Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 Oct 25;18(20):6025–6029. doi: 10.1093/nar/18.20.6025

Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction.

D E Ruffner 1, O C Uhlenbeck 1
PMCID: PMC332400  PMID: 2235484

Abstract

A hammerhead domain of less than 50 nucleotides is responsible for a self-cleavage reaction in the replication of plant RNA pathogens. The hammerhead is composed of three helices joining at a central conserved core of 11 single stranded nucleotides. The core is believed to fold into a tertiary structure that provides functional groups for catalysis and to coordinate one or more divalent metal ions. In this study we use a phosphorothioate substitution interference assay to identify four phosphates in the conserved core which also play a role in the self-cleavage reaction.

Full text

PDF
6029

Images in this article

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Buzayan J. M., Feldstein P. A., Segrelles C., Bruening G. Autolytic processing of a phosphorothioate diester bond. Nucleic Acids Res. 1988 May 11;16(9):4009–4023. doi: 10.1093/nar/16.9.4009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Conway L., Wickens M. Analysis of mRNA 3' end formation by modification interference: the only modifications which prevent processing lie in AAUAAA and the poly(A) site. EMBO J. 1987 Dec 20;6(13):4177–4184. doi: 10.1002/j.1460-2075.1987.tb02764.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Forster A. C., Symons R. H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987 Apr 24;49(2):211–220. doi: 10.1016/0092-8674(87)90562-9. [DOI] [PubMed] [Google Scholar]
  4. Gish G., Eckstein F. DNA and RNA sequence determination based on phosphorothioate chemistry. Science. 1988 Jun 10;240(4858):1520–1522. doi: 10.1126/science.2453926. [DOI] [PubMed] [Google Scholar]
  5. Griffiths A. D., Potter B. V., Eperon I. C. Stereospecificity of nucleases towards phosphorothioate-substituted RNA: stereochemistry of transcription by T7 RNA polymerase. Nucleic Acids Res. 1987 May 26;15(10):4145–4162. doi: 10.1093/nar/15.10.4145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Haseloff J., Gerlach W. L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature. 1988 Aug 18;334(6183):585–591. doi: 10.1038/334585a0. [DOI] [PubMed] [Google Scholar]
  7. Holbrook S. R., Sussman J. L., Warrant R. W., Church G. M., Kim S. H. RNA-ligant interactions. (I) Magnesium binding sites in yeast tRNAPhe. Nucleic Acids Res. 1977 Aug;4(8):2811–2820. doi: 10.1093/nar/4.8.2811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jack A., Ladner J. E., Rhodes D., Brown R. S., Klug A. A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J Mol Biol. 1977 Apr 15;111(3):315–328. doi: 10.1016/s0022-2836(77)80054-5. [DOI] [PubMed] [Google Scholar]
  9. Jeffries A. C., Symons R. H. A catalytic 13-mer ribozyme. Nucleic Acids Res. 1989 Feb 25;17(4):1371–1377. doi: 10.1093/nar/17.4.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Koizumi M., Iwai S., Ohtsuka E. Cleavage of specific sites of RNA by designed ribozymes. FEBS Lett. 1988 Nov 7;239(2):285–288. doi: 10.1016/0014-5793(88)80935-9. [DOI] [PubMed] [Google Scholar]
  11. Latimer L. J., Hampel K., Lee J. S. Synthetic repeating sequence DNAs containing phosphorothioates: nuclease sensitivity and triplex formation. Nucleic Acids Res. 1989 Feb 25;17(4):1549–1561. doi: 10.1093/nar/17.4.1549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Milligan J. F., Groebe D. R., Witherell G. W., Uhlenbeck O. C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987 Nov 11;15(21):8783–8798. doi: 10.1093/nar/15.21.8783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Milligan J. F., Uhlenbeck O. C. Determination of RNA-protein contacts using thiophosphate substitutions. Biochemistry. 1989 Apr 4;28(7):2849–2855. doi: 10.1021/bi00433a016. [DOI] [PubMed] [Google Scholar]
  14. Perreault J. P., Wu T. F., Cousineau B., Ogilvie K. K., Cedergren R. Mixed deoxyribo- and ribo-oligonucleotides with catalytic activity. Nature. 1990 Apr 5;344(6266):565–567. doi: 10.1038/344565a0. [DOI] [PubMed] [Google Scholar]
  15. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796–806. doi: 10.1126/science.790568. [DOI] [PubMed] [Google Scholar]
  16. Quigley G. J., Teeter M. M., Rich A. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A. 1978 Jan;75(1):64–68. doi: 10.1073/pnas.75.1.64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Ruffner D. E., Dahm S. C., Uhlenbeck O. C. Studies on the hammerhead RNA self-cleaving domain. Gene. 1989 Oct 15;82(1):31–41. doi: 10.1016/0378-1119(89)90027-9. [DOI] [PubMed] [Google Scholar]
  18. Sampson J. R., Sullivan F. X., Behlen L. S., DiRenzo A. B., Uhlenbeck O. C. Characterization of two RNA-catalyzed RNA cleavage reactions. Cold Spring Harb Symp Quant Biol. 1987;52:267–275. doi: 10.1101/sqb.1987.052.01.032. [DOI] [PubMed] [Google Scholar]
  19. Uhlenbeck O. C. A small catalytic oligoribonucleotide. Nature. 1987 Aug 13;328(6131):596–600. doi: 10.1038/328596a0. [DOI] [PubMed] [Google Scholar]
  20. Vlassov V. V., Giegé R., Ebel J. P. Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur J Biochem. 1981 Sep;119(1):51–59. doi: 10.1111/j.1432-1033.1981.tb05575.x. [DOI] [PubMed] [Google Scholar]
  21. Waring R. B. Identification of phosphate groups important to self-splicing of the Tetrahymena rRNA intron as determined by phosphorothioate substitution. Nucleic Acids Res. 1989 Dec 25;17(24):10281–10293. doi: 10.1093/nar/17.24.10281. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES