Date of Award

Spring 1-1-2012

Document Type


Degree Name

Doctor of Philosophy (PhD)


Chemistry & Biochemistry

First Advisor

Rob Knight

Second Advisor

Robert Batey

Third Advisor

Michael Yarus

Fourth Advisor

Tommas Cech

Fifth Advisor

Jim A. Goodrich


RNA is a special type of molecule in the sense that it is an information carrier, and is also able to catalyze chemical reactions. It is consequently believed that RNA predated protein and DNA as a catalyst and information carrier in an "RNA World". A greater understanding of evolutionary and functional features of non-coding RNA is not only fundamental to elucidating the evolutionary mechanisms that give rise to RNA function, perhaps giving insight into the origin of life in an RNA World, but is necessary for the advancement of RNA biotechnology and RNA based therapeutics. Recent advancements in high-throughput sequencing technologies have provided the ability to study the function of non-coding RNAs at an unprecedented depth, producing millions to billions of sequences from a single experiment. This poses new challenges to researchers, as traditional biochemical and computational techniques are unable to scale to the massive amounts of data each experiment produces. In this work, I present new computational tools, methods, and their applications in the study of non-coding RNA evolution. I have assembled a gold standard set of non- coding RNA alignments that have been manually curated and aligned to their known 3d structures. These manual alignments address the need for RNA alignments with structural annotation that current automated alignment algorithms do not provide. Next, I present an application of alignments to the study of tRNA evolution. tRNAs, an integral part of the modern translation machinery, are believed to be poor phylogenetic markers. Using UniFrac to cluster genomes based on the collection of tRNAs they contain, I show that these tRNA trees are similar to trees constructed from rRNA from the same organisms, congruent with universal phylogeny. Finally, I describe a technique developed to simultaneously measure the dissociation constant (KD) of a pool of thousands of amino acid binding RNA aptamers obtained by in vitro selection, improving over the traditional laborious process of determining KD one sequence at a time.

Included in

Biochemistry Commons