Abstract
The aim of this chapter is to provide reliable protocols for the study of nonenzymatic oligomerization reactions of ribonucleic acid and its analogs. Traditional radioactive labels are replaced by fluorescent dyes. Product analysis is either based on reversed-phase high-pressure (performance) liquid chromatography or on gel electrophoresis with on-line detection applying a deoxyribonucleic acid sequencer. Three examples of primer extensions are given, one of which demonstrates how the reaction of several primers may be monitored simultaneously.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Gestland, R. F. and Atkins, J. F. (1993) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Bartel, D. P. and Unrau, P. J. (1999) Constructing an RNA world. Trends Cell Biol. 9, M9–M13.
Joyce, G. F. (2002) The antiquity of RNA-based evolution. Nature 418, 214–221.
Cech, T. R. (1990) Self-cleaving and enzymic activity of an intervening RNA sequence from Tetrahymena. Angew. Chem. Int. Ed. Engl. 102, 745–755.
Altmann, S. (1990) Enzymic cleavage of RNA by RNA. Angew. Chem. Int. Ed. Engl. 102, 735–744.
Bartel, D. P., Doudna, J. A., Usman, N., and Szostak, J. W. (1991) Template-directed primer extension catalyzed by the Tetrahymena ribozyme. Mol. Cell. Biol. 11, 3390–3394.
Doudna, J. A., Usman, N., and Szostak, J. W. (1993) Ribozyme-catalyzed primer extension by trinucleotides: a model for the RNA-catalyzed replication of RNA. Biochemistry 32, 2111–2115.
Hager, A. J., Pollard, J. D. J., and Szostak, J. W. (1996) Ribozymes: aiming at RNA replication and protein synthesis. Chem. Biol. 3, 717–725.
Unrau, P. J. and Bartel, D. P. (1998) RNA-catalysed nucleotide synthesis. Nature 395, 260–263.
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, 1319–1324.
McGinness, K. E. and Joyce, G. F. (2003) In search of an RNA replicase ribozyme. Chem. Biol. 10, 5–14.
Reader, J. S. and Joyce, G. F. (2002) A ribozyme composed of only two different nucleotides. Nature 420, 841–844.
Rohategi, R., Bartel, D. P., and Szostak, J. W. (1996) Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc. 118, 3332–3329.
Rohategi, R., Bartel, D. P., and Szostak, J. W. (1996) Nonenzymatic, template directed ligation of oligoribonucleotides is highly regioselective for the formation of 3′-5′ phosphodiester bonds. J. Am. Chem. Soc. 118, 3340–3344.
Eschenmoser, A. and Dobler, M. (1992) Chemistry of-amino nitriles: 5. why pentose and not hexose nucleic acids? part I, introduction to the problem, conformational analysis of oligonucleotide single strands containing 2′,3′-dideoxyglucopyranosyl building blocks (homo-DNA), and reflections on the conformation of A-and B-DNA. Helv. Chim. Acta 75, 218–259.
Eschenmoser, A. (1999) Chemical etiology of nucleic acid structure. Science 284, 2118–2124.
Pitsch, S., Wendeborn, S., Jaun, B., and Eschenmoser, A. (1993) Why pentose-and not hexose-nucleic acids? part VII, pyranosyl-RNA(‘p-RNA’). Helv. Chim. Acta 76, 2161–2183
Pitsch, S., Krishnamurthy, R., Bolli, M., et al. (1995) Pyranosyl-RNA (p-RNA): base pairing selectivity and potential to replicate. Helv. Chim. Acta 78, 1621–1635.
Bolli, M., Micura, R., Pitsch, S., and Eschenmoser, A. (1997) Pyranosyl-RNA: further observations on replication: part 5. Helv. Chim. Acta 80, 1901–1951.
Bolli, M., Micura, R., and Eschenmoser, A. (1997) Pyranosyl-RNA: chiroselective self-assembly of base sequences by ligative oligomerization of tetranucleotide 2′,3′-cyclophosphate. Chem. Biol. 4, 309–321.
Schöing, K.-U., Scholz, P., Wu, X., et al. (2002) The α-L-threofuranosyl-(3′-2′)-oligonucleotide system (TNA’): synthesis and pairing properties. Helv. Chim. Acta 85, 4111–4153
Wu, X., Delgado, G., Krishnamurthy, R., and Eschenmoser, A. (2002) 2,6-Diaminopurine in TNA: effect on duplex stabilities and on the efficiency of template-controlled ligations. Org. Lett. 4, 1283–1286.
von Kiedrowski, G. (1986) A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Ed. Engl. 25, 932–934.
von Kiedrowski, G., Helbing, J., Wlotzka, B., et al. (1992) Parabolic reproduction and the origin of replication. Nachr. Chem. Tech. Lab. 40, 478–588.
Schöeborn, H., Bülle, J., and von Kiedrowski, G. (2001) Kinetic monitoring of self-replicating systems through measurement of fluorescence resonance energy transfer. Chembiochem 12, 922–927.
