Oligodeoxyribonucleoside methylphosphonates derivatized at the 5' end with 4'-(amino-alkyl)-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 for 20 min at 4 degrees 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 nm. The extent of cross-linking increased up to 10 microM 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 extent of cross-linking of oligomers containing varying numbers of noncomplementary bases was greatly diminished or eliminated.(ABSTRACT TRUNCATED AT 250 WORDS)

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The interaction of 4'-N(2-aminoethyl)aminomethyl-4,5',8-trimethylpsoralen-modified oligonucleoside methylphosphonates with synthetic ds-DNA containing a T7 RNA polymerase promoter was studied. The oligomers effectively crosslinked with either coding or noncoding ss-DNA when irradiated at 365 nm, but not with ds-DNA. The extent of the crosslinking reaction, which was complete within 16 min: (a) reached its maximum at an oligomer concentration of 3 microM; (b) remained constant below the Tm of the duplex and then rapidly decreased; and (c) appeared to depend upon the sequence surrounding the psoralen crosslinking site. An oligomer crosslinked to the template strand inhibited transcription by T7 RNA polymerase whereas an oligomer crosslinked to the non-template strand had only a small inhibitory effect. Oligomers did not crosslink to ds-DNA undergoing transcription nor did they inhibit the transcription reaction.