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 'H 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 lineshape and timeresolved techniques. For the amino group of G, the rotational activation enthalpy is equal to +10.6 f 0.3 kcal/mol, and the rotational activation entropy (a',) is equal to -2.5 * 1.4 cal/(mol.T). As A S d 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 f 1.3 kcal/mol, and the rotational activation entropy (LLS',c) is equal to +11.2 3.5 cal/(mol.T). As L!Pmtc 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 pair 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. Although the ground state of DNA is close to the B conformation, DNA is a dynamic molecule which fluctuates between a variety of conformations. Amino groups in DNA rotate, and base pairs flip open and closed. DNA fluctuations are functionally significant, being factors in DNA recognition and reactivity. This *Address correspondence to this author. 'Massachusetts Institute of Technology. *Duke University. )Current address: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 021 15. paper describes one type of DNA fluctuation: rotation of the two amino groups of the cytosine-guanine base pair (Figure 1A). We have used 'H N M R to study the mechanisms of amino proton exchange in a monomeric model system of DNA. The properties of nucleic acid monomers have provided considerable insight into those of polymeric nucleic acids. The hydrogen-bonding interactions in the low-dielectric environment of the interior of polymeric nucleic acids'J can be modeled by nucleic ( 1 ) Levitt, M. Cold Spring Harbor Symp. Quant. Biol. 1982, 47, 251. 0002-7863/90/ 15 12-829$02.50/0