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. 1985 Oct 11;13(19):6919–6936. doi: 10.1093/nar/13.19.6919

Investigation of the tertiary folding of Escherichia coli 16S RNA by in situ intra-RNA cross-linking within 30S ribosomal subunits.

J Atmadja, R Brimacombe, H Blöcker, R Frank
PMCID: PMC322013  PMID: 2997731

Abstract

Intra-RNA cross-links were introduced into E. coli 30S ribosomal subunits by mild ultraviolet irradiation. The subunits were partially digested with cobra venom nuclease, followed in some cases by a second partial digestion with ribonuclease H in the presence of the hexanucleotide d-(CTTCCC). The cross-linked RNA complexes were separated by two-dimensional gel electrophoresis and the sites of cross-linking analysed by our published procedures. Tertiary structural cross-links in the 16S RNA were identified between positions 31 and 48, between oligonucleotides 1090-1094 and 1161-1164, and between oligonucleotides 1125-1127 and 1280-1281. The first of these imposes a rigid constraint on the relative orientations of helices 3 and 4 of the 16S secondary structure. A further tertiary cross-link (which could not be precisely localised) was found between regions 1-72 and 1020-1095, and secondary structural cross-links were identified between positions 497 and 545-548, and positions 1238-1240 and 1298.

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Selected References

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

  1. Brimacombe R., Maly P., Zwieb C. The structure of ribosomal RNA and its organization relative to ribosomal protein. Prog Nucleic Acid Res Mol Biol. 1983;28:1–48. doi: 10.1016/s0079-6603(08)60081-1. [DOI] [PubMed] [Google Scholar]
  2. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A. 1978 Oct;75(10):4801–4805. doi: 10.1073/pnas.75.10.4801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chattopadhyaya J. B., Reese C. B. Chemical synthesis of tridecanucleoside dodecaphosphate sequence of SV40 DNA. Nucleic Acids Res. 1980 May 10;8(9):2039–2053. doi: 10.1093/nar/8.9.2039. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Darlix J. L. Stimultaneous purification of Escherichia coli termination factor rho, RNAase III and RNAase H. Eur J Biochem. 1975 Feb 21;51(2):369–376. doi: 10.1111/j.1432-1033.1975.tb03937.x. [DOI] [PubMed] [Google Scholar]
  5. Donis-Keller H. Site specific enzymatic cleavage of RNA. Nucleic Acids Res. 1979 Sep 11;7(1):179–192. doi: 10.1093/nar/7.1.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Expert-Bezançon A., Milet M., Carbon P. Precise localization of several covalent RNA-RNA cross-link in Escherichia coli 16S RNA. Eur J Biochem. 1983 Nov 2;136(2):267–274. doi: 10.1111/j.1432-1033.1983.tb07737.x. [DOI] [PubMed] [Google Scholar]
  7. Glotz C., Zwieb C., Brimacombe R., Edwards K., Kössel H. Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes. Nucleic Acids Res. 1981 Jul 24;9(14):3287–3306. doi: 10.1093/nar/9.14.3287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Mankin A. S., Skripkin E. A., Chichkova N. V., Kopylov A. M., Bogdanov A. A. An enzymatic approach for localization of oligodeoxyribonucleotide binding sites on RNA. Application to studying rRNA topography. FEBS Lett. 1981 Aug 31;131(2):253–256. doi: 10.1016/0014-5793(81)80378-x. [DOI] [PubMed] [Google Scholar]
  9. Möller K., Brimacombe R. Specific cross-linking of proteins S7 and L4 to ribosomal RNA, by UV irradiation of Escherichia coli ribosomal subunits. Mol Gen Genet. 1975 Dec 9;141(4):343–355. doi: 10.1007/BF00331455. [DOI] [PubMed] [Google Scholar]
