Intercalation and groove binding of an acridine–spermine conjugate on DNA sequences: an FT–Raman and UV–visible absorption study

Abstract

Acridine and acridine derivatives are known as powerful DNA intercalators. Interactions of the acridine–spermine conjugate N1-(Acridin-9-yl)-1,5,9,14,18-pentaazaoctadecane on two 16-mer oligonucleotides containing either alternating guanine–cytosine or adenine–thymine sequences were studied by optical spectroscopies. UV–visible absorption spectra of oligonucleotide/conjugate solutions at different molar ratios were recorded. The conjugate bands in the 350–500 nm region showed strong hypochromism and slight red shift in the presence of the oligonucleotides, thus indicating that the acridine moieties intercalate into adjacent base pairs of the oligonucleotides. These effects stopped near the 1:1 molar ratio, indicating that each oligonucleotide chain can only host one conjugate molecule. Raman spectra of solutions 60 mM (in phosphate) of the oligonucleotides and 3 mM of the conjugate were also recorded. Upon intercalation, the spectra showed relevant wavenumber shifts for skeletal and base vibrations, which have been largely attributed to the interactions of the positively charged side chain groups with the reactive sites of the base residues. Raman data suggested the existence of sequence selectivity induced by the spermine tail. Intercalation together to spermine interaction by the major groove was favoured for the guanine–cytosine sequence, while no groove preference was achieved for the adenine–thymine sequence.