New Ultra-Sensitive Platform Quantifies Damaged DNA Fragments

The Korea Research Institute of Standards and Science (KRISS, President Dr. Lee Ho Seong) has developed an ultra-sensitive immunoassay-based analytical platform that can detect and quantify trace amounts of "Small Excised Damaged DNA (sedDNA)" fragments generated during cellular DNA repair. This technology enables highly sensitive detection with quantification down to the level of several thousand molecules, measuring up to 22 times more DNA fragments than conventional methods. It provides a new analytical foundation for comparing DNA repair capacity between individuals and studying cellular responses to anticancer drugs and carcinogenic agents.

Human DNA is continuously exposed to damage from ultraviolet light, chemical agents, smoking, and normal metabolic processes. If such damage is not properly repaired, mutations can accumulate and lead to aging and diseases such as cancer. To maintain genomic stability, cells activate the Nucleotide Excision Repair (NER) system, which removes damaged DNA segments and replaces them with newly synthesized DNA. The small excised DNA fragments generated during this process serve as important indicators of DNA repair efficiency and kinetics, providing a valuable tool for studying disease mechanisms and predicting treatment responses.

Conventional methods for quantifying these trace fragments rely on labeling the ends of excised DNA molecules and estimating fragment numbers based on signal intensity. However, enzymatic degradation of DNA fragment ends inside cells can prevent proper labeling, leading to underestimation of true fragment abundance.

To overcome this limitation, the KRISS team developed a competitive immunoassay approach. Synthetic DNA mimicking the damaged structure is immobilized on a microplate as a reference. Extracted cellular DNA is then incubated with antibodies specific to damaged DNA structures. A competitive binding mechanism between sample fragments and immobilized reference DNA allows quantitative estimation of fragment abundance, which is converted into molar concentration and subsequently into fragment numbers.

This approach enables researchers to directly quantify the number of DNA repair fragments generated in cells, providing a robust basis for precision analysis of DNA repair dynamics and cellular responses.

Since first detecting trace DNA repair fragments in 2015, the KRISS research team has advanced this field for over a decade. The current study builds on this long-term effort by overcoming fundamental limitations of conventional labeling-based methods.

Quantifying DNA repair efficiency can support early assessment of cancer risk and provide an objective measure of cellular response to anticancer drugs."

Choi Jun-Hyuk, Principal Research Scientist, Korea Research Institute of Standards and Science

He added that further validation using human tissue samples will enable broader applications in personalized cancer treatment.

The study was conducted by the KRISS Biometrology Group and Organic Metrology Group, in collaboration with a researcher from Wright State University, USA. The findings were published in Nucleic Acids Research, a leading journal in the field of molecular biology.