Stability of RNA duplexes containing inosine·cytosine pairs

Nucleic Acids Research
Daniel J WrightBrent M Znosko

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 exocy...Continue Reading

References

Oct 12, 1987·Nucleic Acids Research·P W CorfieldO Kennard
Dec 20, 1985·Nucleic Acids Research·F H MartinI Tinoco
Jul 15, 1974·Journal of Molecular Biology·P N BorerO C Uhlenbeck
Jan 15, 1999·Science·S O Kelley, J K Barton
Dec 6, 2000·Proceedings of the National Academy of Sciences of the United States of America·C WanA H Zewail
Jun 26, 2001·RNA·S K WongD W Lazinski
Jun 5, 2002·Annual Review of Biochemistry·Brenda L Bass
Nov 24, 2004·Nature Structural & Molecular Biology·Frank V Murphy, V Ramakrishnan
Nov 3, 2005·Nucleic Acids Research·Norman E Watkins, John SantaLucia
Nov 23, 2006·RNA Biology·Stefan MaasKazuko Nishikura
Mar 24, 2007·Biochemistry·Daniel J WrightBrent M Znosko
Oct 26, 2007·Biochemistry·Amber R Davis, Brent M Znosko
Jun 11, 2009·Nucleic Acids Research·Martha E Christiansen, Brent M Znosko
Jan 6, 2010·RNA·Justin P SheehyBrent M Znosko
Mar 3, 2010·Annual Review of Biochemistry·Kazuko Nishikura
Oct 26, 2011·Biochemistry. Biokhimii︠a︡·A A H Su, L Randau
Mar 9, 2013·Science·Jacob K GrohmanKevin M Weeks
Dec 3, 2013·Genome Medicine·William Slotkin, Kazuko Nishikura
Apr 11, 2015·Frontiers in Bioengineering and Biotechnology·Giovanni NigitaAlfredo Ferro
Mar 5, 2016·Genome Research·Huiquan LiuJin-Rong Xu
Jul 13, 2016·Proceedings of the National Academy of Sciences of the United States of America·Fang-Chieh ChouRhiju Das

Citations

Aug 19, 2020·Nucleic Acids Research·Melissa C HopfingerBrent M Znosko
Aug 4, 2019·Proceedings of the National Academy of Sciences of the United States of America·Joseph D YesselmanRhiju Das
Apr 18, 2020·Wiley Interdisciplinary Reviews. RNA·Phillip J McCownJessica A Brown

Related Concepts

Adenocard
Adenosine Deaminase
DNA Sequence
Cytosine
Guanosine
Hydrogen Bonding
Inosine
DNA Conformation
Oligoribonucleotides
RNA

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