Predicting U-turns ribosomal RNA with comparative sequence analysis

Journal of Molecular Biology

Volumn 300, Issue 4, 2000, Pages 791-803

  Gutell, Robin R ^a   Cannone, Jamie J ^a   Konings, Danielle ^b   Gautheret, Daniel ^c  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c CNRS Aix Marseille University   (France)

Author keywords

Comparative sequence analysis; Ribosomal RNA; Tertiary interactions; U turns

Indexed keywords

RIBOSOME RNA;

ARTICLE; BASE PAIRING; DNA FLANKING REGION; GENE FUNCTION; MOLECULAR MODEL; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS;

EID: 0034697987     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.3900     Document Type: Article

References (51)

1. Structure of the S15,S6,S18-rRNA complex: Assembly of the 30 S ribosome central domain
2. The uridine in 'U-turn': Contributions to tRNA-ribosomal binding
3. Singly and bifurcated hydrogen-bonded base-pairs in trna anticodon hairpins and ribozymes
4. Identity and geometry of a base triple in 16 S rRNA determined by comparative sequence analysis and molecular modeling
5. Placement of protein and RNA structures into a 5 Å resolution map of the 50 S ribosomal subunit
6. Comparative analysis of ribonuclease P RNA using gene sequences from natural microbial populations reveals tertiary structural elements
7. Solution structure of the conserved 16 S-like ribosomal RNA UGAA tetraloop
8. Crystal structure of a group I ribozyme domain: Principles of RNA packing
9. X-ray crystal structures of 70 S ribosome functional complexes
10. Crystal structure of a conserved ribosomal protein-RNA complex
11. Crystal structure of the ribosomal RNA domain essential for binding elongation factors
12. Frequent use of the same tertiary motif by self folding RNAs
13. Identification of an RNA-protein bridge spanning the ribosomal subunit interface
14. The three-dimensional folding of ribosomal RNA; localization of a series of intra-RNA cross-links in 23 S RNA induced by treatment of Escherichia coli 50 S ribosomal subunits with bis-(2-chloroethyl)-methylamine
15. Structural features of a six-nucleotide RNA hairpin loop found in ribosomal RNA
16. Antisense RNA regulation in prokaryotes: Rapid RNA/RNA interaction facilitated by a general U-turn loop structure
17. Inferring the conformation of RNA base-pairs and triples from patterns of sequence variation
18. In vitro methylation of Escherichia coli 16 S rRNA by tRNA (m5u54)-methyltransferase
19. Collection of small subunit (16 S and 16 S-like) ribosomal RNA structures: 1994
20. Comparative sequence analysis and the structure of 16 S and 23 S rRNA
21. Higher order structure in ribosomal RNA
22. A compilation of large subunit (23 S and 23 S-like) ribosomal RNA structures: 1993
23. Lessons from an evolving rRNA:16 S and 23 S rRNA structures from a comparative perspective
24. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
25. Structure of a hexanucleotide RNA hairpin loop conserved in ribosomal RNAs
26. Involvement of a GNRA tetraloop in long range RNA tertiary interactions
27. GNRA tetraloops make a U-turn
28. The phylogenetically conserved doublet tertiary interaction in domain III of the large subunit rRNA is crucial for ribosomal protein binding
29. In vivo determination of RNA structure-function relationships: Analysis of the 790 loop in ribosomal RNA
30. A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAs
31. Nucleotides in 23 S rRNA protected by the association of 30 S and 50 S ribosomal subunits
32. Interaction of tRNA with 23 S rRNA in the ribosomal A, P, and E sites
33. Intermediate states in the movement of transfer MA in the ribosome
34. GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain
35. Three-dimensional structure of a hammerhead ribozyme
36. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
37. Dynamics of in vitro assembly of 16 S rRNA into 30 S ribosomal subunits
38. Covalent crosslinking of tRNA1Val to 16 S RNA at the ribosomal P site: Identification of crosslinked residues
39. HIV-1 a-rich RNA loop mimics the tRNA anticodon structure
40. Structural domains of transfer RNA molecules
41. Sequence requirement for the hammerhead ribozyme self cleavage reaction
42. Compilation of tRNA sequences and sequences of tRNA genes
43. The structure of an essential splicing element: Stem loop IIa from yeast U2 snRNA
44. Localisation of a series of intra-RNA cross-links in the secondary and tertiary structure of 23 S RNA, induced by ultraviolet irradiation of escherichia coli 50 S ribosomal subunits
45. Investigation of the tertiary folding of Escherichia coli ribosomal RNA by intra-RNA cross-linking in vivo
46. Three-dimensional structure of a transfer RNA in two crystal forms
47. The sarcin/ricin loop, a modular RNA
48. Pseudoknot in the central domain of small subunit ribosomal RNA is essential for translation
49. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
50. A detailed view of a ribosomal active site: The structure of the L11-RNA complex
51. Architecture of ribosomal RNA: Constraints on the sequence of 'tetra-loops'