r-Inosine (Figure 1) is historically considered a universal base, and it is therefore widely used to create „degenerate“ positions in a nucleotide chain. However, Inosine is structurally a guanosine lacking its 2-amino group. Inosine has been shown to bind preferentially to dC and dA, and less strongly to dT and dG. Typically, Inosine is used at the third position of a codon, so to create “degenerate” PCR primers and probes that will anneal to degenerate target sequences. However, as written above, Inosine binds preferentially to dC and dA, especially when it is placed at the third position of a codon. Therefore, it is advisable to mix Inosine-primers with non-Inosine primers, so to ensure sufficient diversity in the PCR products. The base Inosine in RNA has been recognized to be essential for protein translation.
Figure 1. Structure of r-Inosine (R = sequence).
metabion offers r-Inosine in its RNA portfolio:
- Martin FH., Castro MM., Aboul-ela F., Tinoco I Jr. Base pairing involving deoxyinosine: implications for probe design. Nucleic Acids Res. 1985 Dec 20;13(24):8927-38.
- Alseth I., Dalhus B., Bjørås M. Inosine in DNA and RNA. Curr Opin Genet Dev. 2014 Jun;26:116-23.
- Ben-Dov E., Shapiro OH., Siboni N., Kushmaro A. Advantage of using inosine at the 3' termini of 16S rRNA gene universal primers for the study of microbial diversity. Appl Environ Microbiol. 2006 Nov;72(11):6902-6.
- Su AA., Randau L. A-to-I and C-to-U editing within transfer RNAs. Biochemistry (Mosc). 2011 Aug;76(8):932-7.