A proton NMR study of a DNA dumb-bell structure with hairpin loops of only two nucleotides: d(CACGTG- TGTGCGTGCA)

One- and two-dimensional nuclear magnetic resonance (NMR) experiments were used to study the conformation of the DNA hexadecanucleotlde d(C-ACGTGTGTGCGTGCA) In aqueous solution. NMR spectra were recorded for the compound in D2O and in H2O/D2O (90/10) over the temperature range 1°C-60°C. Assignments of imlno proton resonances and of non-exchangeable proton resonances (except for some H4', H5 ' and H5 " resonances) are given. The 1H-NMR spectra indicate that below about 20°C, the compound exists as a single monomolecular species. Between 20°C and 55°C the oligonucleotide occurs as a mixture of structures in fast exchange on the NMR time scale, except for the temperature region 30 °- 34°C, where substantial line broadening indicates intermediate exchange; above 60°C the single strand predominates. The imlno proton spectra, chemical shift values, and scalar coupling and NOE data reveal that the monomeric form, which is exclusively present below 20°C, consists of a structure with a B-DNA double helix region of six base pairs, both ends of which are closed by hairpin loops of only two nucleotides, giving the molecule a dumbbell-like structure