Assessment and detection of nucleotide excision repair capability in human cells: a critical review of current functional methods.

DNA, as the blueprint of the cell, is continuously subjected to damage by chemicals and radiation. Such damage can lead to cell death or mutations, potentially resulting in diseases such as cancer. Fortunately, cells possess various mechanisms to repair different types of DNA damage. Nucleotide excision repair (NER) removes damaged DNA fragments and restores the original DNA sequence, thereby limiting mutagenesis and supporting genome stability. Although NER contributes to cancer prevention, its activity can be altered in a context-dependent manner in cancer cells, with increased NER capacity in some cancers potentially promoting resistance to DNA-damaging therapies. This review summarizes and compares biochemical, cellular, and genome-wide approaches for functional NER analysis, with particular attention to their measured endpoints, methodological characteristics, and interpretive limitations. The assays cover excision-product formation, repair-associated DNA synthesis, transcriptional or reporter gene-expression recovery, lesion removal inferred from restored DNA amplifiability, and genome-wide mapping of DNA damage and excision events. Because these methods interrogate distinct stages or consequences of NER, their selection and interpretation should be guided by the specific research question, with complementary readouts providing a more comprehensive assessment of NER function.