Preparation and characterization of a set of deoxyoligonucleotide 49-mers containing site-specific Cis-syn, Trans-syn-I, (6-4), and dewar photoproducts of thymidylyl(3′ → 5′)-thymidine

Deoxyoligonucleotide 49-mers containing a central cis-syn, trans-syn-I, (6-4), or Dewar photoproduct of TpT were constructed for use in repair and replication studies by ligation of shorter photoproduct-containing oligonucleotides. A (6-4) product-containing 6-mer was prepared in 3.4% yield by 254 nm irradiation of d(AATTAA) and converted in nearly quantitative yield to the Dewar isomer by irradiation with Pyrex- and Mylar-filtered medium-pressure mercury arc light. d(CGAATTAAGC) containing a site-specific cis-syn or trans-syn-I dimer was prepared via automated solid-phase DNA synthesis utilizing photoproduct building blocks. The photoproduct-containing 49-mers were characterized by their susceptibility to base cleavage and a number of enzymes routinely used to map the sites of DNA photoproduct formation. 1 M piperidine at 90°C cleaved the Dewar product faster than the (6-4) product, but did not cleave the cyclobutane dimers. The 3′ → 5′ exonuclease activity of T4 DNA polymerase was completely blocked by all the lesions except the (6-4) product, which it slowly bypassed. T4 endonuclease V did not cleave the (6-4) or Dewar photoproduct, but unexpectedly cleaved the trans-syn-I dimer at most 1% the rate of the cis-syn dimer in double-stranded DNA. The trans-syn-I dimer was cleaved at a 50-fold higher rate in double- than in single-stranded DNA. Eacherichia coli photolyase was found to be specific for the cis-syn dimer at low concentrations. Implications of this work to methodology for mapping and quantifying DNA photoproducts are also discussed.