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Energy migration in the poly(ra-rU)-ethidium complex. determination of the unwinding angle of the polyribonucleic helix

Biophysical Chemistry
Publication Date
DOI: 10.1016/0301-4622(77)85012-6
  • Mathematics


Abstract The polarized fluorescence of the ethidium bromide (EB)-poly(rA-rU) complex has been studied by pulse fluorometry. As expected for a polynucleotide snowing one single kind of intercalation site, the decay of the whole emission is a single exponential (time constant 27 ns). The anisotropy decay is analysed as follows: (1) A brownian contribution having two correlation times, one of which characterizes local motions and the other a macromolecular motion. (2) A contribution due to transfers between EB molecules fixed to the same polynucleotide molecule, is analysed by a method analogous to the method used in previous work on EB-DNA complexes. That method consists in choosing a molecular model of the complex depending on geometrical parameters, and in simulating the energy migration on that model with a Monte Carlo calculation. Poly(rA-rU) is assumed here to adopt the structure A of RNA. Intercalated EB molecules modify the anale between two consecutive base pairs by δ. The angular position of the EB transition moment is defined by an angle φ. One finds that the angle φ is situated between 0° and 30°, which corresponds to a whole intercalation of the chroniophore as opposed to the semi-intercalation which has been proposed for certain dyes. The angle δ is negative; therefore there is an unwinding of the polyribonucleotide helix. Its absolute value is about 38°, sensibly greater than The value previously found for EB-DNA complexes.

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