Poster abstracts

Poster number 41 submitted by Opeyemi Fatunbi

NUCLEOBASE Protonation in RNA Riboregulators

Opeyemi O. Fatunbi (Department of Chemistry & Biochemistry, Ohio University), Md. Ismail Hossain (Department of Chemistry & Biochemistry, Ohio University), Erin R. Murphy (Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University), Jennifer V. Hines (Department of Chemistry & Biochemistry, Ohio University)

Abstract:
Infectious diseases have claimed more than 15 million of the over 57 million annual global deaths,1 and the second leading cause of global death has been associated with bacteria.2 Many pathogens responsible for these infections have RNA riboregulators used to produce virulence factors. Many pathogenic RNA riboregulators have non-canonical base pairs that may be protonated, with their pKa values perturbed toward neutrality.3 The pH dependence and nucleobase protonation have been reported to influence various biological processes, such as miRNA processing4 and viral frameshifting.5 This work focuses on understanding nucleobase protonation in the shuT RNA Thermometer (RNAT)6 and the antiterminator (AM) RNA element of T-box riboswitches,7 which are structured bacterial non-coding RNAs (ncRNAs).
Herein, we employed UV and fluorescence spectroscopy to measure the pKa of shuT RNAT and AM RNA. We observed a clear pH dependence and at least one ionization event in the shuT RNAT and AM RNA. In addition, we observed a pKa shift towards neutrality and identified the nucleobase that may be protonated and responsible for the pH dependence and the upward pKa shift in the shuT RNAT. These findings suggest that the protonation of one of the non-canonical base pairs may be pertinent to the structural stability, function, and interactions of the shuT RNAT. Ongoing work focuses on identifying and characterizing the protonated nucleobases in the AM RNA system.
Understanding the pH-dependent behavior of RNAs is vital to the drug discovery process targeting RNA molecules. The pH at which RNA protonation occurs should be considered when designing small molecules that interact with RNA. This knowledge can guide the development of more effective RNA-targeted drugs, thereby advancing the field of RNA-based drug discovery.

References:
(1) Immunology 2018, 153 (2), 171–178.https://doi.org/10.1111/imm.12841
(2) The Lancet Regional Health - Western Pacific 2024, 43, 100972. https://doi.org/10.1016/j.lanwpc.2023.100972
(3) Acc Chem Res 2011, 44 (12), 1270–1279.https://doi.org/10.1021/ar2000452
(4) Nat Chem Biol 2021, 17 (1), 80–88.https://doi.org/10.1038/s41589-020-00667-5
(5) J Am Chem Soc 2013, 135 (20), 7390–7393.https://doi.org/10.1021/ja3125299
(6) Microbiologyopen 2017, 6 (3), e00442. https://doi.org/10.1002/mbo3.442
(7) Journal of Molecular Biology 2003, 326 (1), 189–201.https://doi.org/10.1016/S0022-2836(02)01339-6

Keywords: Shigella dysenteriae, T-box riboswitch, pH dependence