Internal versus external binding of cationic porphyrins to single-stranded DNA.

Absorbance, induced circular dichroism, and emission studies establish that the tetrasubstituted cationic porphyrin Cu(T4) preferentially binds externally to single-stranded (ss) DNA sequences, except in a purine-rich system like 5'-(dA)10-3' where a degree of internalization occurs. On the other hand, the sterically friendly, disubstituted Cu(tD4) system exclusively binds to ss DNA by internalization, that is, pseudointercalation. By and large the results show that double-stranded DNA hosts decisively outcompete more flexible ss hosts for the uptake of a porphyrin, regardless of the binding motif. The findings are relevant because ss domains of DNA appear during replication, in different types of DNA-secondary structure, and as products of the disassembly of multistranded forms.