Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex

Phensinee Haruehanroengra; Sweta Vangaveti; Srivathsan V Ranganathan; Song Mao; Max Daniel Su; Alan A Chen; Jia Sheng

doi:10.1016/j.isci.2020.101866

Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex

iScience. 2020 Nov 26;23(12):101866. doi: 10.1016/j.isci.2020.101866. eCollection 2020 Dec 18.

Authors

Phensinee Haruehanroengra^{1

2}, Sweta Vangaveti², Srivathsan V Ranganathan², Song Mao^{1

2}, Max Daniel Su^{1

2}, Alan A Chen^{1

2}, Jia Sheng^{1

2}

Affiliations

¹ Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA.
² The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.

Abstract

Geranylation is a hydrophobic modification discovered in several bacteria tRNAs with the function of promoting codon bias during translation. However, why nature selects this C10-geranyl group remains a question. We conduct synthesis, UV-thermal denaturation, and molecular simulation studies in RNA duplexes and reveal possible reasons behind this natural selection. Among methyl-(C1), dimethylallyl-(C5), geranyl-(C10), and farnesyl-(C15) modified 2-thiouridines, only geranyl-group promotes U:G over U:A pair. Molecular simulation shows all the modified terpene groups point to the minor groove of RNA duplexes. The discrimination between U:G and U:A pairs derives from the difference in hydrogen bonding and interactions of the chain with the hydrophobic area in the minor groove. Geranyl group has perfect length to discriminate U:G and U:A pairs, whereas the others are either too long or too short to achieve the same behavior. This work indicates that geranyl group cannot be replaced by other terpene groups in promoting codon-specificity.

Keywords: Biochemistry; Molecular Structure; Structural Biology.

Grants and funding

R35 GM133469/GM/NIGMS NIH HHS/United States