Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons.

The 360 MHz NMR spectra of the base protons and the H1 protons of thirteen trinucleoside diphosphates have been analyzed. The sequences chosen represent all purine-pyrimidine sequences. The chemical shifts of the base protons give evidence for strong next nearest-neighbor effects in some oligonucleotides. Although increasing chain length usually increases nearest-neighbor base-base stacking, it is not always so. Comparing ApCpG, ApUpG and GpUpG to their component dimers, one finds a decrease in stacking of the center pyrimidine with the purine on either side. The coupling constants J 1'2' also show that these three trimers show less stacking for their terminal residues than expected from their component dimers. We conclude that the sequence Pu-Py-Pu favors a conformation in which the pyrimidine is bulged out and the two purines stack on each other.