Discrimination between A-type and B-type conformations of double helical nucleic acid fragments in solution by means of two-dimensional nuclear Overhauser experiments

Abstract

The solution structure of two double helical nucleic acid fragments, viz, r(CGCGCG) and d(CGCGCG), was probed by means of two-dimensional nuclear Overhauser effect spectroscopy. The two compounds were selected as models for the A-type and B-type double helical conformations, respectively, and it is shown that for each of the two model compounds the intensities of the NOE cross peaks between base- and H2' (deoxy)ribose proteins are qualitatively in correspondence with the relative NOE intensities expected on basis of the supposed duplex conformations. Thus our results indicate that NOE-data can be used to differentiate between A-and B-type double helical conformations in solution. Coupling constant data show that, except for G(6), all ribose rings in r(CGCGCG) adopt pure N (C3'-endo) conformations thereby manifesting that this molecule takes up a regular A-type double helical conformation in solution. In contrast, the deoxyribose rings in d(CGCGCG) retain conformational freedom in the duplex state, albeit that the N/S-equilibrium is biased towards the S (C2'-endo) sugar conformation. This finding indicates that in solution the B-DNA backbone is highly dynamic.