD, Letsinger RL (1996) Incorporation of a non-nucleotide bridge into hairpin oligonucleotides capable of high-affinity binding to the REV protein of HIV-1. Biochemistry 35: 5339–5344
Nesbitt S, Hegg LA, Fedor MJ (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis. Chem Biol 4: 619–630
Noller HF, Hoffarth V, Zimniak L (1992) Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256: 1416–1419
Osborne SE, Matsumura I, Ellington AD (1997) Aptamers as therapeutic and diagnostic reagents: problems and prospects. Curr Opin Chem Biol 1: 5–9
Osborne SE, Volker S, Stevens SY, Glick KJ (1996) Design, synthesis and analysis of disulfide cross-linked DNA duplexes. J Am Chem Soc 118: 11993–12003
Otto S, Bertoncin F, Engberts JBFN (1996) Lewis acid catalysis of Diels-Alder reactions in water. J Am Chem Soc 118: 7702–7707
Otto S, Engberts JBFN (1995) Lewis acid catalysis of Diels-Alder reactions in water. Tetrahedron Lett. 36: 2645–2648
Pan T, Uhlenbeck OC (1992) In vitro selection of RNAs that undergo autolytic cleavage with Pb’’. Biochemistry 31: 3887–3895
Peebles CL, Perlman PS, Mecklenburg KL, Petrillio ML, Tabor JH, Jarell KA, Cheng H-L (1986) A self-splicing RNA excises an intron lariat. Cell 44: 213–223
Prody GA, Bakos JT, Buzayan JM, Schneider IR, Bruening G (1986) Autolytic processing of dimeric plant virus satellite RNA. Science 231: 1577–1580
Prudent JR, Uno T, Schultz PG (1994) Expanding the scope of RNA catalysis. Science 264: 1924–1927
Pyle AM (1993) Ribozymes: a distinct class of metalloenzymes. Science 261: 709–714.
Roth A, Breaker RR (1998) An amino acid as cofactor for a catalytic polynucleotide. Proc Natl Acad Sci USA 95: 6027–6031
Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94: 4262–4266
Sassanfar M, Szostak JW (1993) An RNA motif that binds ATP. Nature 364: 550–553
Saville BJ, Collins RA (1990) A site-specific self cleavage reaction performed by a novel RNA in Neurospora Mitochondria. Cell 61: 685–696
Sharmeen L, Kuo MYP, Dinter-Gottlieb G, Taylor J (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62: 2674–2679
Smith D, Kirschenheuter GP, Charlton J, Guidot DM, Repine JE (1995) In vitro selection of RNA-based irreversible inhibitors of human neutrophil elastase. Chem Biol 2: 741–750
Suga H, Lohse PA, Szostak JW (1998) Structural and kinetic characterization of an acyl transferase ribozyme. J Am Chen Soc 120: 1151 - -1156
Symons RH (1992) Small catalytic RNAs. Annu Rev Biochem 61: 641–671
Tang J, Breaker RR (1997a) Rational design of allosteric ribozymes. Chem Biol 4: 453–459
Tang J, Breaker RR (1997b) Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. RNA 3: 914–925
Tang J, Breaker RR (1997b) Examination of the catalytic fitness of the hammerhead ribozyme by in vitro selection. RNA 3: 914–925
Tarasow TM, Tarasow SL, Eaton BE (1997) RNA-catalysed carbon-carbon bond formation. Nature 389: 54–57
Usman N, Beigelman L, McSwiggen JA (1996) Hammerhead ribozyme engineering. Curr Opin Struct Biol 1: 627–533
Walsh C (1979) In: Enzymatic Reaction Mechanisms. WH Freeman, New York, pp. 199–207
Wecker M, Smith D, Gold L (1996) In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide. RNA 2: 982–994
Wiegand TW, Janssen RC, Eaton BE (1997) Selection of RNA amide synthases. Chem Biol 4: 675–683
Williams KP, Bartel (1996) Hi vitro selection of Catalytic RNA. Nucleic Acids Molec Biol 10: 367–381.
Williams KP, Ciafre S, Tocchini-Valentini GP (1995) Selection of novel Mgt -dependent self-cleaving ribozymes. EMBO J 14: 4551–4557
Wilson C, Szostak JW (1995) In vitro evolution of a self-alkylating ribozyme. Nature 374: 777–782
Wright MC, Joyce GF (1997) Continuous in vitro evolution of catalytic function. Science 276: 614–617
Yarus M (1993) How many catalytic RNAs? Ions and the Cheshire cat conjecture. EASES J 7: 31–39
Zhang B, Cech TR (1997) Peptide bond formation by in vitro selected ribozymes. Nature 390: 96–100
Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM (1995) A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility. Cell 83: 529–538
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Breaker, R.R., Kurz, M. (1999). In Vitro Selection of Nucleic Acid Enzymes. In: Famulok, M., Winnacker, EL., Wong, CH. (eds) Combinatorial Chemistry in Biology. Current Topics in Microbiology and Immunology, vol 243. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-60142-2_8
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DOI: https://doi.org/10.1007/978-3-642-60142-2_8
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