Abstract

Small RNA-based Therapeutics

John Burnett, Assistant Research Professor, Beckman Research Institute City of Hope

RNA-based therapeutics offer versatility and unique properties that make them attractive drug candidates. Our lab focuses on developing small interfering RNAs (siRNAs) and RNA aptamers as novel biological therapeutics. We are utilizing advanced technologies, including droplet digital PCR and Solexa deep sequencing, to improve the existing methods for studying RNA-based drugs. For our siRNA therapeutics, we use deep sequencing to understand how the 21-mer siRNAs and Dicer substrate siRNAs are processed and retained by the RNA interference machinery. From these studies, we have identified patterns of nucleotide removal and non-template addition to the 3’-ends of the siRNA guide strand. We are now exploring the effects of these modifications to the stability and potency of the siRNA guide strands. In addition to these studies, we are developing RNA aptamers through a well-established selection process known as SELEX. We have modified the SELEX protocol to utilize droplet digital PCR in place of open PCR in an effort to retain the diversity of the RNA library during selection. Additionally, we have incorporated Solexa deep sequencing into this protocol to characterize our RNA aptamer library after each selection to identify particular RNA sequence motifs that impart the desired aptamer binding properties.