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.