Photoaffinity polyamines: sequence-specific interactions with DNA

ANB-spermine is a photoaffinity analog of the naturally-occurring polyamine, acetylspermine. ANB-spermine was used to determine its binding sites on naked double stranded DNA, at the nucleotide level, using a modification of the primer extension technique. A total of 1,275 nucleotides was examined in 5 sequences of DNA from Saccharomyces cerevisiae. Binding sites were non-random. The primary determinant of binding was the presence of a thymidine residue. Secondary determinants appeared to depend on the secondary structure of the DNA, with runs of thymidines providing unusually poor binding sites while TA and, especially, TATA providing the strongest binding sites. The 'TATA element' upstream of the URA3 gene from S. cerevisiae was the strongest binding site. The data indicate that ANB-spermine binding to DNA is a probe for DNA secondary structure and suggest a role for polyamines in regulating the structure of chromatin in vivo.