NMR studies on DNA hairpin structures with a five nucleotide loop

One- and two-dimensional NMR experiments have been undertaken to investigate the structure of DNA hairpins with a five nucleotide loop. Analysis of proton NMR spectra suggests that the four hairpin structures examined have some common structural features; B-type conformation in the stem region and the same stacking pattern, 5' (XXX-turn-XX) 3', in the loop region. The phosphorus NMR spectra suggest that the conformational changes in the loop region affect the backbone conformation of the stem duplex.