IN A MODEL C-G BASE PAIR, ONE AMINO GROUP ROTATES AND THE OTHER DOES NOT

Cytosine (C) and guanine (G) form Watson-Crick-type complexes in low-dielectric solvents. Dynamics of complexes between 3',5'-bis(triisopropylsilyl) derivatives of 2'-deoxynucleosides in deuteriochloroform were studied with 300-MHz 1H NMR. We have determined rates of rotation about each amino bond of the C:G base pair. From the temperature dependence of the rates of amino group rotation, rotational activation enthalpies and entropies were calculated with line-shape and time-resolved techniques. For the amino group of G, the rotational activation enthalpy is equal to +10.6 ± 0.3 kcal/mol, and the rotational activation entropy (ΔS⋆rotG) is equal to -2.5 ± 1,4 cal/(mol·T). As ΔS⋆rotG is nearly zero, the degree of disorder in the transition state is similar to that of the ground (base paired) state. We propose that rotation of the amino group of G proceeds within the base-paired state. In contrast, for the amino group of C, the rotational activation enthalpy is equal to +18.6 ± 1.3 kcal/mol, and the rotational activation entropy (ΔS⋆rotC) is equal to +11.2 Ω 3.5 cal/(mol·T). AsΔS⋆rotC is large, the degree of disorder in the transition state is greater than that of the ground state. We propose that rotation of the amino group of C proceeds through a transition state in which the base pair is disrupted. The results suggest that the two amino groups of the C:G base air rotate via two different mechanisms. The amino group of G rotates within the base-paired state while the amino group of C rotates only during transient base-pair opening. © 1990, American Chemical Society. All rights reserved.