Abstract

The objective of this project is to determine the three dimensional structure and physical properties of several commonly occurring RNA secondary structure motifs. Among the motifs to be examined are helices containing non-Watson Crick base pairs, and bulged bases, the loops of hairpin structures, and pseudoknots. High field NMR and x-ray crystallography will be the tools used. The structures in question are important components of all naturally occurring RNAs. RNAs serve essential roles as both substrates and catalysts in the gene expression pathway. The information gained should help us understand how these molecules perform their critical biological functions. The systems to be studied are: (1) the helix IV-V region of the 5S RNA from E. coli, which poses interesting questions about base mismatches and protein binding, (2) the pseudoknot structure at the 5' end of U2 RNA, an RNA essential for splicing reactions in eukaryotes, and (3) several purely synthetic RNAs that have simple loops sequences and secondary structure irregularities.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM041651-02
Application #
3299957
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1989-07-01
Project End
1992-06-30
Budget Start
1990-07-01
Budget End
1991-06-30
Support Year
2
Fiscal Year
1990
Total Cost
Indirect Cost

  Institution

Name
Yale University
Department
Type
Schools of Arts and Sciences
DUNS #
082359691
City
New Haven
State
CT
Country
United States
Zip Code
06520

  Publications

Schweisguth, D C; Chelladurai, B S; Nicholson, A W et al. (1994) Structural characterization of a ribonuclease III processing signal. Nucleic Acids Res 22:604-12
Schweitzer, B I; Mikita, T; Kellogg, G W et al. (1994) Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement. Biochemistry 33:11460-75
Szewczak, A A; Kellogg, G W; Moore, P B (1993) Assignment of NH resonances in nucleic acids using natural abundance 15N-1H correlation spectroscopy with spin-echo and gradient pulses. FEBS Lett 327:261-4
Szewczak, A A; Moore, P B; Chang, Y L et al. (1993) The conformation of the sarcin/ricin loop from 28S ribosomal RNA. Proc Natl Acad Sci U S A 90:9581-5
Kellogg, G W; Schweitzer, B I (1993) Two- and three-dimensional 31P-driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides. J Biomol NMR 3:577-95
Cheong, C; Moore, P B (1992) Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry 31:8406-14
White, S A; Nilges, M; Huang, A et al. (1992) NMR analysis of helix I from the 5S RNA of Escherichia coli. Biochemistry 31:1610-21
Szewczak, A A; Chan, Y L; Moore, P B et al. (1991) On the conformation of the alpha sarcin stem-loop of 28S rRNA. Biochimie 73:871-7
Szewczak, A A; Webster, K R; Spicer, E K et al. (1991) An NMR characterization of the regA protein-binding site of bacteriophage T4 gene 44 mRNA. J Biol Chem 266:17832-7
Szewczak, A A; White, S A; Gewirth, D T et al. (1990) On the use of T7 RNA polymerase transcripts for physical investigation. Nucleic Acids Res 18:4139-42