THOSE WHO KNOW, DO; THOSE WHO UNDERSTAND, TEACH: A COMPREHENSIVE STUDY AND PRACTICUM ON THE STRUCTURE, THERMAL STABILITY, AND DYNAMICS OF RNA MOLECULES

Abstract

DNA and RNA are the genetic materials of all living organisms. Due to exogenous and endogenous factors, they are constantly damaged. Because of this, we have repair mechanisms to fix such damage. One such instance is DNA base excision repair (BER), whereby the damaged nucleotide base is excised, leaving an intermediate apurinic/apyrimidinic site, also known as an abasic site. While abasic sites also exist on RNA, research has primarily focused on abasic sites in DNA. RNA abasic sites were previously thought to be rare, but they are now known to exist more frequently than previously believed. Additionally, it was discovered that apurinic/apyrimidinic endonuclease 1 (APE1) can cleave abasic sites in both DNA and RNA. However, the rates of cleavage vary greatly, with the abasic RNA cleavage rate being much slower. Probing the thermodynamics and structure of abasic RNA will further our understanding of the molecular basis for these observed differences. Knowledge of the structure of abasic RNA will lay the foundation for understanding the role of abasic RNA in cellular processes.In addition to studying the structure and dynamics of RNA abasic sites, we have also investigated the dynamics of the HIV-2 TAR RNA element, as there is a gap in knowledge about HIV-2 compared to HIV-1. A more comprehensive dynamics profile of the HIV-2 TAR RNA element will aid further studies on potential drug development for HIV-2. Finally, using the HIV-2 TAR RNA element, we have developed a practicum to teach students about NMR spectroscopy of RNA, as well as the importance of RNA research. In the practicum, students will learn NMR theory, complete structural NMR data analysis to determine partial RNA residue assignments and analyze NMR dynamics data to assess the longitudinal relaxation rate constant (R1). The goal is to expose undergraduate students to graduate-level concepts, which will challenge them, build their technical skills, and provide a better understanding of the capabilities of NMR spectroscopy.