Site-specific Incorporation of p-Azido-L-phenylalanine for Photo-crosslinking Nucleic Acids

Abstract

Current methods for studying RNA binding proteins (RBPs) combine the use of ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) to analyze RNA-protein interactions. An underexplored alternative approach is using site-specific incorporation of photoactivatable non-canonical amino acids (ncAAs) to enhance the crosslinking efficiency of many CLIP protocols. This thesis describes the incorporation of the photo-crosslinking unnatural amino acid p-azido-L-phenylalanine (AzF) into the Hepatitis C Virus (HCV) non-structural protein 3 helicase (NS3h) for photo-crosslinking and in vitro analysis of the potential binding sites found within the HCV RNA genome. From the five potential sites identified from the NS3h crystal structure for AzF incorporation, two sites, E503AzF and Q580AzF, allowed for nucleic acid photo-crosslinking with fluorescently labelled DNA substrates. We further tested if these mutations adversely affected NS3h and binding activity through a molecular beacon helicase assay and fluorescence polarization methods. We found that E503AzF unexpectedly had a faster unwinding rate than wild type (WT) NS3h and managed to have a similar binding affinity to the tested DNA substrate. Finally, we found that there was a 5-fold increase in the photo-crosslinking efficiency of nucleic acids for E503AzF NS3h mutant compared to our WT NS3h at 254 nm UV light. We are currently working on methods for our CLIP-based protocol to ensure quality RNA footprint generation and purification from photo-crosslinked NS3h. Other work contained in this thesis consists of using Prevotella sp. P5-125 Cas13b (PspCas13b), a clustered regularly interspaced short palindromic repeats (CRISPR) RNA-targeting system, which has been previously shown to knockdown viral RNA and mRNA through designable guide CRISPR RNA (crRNA). Here we incorporated the photo-crosslinking ncAA AzF into PspCas13b to irreversibly bind the crRNA in an attempt to enhance knockdown efficiency and longevity of viral and mRNA targets. We were able to design a crRNA that produced significant knockdown targeting the luciferase mRNA of a luciferase rennilla reporter system. When targeting an HCV subgenomic replicon luciferase reporter system, knockdown was not observed. Additionally, the WT PspCas13b had photo-crosslinking to the bound crRNA and requires further optimization for future use.