Oxidative Repair of a Thymine Dimer in DNA from a Distance by a Covalently Linked Organic Intercalator

A thymine cyclobutane dimer, site-specifically incorporated in a DNA duplex, is shown to be repaired upon photoexcitation (at 380 nm) of a naphthalene diimide intercalator (NDI), either bound noncovalently to the duplex or covalently appended to the C4 amine of a methylated cytosine base well separated from the thymine dimer. The repair of the thymine dimer is triggered by photooxidation either directly or by DNA- mediated charge transport over a distance of ∼22 Å, the separation between NDI and the cyclobutane ring. Photooxidative repair with covalently and noncovalently bound NDI is demonstrated using HPLC under denaturing conditions, where the loss of the thymine dimer-containing strand and the formation of the repaired strand are monitored directly, as well as using a novel gel electrophoretic assay. In this assay, two strands of oligonucleotides containing 5′- and 3′-terminal thymidines are first ligated photochemically to yield thymine dimers, and repair is then assayed by monitoring the reversal of the photoligation by intercalators bound either noncovalently or at a distance. Although both NDI and a rhodium intercalator were seen to reverse the photoligation, several anthraquinones and ethidium were unable to promote repair upon irradiation at 350 nm. This photoligation reversal assay provides a rapid screen for thymine dimer repair. The oxidative repair of thymine dimers in a DNA duplex from a distance appears now to be a general phenomenon and requires consideration in developing mechanisms for DNA-mediated charge transport.