Skip to main content
SpringerLink
Log in

What can the New Hammerhead Ribozyme Structures Teach us About Design?

  • Chapter
  • First Online:
RNA Technologies and Their Applications

Part of the book series: RNA Technologies ((RNATECHN))

Abstract

The hammerhead ribozyme is a small, self-cleaving genomic ribozyme whose substrate-targeting properties are quite flexible. It catalyzes a phosphodiester backbone cleavage reaction that can be exploited for antisense-type applications in which it is desirable to cleave the target RNA. To better understand the requirements for rational hammerhead ribozyme design, the natural history, secondary and tertiary structures, and reaction mechanism are reviewed in detail. Specifically, significant advances in our understanding of how the hammerhead ribozyme works have taken place since 2003, rendering previous assumptions about therapeutic hammerhead ribozyme design largely obsolete. The requirement for a tertiary contact between Stems I and II to be present in order to achieve a highly active ribozyme in vivo is described, and design requirements that enable straightforward incorporation of the tertiary contact are explicitly described. This analysis is only possible with crystal structures of two classes of full-length natural hammerhead ribozymes that became available in 2006 and 2008.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Blount KF, Uhlenbeck OC (2005) The structure–function dilemma of the hammerhead ribozyme. Annu Rev Biophys Biomol Struct 34:415–440

    Article  PubMed  CAS  Google Scholar 

  • Canny MD, Jucker FM, Kellogg E et al (2004) Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc 126:10848–10849

    Article  PubMed  CAS  Google Scholar 

  • Chi YI, Martick M, Lares M et al (2008) Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 6:e234

    Article  PubMed  Google Scholar 

  • Cochrane JC, Strobel SA (2008) Catalytic strategies of self-cleaving ribozymes. Acc Chem Res 41:1027–1035

    Article  PubMed  CAS  Google Scholar 

  • Dahm SC, Uhlenbeck OC (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30:9464–9469

    Article  PubMed  CAS  Google Scholar 

  • Dahm SC, Derrick WB, Uhlenbeck OC (1993) Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism. Biochemistry 32:13040–13045

    Article  PubMed  CAS  Google Scholar 

  • Fedor MJ (2009) Comparative enzymology and structural biology of RNA self-cleavage. Annu Rev Biophys 38:271–299

    Article  PubMed  CAS  Google Scholar 

  • Ferbeyre G, Bourdeau V, Pageau M et al (2000) Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank. Genome Res 10:1011–1019

    Article  PubMed  CAS  Google Scholar 

  • Ferbeyre G, Smith JM, Cedergren R (1998) Schistosome satellite DNA encodes active hammerhead ribozymes. Mol Cell Biol 18:3880–3888

    PubMed  CAS  Google Scholar 

  • Forster AC, Davies C, Sheldon CC et al (1988) Self-cleaving viroid and newt RNAs may only be active as dimers. Nature 334:265–267

    Article  PubMed  CAS  Google Scholar 

  • Guerrier-Takada C, Gardiner K, Marsh T et al (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849–857

    Article  PubMed  CAS  Google Scholar 

  • Han J, Burke JM (2005) Model for general acid-base catalysis by the hammerhead ribozyme: pH-activity relationships of G8 and G12 variants at the putative active site. Biochemistry 44:7864–7870

    Article  PubMed  CAS  Google Scholar 

  • Haseloff J, Gerlach WL (1989) Sequences required for self-catalysed cleavage of the satellite RNA of tobacco ringspot virus. Gene 82:43–52

    Article  PubMed  CAS  Google Scholar 

  • Khvorova A, Lescoute A, Westhof E et al (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10:708–712

    Article  PubMed  CAS  Google Scholar 

  • Kim SH, Suddath FL, Quigley GJ et al (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185:435–440

    Article  PubMed  CAS  Google Scholar 

  • Klug A, Ladner J, Robertus JD (1974) The structural geometry of co-ordinated base changes in transfer RNA. J Mol Biol 89:11–16

    Article  Google Scholar 

  • Kruger K, Grabowski PJ, Zaug AJ et al (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell 31:147–157

    Article  PubMed  CAS  Google Scholar 

  • De la Peña M, Gago S, Flores R (2003) Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 22:5561–5570

    Article  PubMed  Google Scholar 

  • Lee TS, Silva López C, Giambasu GM et al (2008) Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation. J Am Chem Soc 130:3053–3064

    Article  PubMed  CAS  Google Scholar 

  • Lee TS, Silva-López C, Martick M et al (2007) Insight into the role of Mg 2 in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation. J Chem Theory Comput 3:325–327

    Article  PubMed  CAS  Google Scholar 

  • Luzi E, Eckstein F, Barsacchi G (1997) The newt ribozyme is part of a riboprotein complex. Proc Natl Acad Sci USA 94:9711–9716

    Article  PubMed  CAS  Google Scholar 

  • Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126:309–320

    Article  PubMed  CAS  Google Scholar 

  • Martick M, Horan LH, Noller HF et al (2008a) A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature 454:899–902

