Design and Modulation of Novel Chemical Probes for RNA SHAPE Analysis: Water Soluble Isatoic Anhydrides and Nicotinic Acid Imidazolides

1 online resource (150 pages) : PDF

2021

University of North Carolina at Charlotte

The growing interest in RNA biology, along with an expansion in computational capabilities, throughput, and sensitivity has provided researchers new tools to probe RNA. RNA selective 2′-hydroxy acylation analyzed by primer extension (SHAPE) utilizes the unique reactivity of the 2′-OH on the ribose sugar at sites of flexibility within an RNA structure to probe the secondary structures of RNA. This work sought to address the limitations of current SHAPE probes including poor aqueous solubility. Several iterations of designs were tested, and these results were used to direct the continued development of new probes. A strategy for modulation of probe reactivity was developed and utilized for isatoic anhydride-based probes and nicotinic acid imidazolide-based probes. The work demonstrated the capability of new RNA probes to provide improved signal to noise of RNA SHAPE both in vivo and in vitro.

doctoral dissertations

Chemistry
Biology

Ph.D.

Bioconjugation
Isatoic Anhydride
Nicotinic Acid Imidazolide
Probing
Rna
Shape

Nanoscale Science

Ogle, Craig

Etzkorn, Markus
Troutman, Jerry
Bejger, Christopher
Steck, Todd

Thesis (Ph.D.)--University of North Carolina at Charlotte, 2021.

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Fessler_uncc_0694D_12870

http://hdl.handle.net/20.500.13093/etd:2951