Effect of the universal base 3-nitropyrrole on the selectivity of neighboring natural bases.

[structure: see text] The effect of the universal base 3-nitropyrrole on the pairing selectivity of neighboring nucleosides has been determined for every combination of complementary and neighboring nucleosides. In a subset of cases the discriminatory ability of the neighboring nucleoside for its Watson-Crick complement is compromised. The results have implications for the hybridization of oligonucleotides that contain 3-nitropyrrole and suggest caution in the use of oligonucleotides that contain other universal bases.