A good appreciation of an RNA's function requires that we understand its secondary and tertiary structure. Thus, the elucidation of this structure from its sequence has broad applications in the study of RNA. Comparative sequence analysis is one method that has yielded accurate and biologically meaningful secondary and tertiary structure models. These models have largely been substantiated in experimental studies, and are now essential in our structural and functional perception of these RNAs. The amount of structural detail that can be deciphered with comparative analysis is proportional to the size and diversity of the sequence database(s), and directly related to the sophistication of the algorithms. Given this, it is important that our sequence collections be large, diverse, and accurate. It is equally important that our comparative methods be able to decipher structural information from the sequence databases. The purpose of this project is (1) to establish and maintain large and structural diverse databases of rRNA and group I intron structures, (2) develop and refine our comparative analysis techniques, and (3) apply these analysis tools to the issue of RNA structure. The overall project described here has general applications to several disciplines. The established databases are utilized by researchers studying the structure, function, and evolution of rRNA and group I intron structures. The development and refinement of the comparative methods are useful for computational biologists studying correlation analysis. And finally, the detained RNA structures that are inferred with comparative analysis will further our understanding of ribosomes and group I introns.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM048207-06
Application #
2459465
Study Section
Special Emphasis Panel (ZRG3-BBCA (01))
Project Start
1992-08-01
Project End
1998-07-31
Budget Start
1997-08-01
Budget End
1998-07-31
Support Year
6
Fiscal Year
1997
Total Cost
Indirect Cost
Name
University of Colorado at Boulder
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
City
Boulder
State
CO
Country
United States
Zip Code
80309
Gutell, R R; Cannone, J J; Shang, Z et al. (2000) A story: unpaired adenosine bases in ribosomal RNAs. J Mol Biol 304:335-54
Trust, T J; Logan, S M; Gustafson, C E et al. (1994) Phylogenetic and molecular characterization of a 23S rRNA gene positions the genus Campylobacter in the epsilon subdivision of the Proteobacteria and shows that the presence of transcribed spacers is common in Campylobacter spp. J Bacteriol 176:4597-609
Cech, T R; Damberger, S H; Gutell, R R (1994) Representation of the secondary and tertiary structure of group I introns. Nat Struct Biol 1:273-80
Ragan, M A; Bird, C J; Rice, E L et al. (1994) A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc Natl Acad Sci U S A 91:7276-80
Laferriere, A; Gautheret, D; Cedergren, R (1994) An RNA pattern matching program with enhanced performance and portability. Comput Appl Biosci 10:211-2
Gutell, R R (1994) Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res 22:3502-7
Gautheret, D; Konings, D; Gutell, R R (1994) A major family of motifs involving G.A mismatches in ribosomal RNA. J Mol Biol 242:1-8
Fan, M; Currie, B P; Gutell, R R et al. (1994) The 16S-like, 5.8S and 23S-like rRNAs of the two varieties of Cryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms. J Med Vet Mycol 32:163-80
Srikantha, T; Gutell, R R; Morrow, B et al. (1994) Partial nucleotide sequence of a single ribosomal RNA coding region and secondary structure of the large subunit 25 s rRNA of Candida albicans. Curr Genet 26:321-8
Damberger, S H; Gutell, R R (1994) A comparative database of group I intron structures. Nucleic Acids Res 22:3508-10

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