Open AccessEffect of B-Z transition and nucleic add structure on the conformational dynamics of bound ethidium dimer measured by hydrogen deuterium exchange kinetics
Author(s) -
Judith Markovits,
Jean Ramstein,
Bernárd P. Roques,
Jean-Bernard Le Pecq
Publication year - 1985
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/13.10.3773
Subject(s) - biology , kinetics , dimer , dynamics (music) , nucleic acid , hydrogen–deuterium exchange , biophysics , transition (genetics) , deuterium , rna , crystallography , biochemistry , chemistry , nuclear magnetic resonance , gene , physics , acoustics , quantum mechanics
Ethidium dimer is shown to bind by intercalation, almost equally well, to the B and Z form of poly[(dG-m5dC)].poly[(dG-m5dC)], whereas the ethidium monomer shows a strong preference for the B form. The hydrogen-deuterium (H-D) exchange kinetics 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 were also modified when ethidium dimer was bound to tRNA and to a triple stranded structure. It is proposed that a dynamic fluctuation at the level of the nucleic acid could modulate the dynamic fluctuation at the level of the bound ligand.