Rotational Dynamics of Adenine Amino Groups in a DNA Double Helix

Abstract

Exocyclic amino groups of the bases undergo conformational fluctuations that affect the recognition and reactivity of nucleic acid molecules. Among these fluctuations, rotation of amino groups around C-N bonds is of special interest. In the present paper, we report the first determination of the rates and energetic parameters for rotation of the N6-amino group of adenine in a DNA double helix. The DNA molecule studied is the dodecamer [d(CGCGAGCTCGCG)] 2. The adenine in each A · T basepair of the dodecamer was labeled with 15N at the N6 position, and the NMR resonances of the two protons in the adenine amino group were selectively observed by 15N-editing methods. The rates of rotation of the amino group were obtained from experiments of transfer of magnetization between the two protons in the same group and from lineshape analysis of 15N-edited amino proton NMR resonances. The results show that, over the temperature range from 0 to 70°C, the rates of rotation of adenine amino groups range from 60 to 24,000 s −1. Formation of the activated state during rotation has a standard enthalpy change of 15.3 ± 0.2 kcal/mol and a standard entropy change of 6.0 ± 0.7 cal/(mol · K). Analysis of the results suggests that rotation of the amino group occurs in the paired, closed state of the adenine in the A · T basepair of the double-helical DNA structure.