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The effect of the universal base 3-nitropyrrole on the pairing selectivity
of neighboring nucleosides has been determined for every combination of com
plementary and neighboring nucleosides, In a subset of cases the discrimina
tory ability of the neighboring nucleoside for its Watson-Crick complement
is compromised. The results have implications for the hybridization of olig
onucleotides that contain 3-nitropyrrole and suggest caution in the use of
oligonucleotides that contain other universal bases.