A Porphyrin Embedded in DNA

Abstract

Oligodeoxynucleotides containing an alkylporphyrin linked to the phosphate groups of DNA via oxypropyl chains have been synthesized. To our knowledge, these are the first porphyrin−nucleic acid conjugates bearing the porphyrin embedded in the backbone of DNA. Chain assembly was achieved by automated solid-phase synthesis using a dimethoxytrityl-protected porphyrin phosphoramidite and standard DNA building blocks. The thermal stability of duplexes involving the octadecamer 5‘-CGCGCCTTC-P-CATTGCGG-3‘, where -P- denotes the porphyrin, was found to depend on the sequence of the complementary strand. A duplex where a thymidine residue in the complementary strand faces the porphyrin gives a higher melting point than duplexes bearing an abasic site or a dT3 loop at this position. Duplex formation is accompanied by 180% hypochromicity at 501 nm, and other spectral changes unprecedented in porphyrinoids interacting with nucleic acids. Footprinting with nuclease S1, together with CD spectropolarimetry, indicates that the alkylporphyrin is embedded in a B-type duplex, with highly nuclease-sensitive phosphates only in the local environment of the porphyrin. Peak shifts in the NMR spectrum of the porphyrin-containing duplex, together with fluorescence data, point toward an interaction between the porphyrin and the stacked nucleobases. Porphyrin-containing DNA- and RNA-duplexes, conveniently prepared with the porphyrin phosphoramidite described here, are expected to be valuable for photochemical and electron-transfer studies, as well as potential cofactor-using nucleic acid-based enzymes which could have had a role in prebiotic evolution.