DNA sequence specificity of 4,5′,8-trimethylpsoralen cross-linking. Effect of neighboring bases on cross-linking the 5′-TA dinucleotide.

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The DNA sequence specificity for 4,5',8-trimethylpsoralen cross-linking of DNA has been examined using chemically synthesized DNA fragments containing all possible pyrimidine and purine base pair combinations. We confirm our previous findings that the 5'-TA dinucleotide represents a preferred cross-link site. Other dinucleotides that form cross-links are 5'-AT much greater than 5'-TG greater than 5'-GT. Although 5'-TA represents a preferred cross-link site, the rate of cross-linking can vary 3-4-fold depending on the base composition flanking the cross-linkable 5'-TA dinucleotide. In some cases, changes in DNA sequence 3 base pairs (bp) away from 5'-TA resulted in significant changes in the rate of cross-linking. We also see evidence for a long-range sequence context effect on the rate of cross-linking. A 30-bp fragment cross-linked at a relative rate of 2.9 compared to the rate of cross-linking of a 20-bp fragment when cloned contiguously in plasmid DNA. When cross-linked as separate fragments, the 30-bp fragment cross-linked at a relative rate of 1.9 compared to the 20-bp fragment. The results suggest that the reactivity of DNA to psoralens, and perhaps other intercalating drugs, is dependent on the dinucleotide sequence, the bases flanking the dinucleotide, and the long-range sequence context of the DNA.