RNA aptamer inhibitors for DNA binding proteins

The main purpose of this thesis is to summarize my five years of doctoral research training focused on small RNA oligonucleotide molecules termed aptamers, selected against various DNA binding proteins. Chapter one serves as an introduction, explaining background information relevant to the crucial cellular process of gene expression and the central dogma of molecular biology. Chapter one goes to describe the proteins that were used as targets for our studies. We then explain the RNA in vitro selection technique utilized and optimized through our studies, and we briefly explain the characteristics of the products of these selections. Chapter 2 reviews ways in which RNA molecules serve to modulate gene expression in vivo, and how these natural examples inspired selection of new artificial RNA aptamers to regulate transcription factors. Chapter 3 explores the selection of RNA aptamers against three example DNA binding proteins, restriction endonucleases. Chapter 4 describes the steps taken to adapt the in RNA vitro selection technique to high-throughput technology utilizing robotics, automation, and next generation sequencing, and the results of selections done simultaneously against hundreds of human transcription factors (TF). Chapter 5 presents our published invited mini-review, an interesting case of an RNA aptamer selected against a G-protein coupled receptor. In Chapter 6 we conclude by summarizing current developments in our understanding of RNA as a regulatory molecule and then propose future experiments.