Müller, D., Pitsch, S., Kittaka, A., Wagner, E., and Eschenmoser, A. (1990) Chemistry of α-aminonitriles: Aldomerization of glycolaldehyde phosphate to rac-hexose 2,4,6-triphosphates and (in presence of formaldehyde) rac-pentose 2,4-diphosphates: rac-allose 2,4,6-triphosphate and rac-ribose 2,4-diphosphate are the main reaction products. Helv. Chim. Acta 73, 1410–1468.
Kozlov, I. A. and Orgel, L. E. (2000) Nonenzymatic template directed synthesis of RNA from monomers. Mol. Biol. 34, 781–789.
Wu, T. and Orgel, L. E. (1992) Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides. J. Am. Chem. Soc. 114, 317–322.
Kurz, M., Göel, K., Hartel, C., and Göel, M. W. (1997) Nonenzymatic oligomerization of ribonucleotides on guanosine-rich templates: supression of the self pairing of guanosine. Angew. Chem Int. Ed. Engl. 36, 842–845
Kurz, M., Göel, K., Hartel, C., and Göel, M. W. (1998) Acridine-labeled primers as tools for the study of nonenzymatic RNA oligomerization. Helv. Chim. Acta 81, 1156–1180.
Kozlov, I. A. and Orgel, L. E. (1999) Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues. Helv. Chim. Acta 82, 1799–1805.
Hartel, C. and Göel, M. W. (2000) Substitution of adenine by purine-2,6-diamin improves the nonenzymatic oligomerization of ribonucleotides on templates containing thymidine. Helv. Chim. Acta 83, 2541–2549.
Hey, M., Hartel, C., and Göel, M. W. (2003) Nonenzymatic oligomerization of ribonucleotides: toward in vitro selection experiments. Helv. Chim. Acta 86, 844–854.
Schmidt, J. G., Nielsen, P. E., and Orgel, L. E. (1997) Information transfer from peptide nucleic acids to RNA by template directed syntheses. Nucl. Acids Res. 25, 4797–4802.
Schmidt, J. G., Christensen, L., Nielsen, P. E., and Orgel, L. E. (1997) Information transfer from DNA to peptide nucleic acids by template-directed syntheses. Nucl. Acids Res. 25, 4792–4796.
Van Aerschot, A., Verheggen, I., Hendrix, C., and Herdewijn, P. (1995) 1,5-Anhydrohexitol nucleic acids, a new promising antisense construct. Angew. Chem. Int. Ed. Engl. 34, 1338–1339.
Hendrix, C., Rosenmeyer, H., de Bouvere, B., van Aerschot, A., Seela, F., and Herdewijn, P. (1997) 1′,5′-Anhydrohexitol oligonucleotides: hybridization and strand displacement with oligoribonucleotides, interaction with RNase H and HIV reverse transcriptase. Chem. Eur. J. 3, 1513–1520.
Allart, B., Khan, K., Rosemeyer, H., et al. (1999) D-altritol nucleic acids (ANA): hybridisation properties, stability, and initial structural Analysis. Chem. Eur. J. 5, 2424–2431.
Winter, H. D., Lescrinier, E., Aerschot, A. V., and Herdewijn, P. (1998) Molecular dynamics simulation to investigate differences in minor groove hydration of HNA/RNA hybrids as compared to HNA/DNA complexes. J. Am. Chem. Soc. 120, 5381–5394.
Kozlov, I. A., Politis, P. K., van Aerschot, A., Busson, R., Herdewijn, P., and Orgel, L. E. (1999) Nonenzymatic synthesis of RNA oligomers on hexitol nucleic acids templates: the importance of the A structure. J. Am. Chem. Soc. 121, 2653–2655.
Kozlov, I. A., de Bouvere, B., van Aerschot, A., Herdewijn, P., and Orgel, L. E. (1999) Efficient transfer of information from hexitol nucleic acids to RNA during nonenzymatic oligomerization. J. Am. Chem. Soc. 121, 5856–5859.
Kozlov, I. A., Zielinski, M., Allart, B., et al. (2000) Nonenzymatic template-directed reactions on altritol oligomers, preorganized analogs of oligonucleotides. Chem. Eur. J. 6, 151–155.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Humana Press Inc.
About this protocol
Cite this protocol
Hey, M., Göel, M. (2005). Nonenzymatic Template-Directed RNA Synthesis. In: Herdewijn, P. (eds) Oligonucleotide Synthesis. Methods in Molecular Biology, vol 288. Humana Press. https://doi.org/10.1385/1-59259-823-4:305
Download citation
DOI: https://doi.org/10.1385/1-59259-823-4:305
Publisher Name: Humana Press
Print ISBN: 978-1-58829-233-9
Online ISBN: 978-1-59259-823-6
eBook Packages: Springer Protocols