Sequence specificity in photoreaction of various psoralen derivatives with DNA: role in biological activity

The sequence specificity in the photoreaction of various psoralen derivatives with DNA is investigated by using DNA sequencing methodology. The 3'-5' exonuclease activity associated with T4 DNA polymerase serves as a probe to map the psoralens' photoaddition (monoadducts plus biadducts) on DNA fragments of defined sequence. This approach has already allowed us to demonstrate a strong sequence context effect on the 8-methoxypsoralen photobinding to DNA [Sage, E., & Moustacchi, E. (1987) Biochemistry 26, 3307-3314]. The psoralens studied include bifunctional derivatives [8-methoxypsoralen, 5-methoxypsoralen, and 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen] and monofunctional derivatives (angelicin, 3-carbethoxypsoralen, and three pyridopsoralens). Maps of photochemical binding on two DNA fragments of the lacI gene of Escherichia coli are established for all the derivatives. These maps demonstrate the following general qualitative rules in the photoreaction of the furocoumarins with DNA: thymine residues in a GC environment are cold, adjacent thymines are better targets, 5'-TpA sites are strongly preferred versus 5'-ApT, and alternating (AT)n sequences are hot spots for photoaddition. Depending on the chemical structure of the derivatives and on their affinity for DNA, some minor differences in the binding spectrum are detected. A most interesting example is 3-carbethoxypsoralen, which specifically reacts with (AT)n sites. Our observations lead us to define two types of target sites: the "strong sites", which are preferential targets for all psoralen derivatives, and the "weak sites", which are targets only for derivatives having a high affinity for DNA. The frequency of DNA lesions is much higher in the former sites.(ABSTRACT TRUNCATED AT 250 WORDS)