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Ribozymes pp 131–143Cite as

Structure-Based Search and In Vitro Analysis of Self-Cleaving Ribozymes

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 848))

Abstract

Detecting functional RNAs is increasingly accomplished through structure-based searches for patterns of conserved secondary structure. With large amounts of new sequencing data becoming available, there is a greater demand for efficient methods of identifying new RNAs. Here we present a method of identifying self-cleaving ribozymes and characterizing the in vitro activity.

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References

  1. Sharp, P. A. (2009) The centrality of RNA, Cell 136, 577–580.

    Article  PubMed  CAS  Google Scholar 

  2. Rivas, E., and Eddy, S. R. (2001) Noncoding RNA gene detection using comparative sequence analysis, BMC Bioinformatics 2, 8.

    Article  PubMed  CAS  Google Scholar 

  3. Doherty, E. A., and Doudna, J. A. (2000) Ribozyme structures and mechanisms, Annu Rev Biochem 69, 597–615.

    Article  PubMed  CAS  Google Scholar 

  4. Waters, L. S., and Storz, G. (2009) Regulatory RNAs in bacteria, Cell 136, 615–628.

    Article  PubMed  CAS  Google Scholar 

  5. Fedor, M. J., and Williamson, J. R. (2005) The catalytic diversity of RNAs, Nat Rev Mol Cell Biol 6, 399–412.

    Article  PubMed  CAS  Google Scholar 

  6. Cech, T. R. (2009) Evolution of biological catalysis: ribozyme to RNP enzyme, Cold Spring Harb Symp Quant Biol 74, 11–16.

    Article  PubMed  CAS  Google Scholar 

  7. Salehi-Ashtiani, K., and Szostak, J. W. (2001) In vitro evolution suggests multiple origins for the hammerhead ribozyme, Nature 414, 82–84.

    Article  PubMed  CAS  Google Scholar 

  8. Cech, T. R. (2002) Ribozymes, the first 20 years, Biochem Soc Trans 30, 1162–1166.

    Article  PubMed  CAS  Google Scholar 

  9. Bourdeau, V., Ferbeyre, G., Pageau, M., Paquin, B., and Cedergren, R. (1999) The distribution of RNA motifs in natural sequences, Nucleic Acids Res 27, 4457–4467.

    Article  PubMed  CAS  Google Scholar 

  10. de la Pena, M., and Garcia-Robles, I. (2010) Intronic hammerhead ribozymes are ultraconserved in the human genome, EMBO Rep 11, 711–716.

    Article  PubMed  Google Scholar 

  11. de la Pena, M., and Garcia-Robles, I. (2010) Ubiquitous presence of the hammerhead ribozyme motif along the tree of life, RNA 16, 1943–1950.

    Article  PubMed  Google Scholar 

  12. Webb, C. H., Riccitelli, N. J., Ruminski, D. J., and Luptak, A. (2009) Widespread occurrence of self-cleaving ribozymes, Science 326, 953.

    Article  PubMed  CAS  Google Scholar 

  13. Martick, M., Horan, L. H., Noller, H. F., and Scott, W. G. (2008) A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA, Nature 454, 899-U857.

    Article  PubMed  CAS  Google Scholar 

  14. Seehafer, C., Kalweit, A., Steger, G., Graf, S., and Hammann, C. (2011) From alpaca to zebrafish: hammerhead ribozymes wherever you look, RNA 17, 21–26.

    Article  PubMed  CAS  Google Scholar 

  15. Yao, Z. Z., Weinberg, Z., and Ruzzo, W. L. (2006) CMfinder - a covariance model based RNA motif finding algorithm, Bioinformatics 22, 445–452.

    Article  PubMed  CAS  Google Scholar 

  16. Bengert, P., and Dandekar, T. (2004) Riboswitch finder - a tool for identification of riboswitch RNAs, Nucleic Acids Research 32, W154-W159.

    Article  PubMed  CAS  Google Scholar 

  17. Turi, A., Loglisci, C., Salvemini, E., Grillo, G., Malerba, D., and D’Elia, D. (2009) Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining, BMC Bioinformatics 10.

    Google Scholar 

  18. Hofacker, I. L. (2003) Vienna RNA secondary structure server, Nucleic Acids Res 31, 3429–3431.

    Article  PubMed  CAS  Google Scholar 

  19. Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., and Schuster, P. (1994) Fast Folding and Comparison of Rna Secondary Structures, Monatsh Chem 125, 167–188.

    Article  CAS  Google Scholar 

  20. Laferriere, A., Gautheret, D., and Cedergren, R. (1994) An RNA pattern matching program with enhanced performance and portability, Comput Appl Biosci 10, 211–212.

    PubMed  CAS  Google Scholar 

  21. Riccitelli, N. J., and Luptak, A. (2010) Computational discovery of folded RNA domains in genomes and in vitro selected libraries, Methods 52, 133–140.

    Article  PubMed  CAS  Google Scholar 

  22. Wu, G., Wolf, J. B., Ibrahim, A. F., Vadasz, S., Gunasinghe, M., and Freeland, S. J. (2006) Simplified gene synthesis: a one-step approach to PCR-based gene construction, J Biotechnol 124, 496–503.

    Article  PubMed  CAS  Google Scholar 

  23. Chadalavada, D. M., Gratton, E. A., and Bevilacqua, P. C. (2010) The Human HDV-like CPEB3 Ribozyme Is Intrinsically Fast-Reacting, Biochemistry 49, 5321–5330.

    Article  PubMed  CAS  Google Scholar 

  24. Kibbe, W. A. (2007) OligoCalc: an online oligonucleotide properties calculator, Nucleic Acids Res 35, W43–46.

    Article  PubMed  Google Scholar 

  25. Doudna, J. A. (1997) Preparation of homogeneous ribozyme RNA for crystallization, Methods Mol Biol 74, 365–370.

    PubMed  CAS  Google Scholar 

  26. Salehi-Ashtiani, K., Luptak, A., Litovchick, A., and Szostak, J. W. (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene, Science 313, 1788–1792.

    Article  PubMed  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA

    Randi M. Jimenez & Andrej Lupták

Authors
  1. Randi M. Jimenez
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  2. Andrej Lupták
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Corresponding author

Correspondence to Andrej Lupták .

Editor information

Editors and Affiliations

  1. Department of Chemistry, Universität Konstanz, Universitätsstr. 10, Konstanz, 78457, Germany

    Jörg S. Hartig

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Jimenez, R.M., Lupták, A. (2012). Structure-Based Search and In Vitro Analysis of Self-Cleaving Ribozymes. In: Hartig, J. (eds) Ribozymes. Methods in Molecular Biology, vol 848. Humana Press. https://doi.org/10.1007/978-1-61779-545-9_9

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  • DOI: https://doi.org/10.1007/978-1-61779-545-9_9

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-544-2

  • Online ISBN: 978-1-61779-545-9

  • eBook Packages: Springer Protocols

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