A Solid-State Deuterium NMR Study of the Localized Dynamics at the C9pG10 Step in the DNA Dodecamer [d(CGCGAATTCGCG)]2

Abstract

A solid-state deuterium NMR study of localized mobility at the C9pG10 step in the DNA dodecamer [d(CGCGAATTCGCG)]2 is described. In contrast to the results of earlier deuterium NMR studies of furanose ring and backbone dynamics within the d(AATT) moiety, the furanose ring and helix backbone of dC9 display large amplitudes of motion on the 0.1 ms time scale at hydration levels characteristic of the B form structure. Solid-state deuterium NMR line shape data obtained from labeled dC9 DNA are interpreted using a composite motion model, in which the DNA oligomer is treated as rotating as a whole about the helix axis, while the base, furanose ring, and phosphodiester backbone execute localized motions. Consistent with past solid-state NMR studies, the amplitude and rate of the uniform rotation of the dC9-labeled oligomer are found to be sensitive to hydration level. Amplitudes of localized reorientational motions of C−D bonds in the furanose ring and backbone of dC9 are found to be larger than the librational amplitudes for the C−D bonds in the base of dC9, indicating that the pyrimidine base sugar does not move as a rigid entity and intersects a locally flexible region of the phosphodiester backbone. At hydration levels corresponding to 10−12 waters per nucleotide, Zeeman relaxation times for the furanose ring and backbone deuterons of dC9 in B form DNA equal 0.025 and 0.03 ms, respectively, and are the shortest relaxation times observed thus far for any deuteron in the DNA dodecamer at comparable hydration levels. The results of this solid-state NMR study suggest the existence of a significant dynamic component of sequence-specific recognition in this system.