Modeling Furanose Ring Dynamics in DNA

Abstract

Determination of the conformational flexibility of the furanose ring is of vital importance in understanding the structure of DNA. In this work we have 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 describes the angular trajectories of the atoms in the furanose ring in terms of pseudorotation puckering amplitude (q) and the pseudorotation puckering phase φ. Fixing q, the motion is thus treated as Brownian diffusion through an angular-dependent potential U(φ). We have simulated numerous line shapes varying the adjustable parameters, including the diffusion coefficient D, pseudorotation puckering amplitude q, and the form of the potential U(φ). We have used several forms of the potential, including equal double-well potentials, unequal double-well potentials, and a potential truncated to “second order” in the Fourier series. To date, we have obtained best simulations for both equilibrium and nonequilibrium (partially relaxed) solid-state deuterium NMR line shapes for the sample [2‘ ‘-2H]-2‘-deoxycytidine at the position C3 (underlined) in the DNA sequence [d(CGCGAATTCGCG)]2, using a double-well potential with an equal barrier height of U0 = 5.5kBT (∼3.3 kcal/mol), a puckering amplitude of q = 0.4 Å, and a diffusion coefficient characterizing the underlying stochastic jump rate D = 9.9 × 108 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 × 107 Hz.

Document Type

Article

DOI

https://doi.org/10.1021/ja010721d

Keywords

transport properties, hydrogen isotopes, diffusion, equilibrium, genetics

Publication Date

2001

Journal Title

Journal of the American Chemical Society

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