A PORPHYRIN EMBEDDED IN DNA

Oligodeoxynucleotides containing an alkylporphyrin linked to the phosp hate groups of DNA via oxypropyl chains have been synthesized. To our knowledge, these are the first porphyrin-nucleic acid conjugates beari ng the porphyrin embedded in the backbone of DNA. Chain assembly was a chieved by automated solid-phase synthesis using a dimethoxytrityl-pro tected 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 highe r melting point than duplexes bearing an abasic site or a dT(3) loop a t this position. Duplex formation is accompanied by 180% hypochromicit y at 501 nm, and other spectral changes unprecedented in porphyrinoids interacting with nucleic acids. Footprinting with nuclease S1, togeth er with CD spectropolarimetry, indicates that the alkylporphyrin is em bedded in a B-type duplex, with highly nuclease-sensitive phosphates o nly in the local environment of the porphyrin. Peak shifts in the NMR spectrum of the porphyrin-containing duplex, together with. fluorescen ce data, point toward an interaction between the porphyrin and the sta cked nucleobases. Porphyrin-containing DNA-and RNA-duplexes, convenien tly prepared with the porphyrin phosphoramidite described here, are ex pected 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.