Conformational perturbation due to an extra adenosine in a self-complementary oligodeoxynucleotide duplex

Abstract

The conformation of an oligodeoxynucleotide pentadecamer, d(CGCGAAATTTACGCG), self-complementary except for an additional adenosine nucleotide at position 11, has been investigated with nmr spectroscopy. This oligomer was found to exist predominantly in the duplex form in solution rather than in the hairpin loop form, as observed previously for an analogous 13-mer sequence. Nuclear Overhauser effects indicate that the B-form conformation is disrupted by the extra A base, which forms a wedge within the duplex, producing a bent junction and an overall S-like structure. A downfield-shifted phosphate resonance was assigned using a two-dimensional ¹H-³¹P correlation method, and was found to be P12-13. This and other results indicate that the extra A causes conformational distortions at some distance along the duplex structure.