| Description |
The activity of RNA dependant protein kinase, PKR, in the interferon signaling system has been shown to lead to inhibition of cell growth in response to a viral infection. It has been hypothesized that it is possible to control the interaction of PKR with viral RNA's using small molecular intercalators such as acridine orange. I have performed a series of experiments to study the effects of acridine orange (an intercalator of RNA) on RNA-protein complexes. These experiments complement the work of a graduate student who has designed a series of experiments referred to as SELEX to choose RNAs which are sensitive to acridine orange. In my part of the project, I was able to show that the SELEX was in fact effective at screening those RNAs whose binding to protein is sensitive to acridine orange. The study has focused on four RN As: V Al, Clone 2, 2ACR, and 2A/N. V Al and Clone 2 were chosen randomly, they were used to study the behavior of a typical small RNA molecule in the presence and absence of acridine orange. 2 ACR is an RNA chosen in the SELEX for sensitivity to acridine orange. 2 AIN was chosen as a very insensitive RNA. For the two randomly selected RNAs (VAl and Clone 2), acridine was shown to increase the Kd concentration of RBD approximately by a factor of four. However, for 2ACR acridine shifted the Kd by factor of forty, approximately ten times the normal. Gel shifts with 2A/N showed that this RNA was more resistant to acridine than either Clone 2 or V Al. Furthermore, it was shown that 56% of 2A/N bound to RBD, while 51% bound in the presence of acridine orange and 50% bound in presence of acridine yellow. |
