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Ethidium bromide–dinucleotide complexes. Evidence for intercalation and sequence preferences in binding to double‐stranded nucleic acids
Author(s) -
Krugh Thomas R.,
Wittlin Frederick N.,
Cramer Stephen P.
Publication year - 1975
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1975.360140114
Subject(s) - ethidium bromide , chemistry , intercalation (chemistry) , cpg site , nucleic acid , dna , cooperative binding , stereochemistry , rna , binding site , biochemistry , organic chemistry , dna methylation , gene expression , gene
The solution complexes of ethidium bromide with nine different deoxydinucleotides and the four self‐complementary ribodinucleoside monophosphates as well as mixtures of complementary and noncomplementary deoxydinucleotides were studied as models for the binding of the drug to DNA and RNA. Ethidium bromide forms the strongest complexes with pdC‐dG and CpG and shows a definite preference for interaction with pyrimidine–purine sequence isomers. Cooperativity is observed in the binding curves of the self‐complementary deoxydinucleotides pdC‐dG and pdG‐dC as well as the ribodinucleoside monophosphates CpG and GpC, indicating the formation of a minihelix around ethidium bromide. The role of complementarity of the nucleotide bases was evident in the visible and circular dichroism spectra of mixtures of complementary and noncomplementary dinucleotides. Nuclear magnetic resonance measurements on an ethidium bromide complex with CpG provided evidence for the intercalation model for the binding of ethidium bromide to double‐stranded nucleic acids. The results also suggest that ethidium bromide may bind to various sequences on DNA and RNA with significantly different binding constants.