Interaction of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates with single-stranded DNA

Abstract

Oligodeoxyribonucleoside methylphosphonates derivatized at the 5'' end with 4''-(aminoalkyl)-4,5'',8-trimethylpsoralen were prepared. The interaction of these psoralen-derivatized methylphosphonate oligomers with synthetic single-stranded DNAs 35 nucleotides in length was studied. Irradiation of a solution containing the 35-mer and its complementary methylphosphonate oligomer at 365 nm gave a cross-linked duplex produced by cycloaddition between the psoralen pyrone ring of the derivatized methylphosphonate oligomer and a thymine base of the DNA. Photoadduct formation could be reversed by irradiation at 254 nm. The rate and extent of cross-linking were dependent upon the length of the aminoalkyl linker between the trimethylpsoralen group and the 5'' end of the methylphosphonate oligomer. Methylphosphonate oligomers derivatized with 4''-[[N-(2-aminoethyl)amino]methyl]-4,5'',8-trimethylpsoralen gave between 70% and 85% cross-linked product when irradiated fro 20 min at 4.degree. C. Further irradiation did not increase cross-linking, and preirradiation of the psoralen-derivatized methylphosphonate oligomer at 365 nm reduced or prevented cross-linking. These results suggest that the methylphosphonate oligomers undergo both cross-linking and deactivation reactions when irradiated at 365 mm. The extent of cross-linking increased up to 10 .mu.M oligomer concentration and dramatically decreased at temperatures above the estimated Tm of the methylphosphonate oligomer-DNA duplex. The cross-linking reaction was dependent upon the fidelity of base-pairing interactions between the methylphosphonate oligomers and the single-stranded DNA. Noncomplementary oligomers did not cross-link, and the extend of cross-linking of oligomers containing varying numbers of noncomplementary bases was greatly diminished or eliminated. The extent and sequence specificity of photoinduced cross-linking, combined with the known ability of methylphosphonate oligomers to be taken up by living cells, suggest that psoralen-derivatized oligonucleoside methylphosphonates may be useful probes of cellular gene expression.