When using an inosine base within a hybridization probe, this residue can form base-pairs with dA, dC, dG, or dT residues on the target strand. Inosine bases can be used instead of wobbles and have the advantage that the hybridization probe is not "diluted" by the non-pairing components of the wobbles. Deoxyinosine might be an "inert" base, its presence in an oligonucleotide sequence seems neither to disturb DNA duplex formation nor to destabilize the duplex.

Independent of sequence effects, the order of stability of base-pairings is I-C >> I-A > I-T = I-G.

Inosine bases are available at any position in an oligonucleotide, and can be used multiple times within a sequence.