Date of Award

1-1-2019

Language

English

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College/School/Department

Department of Chemistry

Content Description

1 online resource (xxi, 144 pages) : illustrations (some color)

Dissertation/Thesis Chair

Li Niu

Committee Members

Maksim Royzen, Ting Wang, Gabriele Fuchs

Keywords

geranylated-2-thiouridine, geranylation, modified RNA, Ribosomal binding, SelU, tRNA modification, Organic compounds, Transfer RNA, Transferases, Escherichia coli

Subject Categories

Biochemistry | Chemistry

Abstract

Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. Geranylated-2-thiouridine is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, namely E. coli, E. aerogenes, P. aeruginosa and S. typhimurium by Liu group. It has been found as a post-transcription modification on the wobble position of anticodon of tRNAs specific for glutamic acid, glutamine and lysine. Geranylated-tRNA was shown to correct the frameshifting during the translation of E. coli. However, the reason of the existing of the modification is still largely unclear. To understand why nature incorporates such a hydrophobic group in tRNA system, chemical synthesis approaches were developed to obtain large quantity of geranylated RNA oligonucleotides. The biophysical property of geranylated-RNA was then investigated. The systematic study of the effect of terpene chain length on base-pairing specificity and stability revealed the importance of geranyl group in providing base-pairing discrimination of U:G pair over U:A one. The role of geranyl group of E. coli tRNA in ribosomal binding was also reported in this dissertation to fully understand the involvement of geranyl group on codon-anticodon recognition in the presence of 70S E. coli ribosome complex. Understanding of biosynthesis pathway of tRNA geranylation modification will set up a foundation for future tool developments and their biochemical applications. The enzymatic geranylation by selenouridine synthase (SelU) was also investigated in term of enzymatic efficiency, anticodon dependency, geranyl pyrophosphate analogues recognition and tRNA bound-SelU identification. In addition, geranyl group was observed to facilitate the HEK-293 cell permeability of 17nt RNA oligonucleotides, which might be useful for cell imaging studies and drug delivery.

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