OLIGO(A), OLIGO(TG), AND ALU REPEATS OF DNA IN CHROMATIN ARE AVAILABLE FOR SEQUENCE-SPECIFIC CHEMICAL MODIFICATION WITH OLIGODEOXYNUCLEOTIDE DERIVATIVES

Reaction of 4-(N-2-chloroethyl-N-methylamino) benzylphosphamides of ol igonucleotides, which are targeted to the poly(A), poly(TG), and Alu r epeats of eukaryotic DNA in chromatin and isolated nuclei from HeLa ce lls, has been investigated. It was found that the reagents alkylate DN A and some proteins due to specific complex formation. The affinity ch aracter of the reaction was proved by the fact that free corresponding oligonucleotides taken in excess or preliminary treatment of chromati n with S1 nuclease both prevent the biopolymers from the modification. Deproteinated DNA from the same cells does not react with oligonucleo tide derivatives. This suggests that the chromatin DNA must have some structural features allowing oligonucleotide binding. Reactivity may b e attributed to the existence of strongly negative supercoiled DNA reg ions containing single-stranded sequences or regions where DNA can unw ind in the presence of complementary oligonucleotides, Results obtaine d suggest that in eukaryotic chromatin there are open DNA sequences av ailable for affinity modification with oligonucleotide derivatives not only due to formation of triple helixes,