Orientation of the tRNA anticodon in the ribosomal P-site: Quantitative footprinting with U33-modified, anticodon stem and loop domains

RNA

Volumn 5, Issue 9, 1999, Pages 1191-1199

  Ashraf, S Salman ^a,b   Guenther, Richard ^a   Agris, Paul F ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b Novalon Pharmaceutical Corporation   (United States)

Author keywords

Anticodon stem loops; Modified nucleosides; Quantitative footprinting; Ribosome

Indexed keywords

3 METHYLURIDINE; AMINO ACID; PHENYLALANINE TRANSFER RNA; RNA 16S; UNCLASSIFIED DRUG; URIDINE DERIVATIVE;

ANTICODON; ARTICLE; BINDING SITE; CHEMICAL REACTION KINETICS; CONTROLLED STUDY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; RIBOSOME; RNA ANALYSIS; RNA BINDING; RNA CONFORMATION; STRUCTURE ACTIVITY RELATION; TEMPERATURE DEPENDENCE;

ALDEHYDES; ANTICODON; ANTIVIRAL AGENTS; BASE SEQUENCE; DOSE-RESPONSE RELATIONSHIP, DRUG; GENETIC TECHNIQUES; KINETICS; MOLECULAR SEQUENCE DATA; MUTAGENS; RIBOSOMES; RNA, FUNGAL; RNA, RIBOSOMAL, 16S; RNA, TRANSFER; RNA, TRANSFER, PHE; SULFURIC ACID ESTERS; TEMPERATURE;

EID: 0032865754     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838299990933     Document Type: Article

References (24)

1. Agris PF, Malkiewicz A, Kraszewski A, Everett K, Nawrot B, Sochacka E, Jankowska J, Guenther R. 1995. Site-selected introduction of modified purine and pyrimidine ribonucleosides into RNA by automated phosphoramidite chemistry. Biochimie 77:125-134.
2. Ashraf SS, Ansari G, Guenther R, Sochacka E, Malkiewicz A, Agris PF. 1999. The uridine in "U-turn": Contributions to tRNA-ribosomal binding. RNA 5:503-511.
3. Banerjee AR, Turner DH. 1995. The time dependence of chemical modification reveals slow steps in the folding of a group I ribozyme. Biochemistry 34:6504-6512.
4. Barta A, Steiner G, Brosius J, Noller HF, Kuechler E. 1984. Identification of a site on 23S ribosomal RNA located at the peptidyl transferase center. Proc Natl Acad Sci USA 81:3607-3611.
5. Brenowitz M, Senear DF, Shea MA, Ackers GK. 1986. "Footprint" titrations yield valid thermodynamic isotherms. Proc Natl Acad Sci USA 83:8462-8466.
6. Doring T, Mitchell P, Osswald M, Bochkariov D, Brimacombe R. 1994. The decoding region of 16S RNA; a cross-linking study of the ribosomal A, P, and E sites using tRNA derivatized at position 32 in the anticodon loop. EMBO J 13:2677-2685.
7. Ericson G, Minchew P, Wollenzien P. 1995. Structural changes in base-paired region 28 in 16 S rRNA close to the decoding region of the 30 S ribosomal subunit are correlated to changes in tRNA binding. J Mol Biol 250:407-419.
8. Green R, Samaha RR, Noller HF. 1997. Mutations at nucleotides G2251 and U2585 of 23 S rRNA perturb the peptidyl transferase center of the ribosome. J Mol Biol 266:40-50.
9. Huttenhofer A, Noller HF. 1992. Hydroxyl radical cleavage of tRNA in the ribosomal P site. Proc Natl Acad Sci USA 89:7851-7855.
10. Moazed D, Noller HF. 1986. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47:985-994.
11. Moazed D, Noller HF. 1990. Binding of tRNA to the ribosomal A and P sites protects two distinct sets of nucleotides in 16 S rRNA. J Mol Biol 211:135-145.
12. Noller HF. 1993. tRNA-rRNA interactions and peptidyl transferase. FASEB J 7:87-89.
13. Noller HF, Hoffarth V, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-1419.
14. Osswald M, Doring T, Brimacombe R. 1995. The ribosomal neighborhood of the central fold of tRNA: Cross-links from position 47 of tRNA located at the A, P, or E site. Nucleic Acids Res 23:4635-4641.
15. Petri V, Brenowitz M. 1997. Quantitative nucleic acids footprinting: Thermodynamic and kinetic approaches. Curr Opin Biotechnol 8:36-44.
16. Podkowinski J, Gornicki P. 1989. Ribosomal proteins S7 and L1 are located close to the decoding site of E. coli ribosome: Affinity labeling studies with modified tRNAs carrying photoreactive probes attached adjacent to the 3′-end of the anticodon. Nucleic Acids Res 17:8767-8782.
17. 1Val to 16S RNA at the ribosomal P site: Identification of cross-linked residues. Proc Natl Acad Sci USA 79:5450-5454.
18. Phe anticodon arm to Escherichia coli 30 S ribosomes. J Mol Biol 167:103-117.
19. Sclavi B, Sullivan M, Chance MR, Brenowitz M, Woodson SA. 1998. RNA folding at millisecond intervals by synchrotron hydroxyl radical footprinting. Science 279:1940-1943.
20. Sergiev PV, Lavrik IN, Wlasoff VA, Dokudovskaya SS, Dontsova OA, Bogdanov AA, Brimacombe R. 1997. The path of mRNA through the bacterial ribosome: A site-directed cross-linking study using new photoreactive derivatives of guanosine and uridine. RNA 3:464-475.
21. von Ahsen U, Green R, Schroeder R, Noller HF. 1997. Identification of 2′-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome. RNA 3:49-56.
22. von Ahsen U, Noller HF. 1995. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 267:234-237.
23. Wallis MG, von Ahsen U, Schroeder R, Famulok M. 1995. A novel RNA motif for neomycin recognition. Chem Biol 2:543-552.
24. Woodson SA, Leontis NB. 1998. Structure and dynamics of ribosomal RNA. Curr Opin Struct Biol 8:294-300.