RNA self-ligation: From oligonucleotides to full length ribozymes

Biochimie

Volumn 94, Issue 7, 2012, Pages 1457-1463

  Gwiazda, Slawomir ^a   Salomon, Kristina ^a   Appel, Bettina ^a   Müller, Sabine ^a  

^a UNIVERSITY OF GREIFSWALD   (Germany)

Author keywords

Cyclic phosphate; RNA ligation; RNA world; Self organization; Self replication

Indexed keywords

PHOSPHODIESTERASE; RIBOZYME; RNA; SHORT HAIRPIN RNA;

ARTICLE; CHEMICAL BOND; MOLECULAR INTERACTION; PROTEIN SECONDARY STRUCTURE; RNA CONFORMATION; RNA STRUCTURE; TEMPERATURE;

BASE SEQUENCE; BIOCATALYSIS; COMPUTATIONAL BIOLOGY; NUCLEIC ACID CONFORMATION; OLIGORIBONUCLEOTIDES; PHOSPHATES; POLYMERIZATION; RNA, CATALYTIC; TEMPERATURE;

EID: 84861606024     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2012.03.015     Document Type: Article

References (33)

1. G. Witzany The agents of natural genome editing J. Mol. Cell. Biol. 3 2011 181 189
2. J.L. Shim, R. Lohrmann, and L.E. Orgel Poly(U)-directed transamidation between adenosine 5′-phosphorimidazolide and 5′-phosphoadenosine 2′(3′)-glycine ester J. Am. Chem. Soc. 96 1974 5283 5284
3. W. Huang, and J.P. Ferris Synthesis of 35-40mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world Chem. Commun. 12 2003 1458 1459
4. W.K. Johnston, P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension Science 292 2001 1319 1325
5. G. von Kiedrowski A self-replicating hexadeoxynucleotide Angew. Chem. Int. Ed. 25 1986 932 935
6. N. Paul, and G.F. Joyce A self-replicating ligase ribozyme Proc. Natl. Acad. Sci. U S A 99 2002 12733 12740
7. D.E. Kim, and G.F. Joyce Cross-catalytic replication of an RNA ligase ribozyme Chem. Biol. 11 2004 1505 1512
8. T.A. Lincoln, and G.F. Joyce Self-sustained replication of an RNA enzyme Science 323 2009 1229 1232
9. B.J. Lam, and G.F. Joyce Autocatalytic aptazymes enable ligand-dependent exponential amplification of RNA Nat. Biotech. 27 2009 288 292
10. B.J. Lam, and G.F. Joyce An isothermal system that couples ligand-dependent catalysis to ligand-independent exponential amplification J. Am. Chem. Soc. 133 2011 3191 3197
11. R. Rohatgi, D.P. Bartel, and J.W. Szostak Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation J. Am. Chem. Soc. 118 1996 3332 3339
12. P.A. Monnard, A. Kanavarioti, and D.W. Deamer Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases J. Am. Chem. Soc. 125 2003 13734 13740
13. S.R. Vogel, C. Deck, and C. Richert Accelerating chemical replication steps of RNA involving activated ribonucleotides and downstream-binding elements Chem. Commun. 39 2005 4922 4924
14. C. Deck, M. Jauker, and C. Richert Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA Nat. Chem. 3 2011 603 608
15. M.W. Powner, B. Gerland, and J.D. Sutherland Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Nature 459 2009 171 172
16. M.W. Powner, J.D. Sutherland, and J.W. Szostak Chemoselective multicomponent one-pot assembly of purine precursors in water J. Am. Chem. Soc. 132 2010 16677 16688
17. S. Pieper, S. Vauléon, and S. Müller RNA self-processing towards changed topology and sequence oligomerization Biol. Chem. 388 2007 743 746
18. A. Feldstein, J.M. Buzayan, and G. Bruening Two sequences participating in the autolytic processing of satellite tobacco ringspot virus complementary RNA Gene 82 1989 53 61
19. A. Hampel, and R. Tritz RNA catalytic properties of the minimum (-)sTRSV sequence Biochemistry 28 1989 4929 4933
20. S.M. Nesbitt, H.A. Erlacher, and M.J. Fedor The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects J. Mol. Biol. 286 1999 1009 1024
21. R. Welz, K. Bossmann, C. Klug, C. Schmidt, H.-J. Fritz, and S. Müller Site-directed alteration of RNA sequence mediated by an engineered twin ribozyme Angew. Chem. Int. Ed. 42 2003 2424 2427
22. S.A. Ivanov, S. Vauléon, and S. Müller Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units FEBS J. 27 2005 4464 4474
23. S. Vauléon, S.A. Ivanov, S. Gwiazda, and S. Müller Site-specific fluorescent and affinity labeling of RNA mediated by an engineered twin ribozyme ChemBioChem 6 2005 2158 2162
24. I. Drude, S. Vauléon, and S. Müller Twin ribozyme mediated removal of nucleotides from an internal RNA site Biochem. Biophys. Res. Commun. 363 2007 24 29
25. C. Schmidt, R. Welz, and S. Müller RNA double cleavage by a hairpin-derived twin ribozyme Nucleic Acids Res. 28 2000 886 894
26. R. Welz, and S. Müller 5-(Benzylmercapto)-1H-tetrazole as activator for 2′-O-TBDMS phosphoramidite building blocks in RNA synthesis Tetrahedron Lett. 43 2002 795 797
27. N. Rublack, H. Nguyen, B. Appel, D. Springstubbe, D. Strohbach, and S. Müller Synthesis of specifically modified oligonucleotides for application in structural and functional analysis of RNA article ID 805253 J. Nucleic Acids 2011 19 doi: 10.4061/2011/805253
28. J. Haseloff, and W.L. Gerlach Sequences required for self-catalyzed cleavage of the satellite RNA of tobacco ringspot virus Gene 82 1989 43 52
29. A. Berzal-Herranz, S. Joseph, B.M. Chowrira, S.E. Butcher, and J.M. Burke Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme EMBO J. 12 1993 2567 2573
30. S. Müller, B. Appel, T. Krellenberg, and S. Petkovic The many faces of the hairpin ribozyme: structural and functional variants of a small catalytic RNA IUBMB Life 64 2012 36 47
31. R. Ohmori, H. Saito, Y. Ikawa, Y. Fujita, and T. Inoue Self-replication reactions dependent on tertiary interaction motifs in an RNA ligase ribozyme J. Mol. Evol. 73 2011 221 229
32. P. Yin, H.M.-T. Choi, C.R. Calvert, and N.A. Pierce Programming biomolecular self-assembly pathways Nature 451 2008 318 322
33. N.C. Seeman Nanomaterials based on DNA Annu. Rev. Biochem. 79 2010 65 87