Sequence specificity of 125I-labelled Hoechst 33258 damage in six closely related DNA sequences

The sequence selectivity of [125I]Hoechst 33258 in six 340 base-pair DNA sequences has been investigated. [125I]Hoechst 33258, which is a bis-benzimidazole and binds to the minor groove of B-DNA, preferentially binds to A + T-rich regions of DNA. Six out of nine strong binding sites contained four or more consecutive A.T base-pairs, while the other three strong binding sites were AAGGATT, TATAGAAA (the peak of damage was in the run of 3 A residues) and AAA. One of the six weak binding sites had five consecutive A.T base-pairs, two of the weak binding sites had three, and three did not have any. In addition to genomic 340 base-pair alpha RI-DNA (which is a tandem repeat in human cells), five 340 base-pair alpha RI-DNA clones were generated that differed from the genomic "consensus" sequence by a number of random base alterations. The effect of these base changes on the sequence specificity of [125I]Hoechst 33258 damage indicated that of the base changes that interrupted 14 binding sites, six decreased and eight did not change the extent of damage, while two sites changed position. Of the base alterations that augmented 17 binding sites, five increased, two decreased and ten did not alter the degree of cleavage, while ten sites changed position. It was concluded from the data that, while runs of consecutive A.T base-pairs was the most important parameter that determines [125I]Hoechst 33258 binding, other factors including position in the DNA sequence, nearest neighbour and long-range interactions were also important.