    Article  PubMed  CAS  Google Scholar 

  • Martick M, Lee TS, York DM et al (2008b) Solvent structure and hammerhead ribozyme catalysis. Chem Biol 15:332–342

    Article  PubMed  CAS  Google Scholar 

  • McKay DB (1996) Structure and function of the hammerhead ribozyme: an unfinished story. RNA 2:395–403

    PubMed  CAS  Google Scholar 

  • Murray JB, Dunham CM, Scott WG (2002) A pH-dependent conformational change, rather than the chemical step, appears to be rate-limiting in the hammerhead ribozyme cleavage reaction. J Mol Biol 315:121–130

    Article  PubMed  CAS  Google Scholar 

  • Murray JB, Seyhan AA, Walter NG et al (1998a) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol 5:587–595

    Article  PubMed  CAS  Google Scholar 

  • Murray JB, Szöke H, Szöke A et al (2000) Capture and visualization of a catalytic RNA enzyme–product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol Cell 5:279–287

    Article  PubMed  CAS  Google Scholar 

  • Murray JB, Terwey DP, Maloney L et al (1998b) The structural basis of hammerhead ribozyme self-cleavage. Cell 92:665–673

    Article  PubMed  CAS  Google Scholar 

  • Nelson JA, Uhlenbeck OC (2006) When to believe what you see. Mol Cell 23:447–450

    Article  PubMed  CAS  Google Scholar 

  • Nelson JA, Uhlenbeck OC (2008) Hammerhead redux: does the new structure fit the old biochemical data? RNA 14:605–615

    Article  PubMed  CAS  Google Scholar 

  • Noller HF, Hoffarth V, Zimniak L (1992) Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416–1419

    Article  PubMed  CAS  Google Scholar 

  • Peracchi A, Beigelman L, Scott EC et al (1997) Involvement of a specific metal ion in the transition of the hammerhead ribozyme to its catalytic conformation. J Biol Chem 272:26822–26826

    Article  PubMed  CAS  Google Scholar 

  • Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372:68–74

    Article  PubMed  CAS  Google Scholar 

  • Prody GA, Bakos JT, Buzayan JM et al (1986) Autolytic processing of dimeric plant virus satellite RNA. Science 231:1577–580

    Article  PubMed  CAS  Google Scholar 

  • Pyle AM (1993) Ribozymes: a distinct class of metalloenzymes. Science 261:709–714

    Article  PubMed  CAS  Google Scholar 

  • Robertus JD, Ladner JE, Finch JT et al (1974) Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 250:546–551

    Article  PubMed  CAS  Google Scholar 

  • Scott WG (1999) RNA structure, metal ions, and catalysis. Curr Opin Chem Biol 3:705–710

    Article  PubMed  CAS  Google Scholar 

  • Scott WG (2002) Visualizing the structure and mechanism of a small nucleolytic ribozyme. Methods 28:302–306

    Article  PubMed  CAS  Google Scholar 

  • Scott WG, Finch JT, Klug A (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81:991–1002

    Article  PubMed  CAS  Google Scholar 

  • Scott WG, Martick M, Chi YI (2009) Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. Biochim Biophys Acta 1789:634–641

    Article  PubMed  CAS  Google Scholar 

  • Scott WG, Murray JB, Arnold JR et al (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274:2065–2069

    Article  PubMed  CAS  Google Scholar 

  • Stage-Zimmermann TK, Uhlenbeck OC (1998) Hammerhead ribozyme kinetics. RNA 4:875–889

    Article  PubMed  CAS  Google Scholar 

  • Steitz TA, Moore PB (2003) RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci 28:411–418

    Article  PubMed  CAS  Google Scholar 

  • Tedeschi L, Lande C, Cecchettini A et al (2009) Hammerhead ribozymes in therapeutic target discovery and validation. Drug Discov Today 14:776–783

    Article  PubMed  CAS  Google Scholar 

  • Uhlenbeck OC (1987) A small catalytic oligoribonucleotide. Nature 328:596–600

    Article  PubMed  CAS  Google Scholar 

  • Wang S, Karbstein K, Peracchi A et al (1999) Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate. Biochemistry 38:14363–14378

    Article  PubMed  CAS  Google Scholar 

  • Wedekind JE, McKay DB (1998) Crystallographic structures of the hammerhead ribozyme: relationship to ribozyme folding and catalysis. Annu Rev Biophys Biomol Struct 27:475–502

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA, University of California at Santa Cruz, 228 Sinsheimer Laboratories, Santa Cruz, CA, 95064, USA

    William G. Scott

Authors
  1. William G. Scott
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to William G. Scott .

Editor information

Editors and Affiliations

  1. Inst. Chemie und Biochemie, FU Berlin, Thielallee 63, Berlin, 14195, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Scott, W.G. (2010). What can the New Hammerhead Ribozyme Structures Teach us About Design?. In: Erdmann, V., Barciszewski, J. (eds) RNA Technologies and Their Applications. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12168-5_14

Download citation

Publish with us

Policies and ethics

Search

Navigation