The amplitude of local angular motions of intercalated dyes and bases in DNA.

Abstract

AbstractThe orientation of ethidium dye in DNA and the amplitude of its local internal angular motion are estimated from fluorescence polarization anisotropy and reduced linear dichroism data. When the local internal motion is assumed to be isotropic, the acceptable range of polar angles of the transition dipole is ϵ = 70°−72°, and the acceptable range of root mean squared (rms) amplitudes of local internal motion is 〈δϵ2〉1/2 = 6.9°–8°, in agreement with earlier estimates. The nmr relaxation data reported by Kearns and co‐workers for the imino protons of duplex (dAdT)26.5 and (dGdC)30 are analyzed using recent theoretical results for flexible filaments. For typical, or reasonable, assumed geometrical parameters, large rms amplitudes of local internal motion of the bases are not required to be superimposed on the collective motions due to twisting and bending deformations. For the particular geometrical parameters considered herein, rms amplitudes greater than about 12° are precluded by the data, but values as low as 0° are not. The low precision of present knowledge about solution structures does not allow a definitive statement about the rms amplitudes of local angular motion of the bases to be made independent of any structural or geometric assumptions.