Stability of RNA duplexes containing inosine·cytosine pairs

Abstract

Inosine is found naturally in the anticodon loop of tRNA, is a product of adenosine deaminases that act on RNA, and can be used in oligonucleotide probes or to investigate the role of the exocyclic amino group of guanosine. Although the thermodynamics of I·U pairs in RNA have been systematically studied [Wright, D. J., Rice, J. L., Yanker, D. M., and Znosko, B. M. (2007) Biochemistry 46, 4625–4634], the thermodynamics of I·C pairs in RNA have not. Here, we have performed optical melting experiments on a series of RNA duplexes containing I·C pairs and compared their thermodynamics to the same duplexes containing A·C and G–C pairs. Nearest neighbor parameters for single I·C pairs adjacent to Watson-Crick pairs were derived. The derived nearest neighbor parameters are compared to those previously predicted blindly through a reweighting of energy-function collection with conformational ensemble sampling in Rosetta [Chou, F.-C., Kladwang, W., Kappel, K., and Das, R. (2016) Proc. Natl. Acad. Sci. U.S.A. 113, 8430–8435]. Scientists can use these nearest neighbor parameters to calculate the stability of ADAR products and to calculate the stability of an RNA duplex in which G-to-I substitution was used to determine the role of the exocyclic amino group of G.