EFFECT OF THE 1-(2'-DEOXY-BETA-D-RIBOFURANOSYL)-3-NITROPYRROLE RESIDUE ON THE STABILITY OF DNA DUPLEXES AND TRIPLEXES

3-Nitropyrrole (M) was introduced as a non-discriminating 'universal' base in nucleic acid duplexes by virtue of small size and a presumed t endency to stack but not hydrogen bond with canonical bases. However, the absence of thermally-induced hyperchromic changes by single-strand ed deoxyoligomers in which M alternates with A or C residues shows tha t Rn does not stack strongly with A or C nearest neighbors. Yet, the i nsertion of a centrally located M opposite any canonical base in a dup lex is sometimes even less destabilizing than that of some mismatches, and the variation in duplex stability is small. in triplexes, on the other hand, an M residue centrally located in the third strand reduces tripler stability drastically even when the X.Y target base pair is A .T or G.C in a homopurine homopyrimidine segment. But, when the target duplex opposition is M-T and the third strand residue is T, the prese nce of M in the test triplet has little effect on tripler stability. T herefore, a lack of hydrogen bonding in an otherwise helix-compatible test triplet cannot be responsible for tripler destabilization when RA is the third strand residue. Thus, M is non-discriminating and none-t oo-destabilizing in a duplex, but in a tripler it is extremely destabi lizing when in the third strand.