Poster abstracts
Poster number 111 submitted by Dan Seith
Probing the role of guanine deprotonation in ribozyme mechanism
Dan Seith (Chemistry at Pennsylvania State University), Jamie Bingaman (Chemistry at Pennsylvania State University), Yin Tang (Center for RNA Molecular Biology at Pennsylvania State University), Phillip C. Bevilacqua (Chemistry at Pennsylvania State University), Sarah Assmann (Biology at Pennsylvania State University)
Abstract:
This work is focused on deprotonation of guanines in functional RNAs. One of the biological motivations for understanding guanine deprotonation is that anionic guanines can act as proton acceptors in ribozyme mechanisms. This is especially true for most of the small ribozymes where guanines appear to be poised in an ideal position in the active site to participate in a chemical step during cleavage. To gain a better understanding of guanine ionization at the N1 position, genome-wide data from dimethyl sulfate (DMS) methylation experiments on Arabidopsis thaliana rRNA were subjected to a scoring procedure to reveal possible correlations between DMS reactivity scores at guanines and RNA secondary structure. The procedure showed what nucleotide positions revealed reverse transcription stops. After investigating supposed guanine N1 reactivity upon DMS treatment in multiple rRNAs, no correlations were found between DMS reactivity at the N1 of guanines and RNA secondary structure. The mechanistic basis for reverse transcription stops one nucleotide before guanine at neutral pH is now being assessed by other models. Also presented in this work is progress that has been made towards developing a new chemical assay for detecting guanine deprotonation in functional ribozymes.
Keywords: ribozyme, guanine