Modeling furanose ring dynamics in DNA

Determination of the conformational flexibility of the furanose ring is of vital importance in understanding the structure of DNA. In this work we hav e applied a model of furanose ring motion to the analysis of deuterium line shape data obtained from sugar rings in solid hydrated DNA. The model desc ribes the angular trajectories of the atoms in the furanose ring in terms o f pseudorotation puckering amplitude (q) and the pseudorotation puckering p hase phi. Fixing q, the motion is thus treated as Brownian diffusion throug h an angular-dependent potential U(phi). We have simulated numerous line sh apes varying the adjustable parameters, including the diffusion coefficient D, pseudorotation puckering amplitude q, and the form of the potential U(p hi). We have used several forms of the potential, including equal double-we ll potentials, unequal double-well potentials, and a potential truncated to "second order" in the Fourier series. To date, we have obtained best simul ations for both equilibrium and nonequilibrium (partially relaxed) solid-st ate deuterium NMR line shapes for the sample [2"-H-2]-2'-deoxycytidine at t he position C3 (underlined) in the DNA sequence [d(CGCGAATTCGCG)](2), using a double-well potential with an equal barrier height of U-0 = 5.5k(B)T (si milar to3.3 kcal/mol), a puckering amplitude of q = 0.4 Angstrom, and a dif fusion coefficient characterizing the underlying stochastic jump rate D = 9 .9 x 10(8) Hz. Then the rate of flux for the C-D bond over the barrier, i.e ,, the escape velocity or the overall rate of puckering between modes, was found to be 0.7 x 10(7) Hz.