Effect of B-Z transition and nucleic add structure on the conformational dynamics of bound ethidium dimer measured by hydrogen deuterium exchange kinetics
Open Access
- 1 January 1985
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 13 (10) , 3773-3788
- https://doi.org/10.1093/nar/13.10.3773
Abstract
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.Keywords
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