Heteronuclear N-15 and H-1 magnetic resonance study of a DNA dodecamer containing an A(3)T(3) tract

Two related DNA dodecamers, [d(CGCAAATTTGCG)](2) and [d(CGCGAGCTCGCG)](2), with all adenine residues N-15-labeled at the amino groups were synthesized, The dynamics and conformational transitions in both dodecamers were investigated using N-15 and H-1 NMR spectroscopy, It was found that, in the premelting temperature range, the N-15 resonances of the first and second adenines in the A(3)T(3) tract of [d(CGCAAATTTGCG)](2) shift downfield with increase in temperature, The change in the N-15 chemical shift of the central adenine in the A(3)T(3) tract was an order of magnitude smaller and was similar to that of the single adenine in [d(CGCGAGCTCGCG)](2). These premelting N-15 chemical shift changes parallel the pattern of three-centered hydrogen bonds that could form in the [d(CGCAAATTTGCG)](2) dodecamer. The dynamics of adenine amino groups in both dodecamers were also characterized using N-15 T-1 and H-1-N-15 NOE measurements. The data are consistent with the presence of internal motions for adenine amino groups. The motions are highly restricted, with an order parameter S-2 of 0.8, and occur on the picosecond time-scale. The internal motions of the three adenine amino groups in [d(CGCAAATTTGCG)](2) are similar and parallel that of the amino group in the single adenine in [d(CGCGAGCTCGCG)](2).