This proposal requests continued funding for ongoing studies of RNA pseudoknots, directed toward understanding the relationships between structure, stability, dynamics and function within this important and widespread RNA motif. The research plan focuses on the pseudoknots from the autoregulatory gene 32 mRNAs of T-even bacteriophages, and the frameshift-stimulating pseudoknots from the pathogenic retroviral gag-pro mRNA mu1 frameshift sites. The following experiments are proposed: 1) Multi-dimensional NMR spectroscopy will be used to determine the solution structure of the gag-pro frameshifting pseudoknot of mouse intracisternal A-particle (mIAP), complementing the applicant's recently published NMR investigations of the pseudoknot at the simian retrovirus gag-pro frameshift site; 2) Thermodynamics of folding of the bacteriophage and retroviral pseudoknots will be investigated using optical melting techniques and differential scanning calorimetry to define stability determinants; 3, 4) The conformational dynamics and kinetics of pseudoknot unfolding will be investigated using NMR-based and steady-state fluorescence spectroscopies. Results will indicate whether conformational switching occurs on a time scale which is compatible with translational elongation and therefore ribosomal frameshifting; 5) Fluorescence resonance energy transfer (FRET) spectroscopy will be used to compare the global flexibilities of the bacteriophage gene 32, MMTV and mIAP pseudoknots, as well as define the distribution of end-to-end distances compatible with the pseudoknot structures, thus providing a direct comparison of """"""""straight"""""""" pseudoknots with coaxial stems and the """"""""bent"""""""" pseudoknots that stimulate frameshifting at the retroviral gag-pro interface. In the case of the retroviral pseudoknots, results will provide insight into the requirements for stimulating a frameshift upon translation of mRNA by the ribosome, and may ultimately provide insight as to how to target the pseudoknot in order to interfere with its essential function.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
5R01AI040187-07
Application #
6532727
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Meegan, James M
Project Start
1996-08-01
Project End
2003-07-31
Budget Start
2002-08-01
Budget End
2003-07-31
Support Year
7
Fiscal Year
2002
Total Cost
$219,116
Indirect Cost
Name
Texas A&M University
Department
Biochemistry
Type
Schools of Earth Sciences/Natur
DUNS #
047006379
City
College Station
State
TX
Country
United States
Zip Code
77845
Stammler, Suzanne N; Cao, Song; Chen, Shi-Jie et al. (2011) A conserved RNA pseudoknot in a putative molecular switch domain of the 3'-untranslated region of coronaviruses is only marginally stable. RNA 17:1747-59
Grossoehme, Nicholas E; Li, Lichun; Keane, Sarah C et al. (2009) Coronavirus N protein N-terminal domain (NTD) specifically binds the transcriptional regulatory sequence (TRS) and melts TRS-cTRS RNA duplexes. J Mol Biol 394:544-57
Giedroc, David P; Cornish, Peter V (2009) Frameshifting RNA pseudoknots: structure and mechanism. Virus Res 139:193-208
Liu, Pinghua; Li, Lichun; Keane, Sarah C et al. (2009) Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. J Virol 83:12084-93
Li, Lichun; Kang, Hyojeung; Liu, Pinghua et al. (2008) Structural lability in stem-loop 1 drives a 5'UTR-3'UTR interaction in coronavirus replication. J Mol Biol 377:790-803
Tang, Xinyu; Thomas, Shawna; Tapia, Lydia et al. (2008) Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol 381:1055-67
Scott, Lincoln G; Hennig, Mirko (2008) RNA structure determination by NMR. Methods Mol Biol 452:29-61
Liu, Pinghua; Li, Lichun; Millership, Jason J et al. (2007) A U-turn motif-containing stem-loop in the coronavirus 5'untranslated region plays a functional role in replication. RNA 13:763-80
Cornish, Peter V; Stammler, Suzanne N; Giedroc, David P (2006) The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical. RNA 12:1959-69
Liu, Pinghua; Millership, Jason J; Li, Lichun et al. (2006) A previously unrecognized UNR stem-loop structure in the coronavirus 5' untranslated region plays a functional role in replication. Adv Exp Med Biol 581:25-30

Showing the most recent 10 out of 32 publications