THE DEVELOPMENT AND APPLICATION OF SITE-SELECTIVELY ISOTOPICALLY LABELED NUCLEOTIDES TO PROBLEMS IN NMR SPECTROSCOPY:STRUCTURAL INSIGHTS INTO THE EPSILON RNA AND TARGET COMPOUND INTERACTIONS

Abstract

RNA plays a central role in a multitude of cellular processes. Understanding the complex interplay between its structure and function is a requisite for understanding these cellular roles mechanisms of action. Herein we describe technologies that we have developed to help better study RNA structure and function via NMR. Our development of site-selectively isotopically labeled pyrimidine and purine nucleotides has reduced spectral crowding, eliminated problems associated with scalar coupling, and led to novel assignment protocols. We have applied these labels to a 61-nucleotide viral RNA element, HBV-ε. This RNA is central Hepatitis B’s viral life cycle. Its NMR resonances have been assigned and initial structure calculations have begun to show how it interacts with compounds screened to bind to an internal six nucleotide bulge.