Dynamics, Degradation, and Chemical Modification of Non-Coding RNA

Abstract

Our understanding of the function of RNA has grown significantly since the central dogma of molecular biology described RNA as a rudimentary conveyor of the genetic message. In the genomic era, we are beginning to learn the true depth and breadth of the non-coding (nc)RNA repertoire. A key attribute of RNA molecules is the conformational dynamics that they explore. Here, we have applied studies of structure, dynamics, and metal binding to models of helix 27 from 16S rRNA to elucidate the function of this important component of the ribosome. Our studies reveal the kinetic and thermodynamic framework within which this isolated helix undergoes secondary structure rearrangement. Both NMR and fluorescence techniques demonstrate millisecond exchange between the 885 and 888 conformations, defining an equilibrium constant close to one. Fluorescence studies also show that the antibiotic tetracycline interferes with this conformational exchange. Metal binding studies of helix 27 have confirmed data from ribosomal crystal structures and further correlated local and global metal binding features of this RNA. Another general attribute of RNA is its inherent lability. The great promise of a new class of therapeutics based on small interfering (si)RNA molecules and the RNA interference pathway has forced researchers to overcome the nucleolytic vulnerability of RNA molecules, primarily by introducing chemical modifications. Work in this thesis demonstrates that siRNA degradation in blood serum is asymmetric, where the guide strand is predisposed to efficient degradation due to differential stability of the terminal base pairs. We further show that a simple pattern of chemical modifications greatly stabilizes siRNAs in regions particularly susceptible to nuclease cleavage. We have shown that 21 and 24-nucleotide siRNA-like double-stranded RNAs are specifically protected in cell extract, a result which demonstrates intracellular siRNA stability and may help explain recent results suggesting that, once inside the cell, chemical modifications to siRNAs do not significantly increase the potency of the silencing effect. Taken together, the work presented in this thesis has helped to illuminate the function of important ncRNA molecules, furthering our understanding of how ncRNA contributes to the structural, catalytic, and regulatory landscape that defines the cellular lifecycle.