  10. Stiege W., Glotz C., Brimacombe R. Localisation of a series of intra-RNA cross-links in the secondary and tertiary structure of 23S RNA, induced by ultraviolet irradiation of Escherichia coli 50S ribosomal subunits. Nucleic Acids Res. 1983 Mar 25;11(6):1687–1706. doi: 10.1093/nar/11.6.1687. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Stiege W., Zwieb C., Brimacombe R. Precise localisation of three intra-RNA cross-links in 23S RNA and one in 5S RNA, induced by treatment of Escherichia coli 50S ribosomal subunits with bis-(2-chloroethyl)-methylamine. Nucleic Acids Res. 1982 Nov 25;10(22):7211–7229. doi: 10.1093/nar/10.22.7211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Thompson J. F., Hearst J. E. Structure of E. coli 16S RNA elucidated by psoralen crosslinking. Cell. 1983 Apr;32(4):1355–1365. doi: 10.1016/0092-8674(83)90316-1. [DOI] [PubMed] [Google Scholar]
  13. Turner S., Noller H. F. Identification of sites of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen cross-linking in Escherichia coli 23S ribosomal ribonucleic acid. Biochemistry. 1983 Aug 16;22(17):4159–4164. doi: 10.1021/bi00286a026. [DOI] [PubMed] [Google Scholar]
  14. Turner S., Thompson J. F., Hearst J. E., Noller H. F. Identification of a site of psoralen crosslinking in E. coli 16S ribosomal RNA. Nucleic Acids Res. 1982 May 11;10(9):2839–2849. doi: 10.1093/nar/10.9.2839. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Vasilenko S. K., Ryte V. C. [Isolation of highly purified ribonuclease from cobra (Naja oxiana) venom]. Biokhimiia. 1975 May-Jun;40(3):578–583. [PubMed] [Google Scholar]
  16. Vassilenko S. K., Carbon P., Ebel J. P., Ehresmann C. Topography of 16 S RNA in 30 S subunits and 70 S ribosomes accessibility to cobra venom ribonuclease. J Mol Biol. 1981 Nov 15;152(4):699–721. doi: 10.1016/0022-2836(81)90123-6. [DOI] [PubMed] [Google Scholar]
  17. Volckaert G., Fiers W. Micro thin-layer techniques for rapid sequence analysis of 32P-labeled RNA: double digestion and pancreatic ribonuclease analyses. Anal Biochem. 1977 Nov;83(1):228–239. doi: 10.1016/0003-2697(77)90531-0. [DOI] [PubMed] [Google Scholar]
  18. Wollenzien P., Hearst J. E., Thammana P., Cantor C. R. Base-pairing between distant regions of the Escherichia coli 16 S ribosomal RNA in solution. J Mol Biol. 1979 Nov 25;135(1):255–269. doi: 10.1016/0022-2836(79)90351-6. [DOI] [PubMed] [Google Scholar]
  19. Wower I., Brimacombe R. The localization of multiple sites on 16S RNA which are cross-linked to proteins S7 and S8 in Escherichia coli 30S ribosomal subunits by treatment with 2-iminothiolane. Nucleic Acids Res. 1983 Mar 11;11(5):1419–1437. doi: 10.1093/nar/11.5.1419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Yuki A., Brimacombe R. Nucleotide sequences of Escherichia coli 16-S RNA associated with ribosomal proteins S7, S9, S10, S14 and S19. Eur J Biochem. 1975 Aug 1;56(1):23–34. doi: 10.1111/j.1432-1033.1975.tb02203.x. [DOI] [PubMed] [Google Scholar]
  21. Zwieb C., Brimacombe R. Localisation of a series of intra-RNA cross-links in 16S RNA, induced by ultraviolet irradiation of Escherichia coli 30S ribosomal subunits. Nucleic Acids Res. 1980 Jun 11;8(11):2397–2411. doi: 10.1093/nar/8.11.2397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Zwieb C., Brimacombe R. Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin-Dahlem, GFR. Nucleic Acids Res. 1979;6(5):1775–1790. doi: 10.1093/nar/6.5.1775. [DOI] [PMC free article] [PubMed] [Google Scholar]

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