Hudak, Katalin A.2015-08-282015-08-282015-04-212015-08-28http://hdl.handle.net/10315/30070The pokeweed antiviral protein (PAP) is an N-glycosidase that removes an adenine residue from the sarcin/ricin loop (SRL) of rRNA through a process called depurination. PAP has also been shown to depurinate the ORF of Rev RNA of HIV-1 in vivo without causing toxicity. The sequence and structure of Rev RNA that PAP interacts is identified and compared to the sarcin/ricin loop in order to describe the importance of RNA structure for PAP specificity. My results show that PAP binds to a short GGGAA sequence at the site of depurination of Rev RNA. Structural analysis reveals that the binding site is within a 15 nt hairpin pentaloop. The pentaloop contains a pseudo GNRA loop structure that swings G and A residues out of the hairpin, allowing PAP access to these purines for binding and depurination. These data provide new insight into the specificity of PAP to target an RNA.enAuthor owns copyright, except where explicitly noted. Please contact the author directly with licensing requests.BiochemistryMolecular biologyBiologyElectronic Thesis or Dissertation2015-08-28RNAProtein RNA interactionHIV-1BiochemistryPokeweed antiviral proteinPhytolacca americanaSarcin/Ricin loopRNA structure.