Synthesis and characterization of water-soluble free-base, zinc and copper porphyrin–oligonucleotide conjugates

Abstract

We describe the synthesis and characterization of a series of water-soluble free-base, zinc, and copper porphyrin–oligonucleotide (ODN) conjugates. A non-charged tetraarylporphyrin was directly attached to the 5′-position of thymine via a short amide linker. Such a linker should allow for rigid connection to the adjacent nucleobases, thus increasing the sensitivity for monitoring conformational changes of the ODNs by electronic circular dichroism due to capping effects or ligand binding. Two complementary synthetic approaches have been used to incorporate porphyrin chromophores into the DNA. In the first approach a porphyrin carboxylic acid is conjugated to 5′-amino-ODN. In the second approach the phosphoramidite of the porphyrin-amido-thymidine is coupled to 5′-hydroxy-ODN using standard automated phosphoramidite chemistry. In both cases a spontaneous metallation of the free-base porphyrin in porphyrin–DNA conjugates was observed during the porphyrin–DNA conjugate cleavage from the solid support and its consequent deprotection using concentrated aqueous ammonia. Zinc and copper porphyrin–DNA conjugates were isolated by HPLC and characterized together with the anticipated free-base porphyrin–DNA conjugate. Authentic zinc and copper porphyrin–DNA conjugates were intentionally prepared from intentionally metallated porphyrins to compare their spectroscopic and HPLC characteristics with isolated metallospecies and to confirm the spontaneous metallation.