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2005
LSU-HHMI Summer Undergraduate Research Program |
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Waqar Haque (University of Houston) and Fareed Aboul-ela, Biological Sciences
Stability of an RNA Stem Loop in the West Nile Virus RNA
The West Nile virus is a potentially lethal disease, and since being introduced to the U.S. in 1999, it has afflicted thousands of people each year. My project involved working with the penta-nucleotide sequence in the 3' stem-loop of the West Nile virus genome. I examined the folding in 2 different sequences of the mRNA transcript of the 3' stem loop. One of the mutants involved flipping a six nucleotide sequence that contained the flavivirus-conserved penta-nucleotide sequence. This mutation eliminated RNA replication. I observed the folding of the mRNA sequence of the entire West Nile Virus gene sequence, the 3' stem loop of the mutant, and the 3' stem loop of the wild type. Later, I did temperature folding experiments. This way, I was able to determine the conformation of the mRNA secondary structure at different temperatures, elucidating the stability of the 3' stem-loop. The temperature experiments showed the WNV mutant sequence to be less stable than the WNV wild type. The NMR experiments proved that there is a three dimensional structural difference between the WNV mutant and wild type, leading to the elimination of RNA replication.
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