An extended sequence specificity for UV-induced DNA damage

Abstract

The sequence specificity of UV-induced DNA damage was determined with a higher precision and accuracy than previously reported. UV light induces two major damage adducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6–4)pyrimidone photoproducts (6–4PPs). Employing capillary electrophoresis with laser-induced fluorescence and taking advantages of the distinct properties of the CPDs and 6–4PPs, we studied the sequence specificity of UV-induced DNA damage in a purified DNA sequence using two approaches: end-labelling and a polymerase stop/linear amplification assay. A mitochondrial DNA sequence that contained a random nucleotide composition was employed as the target DNA sequence. With previous methodology, the UV sequence specificity was determined at a dinucleotide or trinucleotide level; however, in this paper, we have extended the UV sequence specificity to a hexanucleotide level. With the end-labelling technique (for 6–4PPs), the consensus sequence was found to be 5′-GCTC*AC (where C* is the breakage site); while with the linear amplification procedure, it was 5′-TCTT*AC. With end-labelling, the dinucleotide frequency of occurrence was highest for 5′-TC*, 5′-TT* and 5′-CC*; whereas it was 5′-TT* for linear amplification. The influence of neighbouring nucleotides on the degree of UV-induced DNA damage was also examined. The core sequences consisted of pyrimidine nucleotides 5′-CTC* and 5′-CTT* while an A at position “1” and C at position “2” enhanced UV-induced DNA damage.