Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S13 using tethered Fe(II)

RNA

Volumn 2, Issue 6, 1996, Pages 597-602

  Heilek, Gabriele M ^a,b   Noller, Harry F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b AMGEN INC   (United States)

Author keywords

crosslinking; hydroxyl radical probing; ribosomal protein S13

Indexed keywords

CYSTEINE; EDETATE IRON; FERROUS ION; HYDROXYL RADICAL; RIBOSOME PROTEIN; RIBOSOME RNA;

ARTICLE; NONHUMAN; PRIORITY JOURNAL; RIBOSOME SUBUNIT; RNA CLEAVAGE; RNA PROBE;

BACTERIAL PROTEINS; CYSTEINE; EDETIC ACID; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HYDROGEN PEROXIDE; HYDROXYL RADICAL; IRON; MODELS, MOLECULAR; MOLECULAR PROBES; NUCLEIC ACID CONFORMATION; ORGANOMETALLIC COMPOUNDS; RIBOSOMAL PROTEINS; RNA, BACTERIAL; RNA, RIBOSOMAL; ULTRACENTRIFUGATION;

EID: 0029853765     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (16)

1. Bollen A, Heimark RL, Cozzone A, Traut RR, Hershey JWB. 1975. Cross-linking of initiation factor IF-2 to Escherichia coli 30 S ribosomal proteins with dimethylsuberimidate. J Biol Chem 250:4310-4314.
2. Brimacombe R, Greuer B, Mitchell P, Osswald M, Rinke-Appel J, Schüler D, Stade K. 1990. Three-dimensional structure and function of Escherichia coli 16S and 235 rRNA as studied by crosslinking techniques. In: Hill WE et al., eds. The ribosome: Structure, function and evolution. American Society of Microbiology, pp 93-106.
3. Capel MS, Engelman DM, Freeborn BR, Kjeldgaard M, Langer JA, Ramakrishnan V, Schindler DP, Schneider DK, Schoenborn BP, Sillers IY, Yabuki S, Moore PB. 1987. A complete mapping of the proteins in the small ribosomal subunit of Escherichia coli. Science 238:1403-1440.
4. Craven GR, Voynow P, Hardy SJ, Kurland CG. 1969. The ribosomal proteins of Escherichia coli. II. Chemical and physical characterization of the 30S ribosomal proteins. Biochemistry 8:2906-2915.
5. DeRiemer LH, Meares CF, Goodwin DA, Diamanti CJ. 1981. BLEDTA-II synthesis of a new tumor-visualizing derivative of CO(III)-bleomycin. J Laeled Compd Radiopharm 75:1517-1534.
6. Dijk J, Littlechild J, Garrett JA. 1977. The RNA binding properties of "native" protein-protein complexes isolated from the Escherichia coli ribosome. FEBS Lett 77:295-300.
7. Dreyer GB, Dervan PB. 1985. Sequence-specific cleavage of single-stranded DNA: oligodeoxynucleotide-EDTA X Fe(II). Proc Natl Acad Sci USA 82:968-972.
8. Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK. 1995. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Nature 376:441-444.
9. Hardy SJ, Kurland CG, Voynow P, Mora G. 1969. The ribosomal proteins of Escherichia coli. I. Purification of the 30S ribosomal proteins. Biochemistry 8:2897-2905.
10. Heilek G, Marusak R, Meares CF, Noller HF. 1995. Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc Natl Acad Sci USA 92:1113-1116.
11. Imlay JA, Chin SM, Linn S. 1988. Toxic DNA damage by hydrogen peroxide through the Fenton reaction in vivo and in vitro. Science 240:640-642.
12. Moazed D, Noller HF. 1986. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell 47:985-994.
13. Moazed D, Noller HF. 1990. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16S rRNA. J Mol Biol 211:135-145.
14. Moazed D, Stern S, Noller HF. 1986. Rapid chemical probing of conformations in 16S ribosomal RNA and 30S ribosomal subunits using primer extensions. J Mol Biol 187:399-416.
15. Osswald M, Greuer B, Brimacombe R, Stöffler G, Bäumert H, Fasold H. 1987. RNA-protein crosslinking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are crosslinked to proteins S3, S4, S5, S7, S8, S9, S11, S13, S19 and S21 by treatment with methyl p-azidophenyl acetimidate. Nucleic Acids Res 75:3221-3240.
16. Podkowinski J, Gornicki P. 1991. Neighbourhood of the central fold of the tRNA moleculae bound to the E. coli ribosome - affinity labeling studies with modified tRNAs carrying photoreactive probes attached to the dihydrouridine loop. Nucleic Acids Res 19: 801-808.