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Nucleic Acids Research, 1985, Vol. 13, No. 10 3773-3788
© 1985

Articles

Effect of B-Z transition and nucleic add structure on the conformational dynamics of bound ethidium dimer measured by hydrogen deuterium exchange kinetics

Judith Markovits, Jean Ramstein1, Bernard P. Roques2 and Jean-Bernard Le Pecq

Lahoratoire de Physico-chimie macromoléculaire, LA 147 CNRS, U 140 INSERM, Institut Gustave Roussy 94805 Villejuif Cedex 1Centre de Biophysique Moléculaire du CNRS 45000 Orlé 2Department of Chimie Organique, ERA 613 CNRS, U 266 INSERM, UER des Sciences, Pharmaceutiques Biologiques, Université Paris V75006 France

Received August 6, 1984. Revised April 16, 1985. Accepted April 30, 1985.

Ethidium dimer is shown to bind by intercalation. almost equally well, to the B and Z form of po1y[(dG-m5dC)].poly[(dG-m5dC)], whereas the ethidium monomer shows a strong preference for the B form. The hydrogendeuterium (H-D ) exchange kinetic of the ethidium dimer bound to the B and Z form of poly[(dG-m5dC)]. poly [(dG-m5dC)] could then be compared. The kinetics of the H-D exchange were strikingly slower when the dye was bound to Z DNA as compared to B DNA. The exchange kinetics ware also modified when ethidium dimer was bound to tRNA and to a triple stranded structure. It is proposed that a dynamic flucthatia at the level of the nucleic acid could modulate the dynamic fluctuation at the level of the bound ligand.


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