Binding of Hoechst with nucleic acids using fluorescence spectroscopy

It has been shown that polarity of environment around Hoechst 33342 is almost unchanged while sorption of this fluorescent dye on a surface of the hairpin oligonucleotide HP1, t-RNA and DNA. At small concentrations, this dye, adsorbed on the surface of DNA, RNA or HP1, does not show any specificity to certain nucleotides. In the case of unwound sites of DNA or HP1, it can bind inside, but without the intercalation stacking with nucleotides. The energy transfer from nucleotide chromophores to Hoechst is absent due to their remoteness and also “bad” (non-stacking) orientation. The mutual fluorescence quenching of Hoechst by actinomycin D (AMD) and, vice versa, of 7-amino-actinomycin D (7AAMD) by Hoechst in DNA and HP1 is observed. It is due to dynamic deactivation and mutual replacing in binding sites.