Discovery Unveils Protein Duo Detecting UV-DNA Damage

Abstract

Ultraviolet-induced DNA lesions are removed by the nucleotide excision repair (NER) pathway. In global-genome NER (GG-NER), XPC-RAD23B recognizes the lesions and initiates NER. However, cyclobutane pyrimidine dimers (CPDs), which do not significantly destabilize the DNA duplex, are not bound by XPC-RAD23B with high selectivity. Instead, CPD is preferentially sensed by UV-DDB, which is believed to hand over the lesion to XPC-RAD23B via ubiquitination of both proteins. Here, by combining biochemical and single-molecule DNA curtain assays, we investigate the interactions between UV-DDB and XPC-RAD23B on DNA. Surprisingly, we discover that XPC-RAD23B enhances the binding of UV-DDB to DNA. We demonstrate that this enhancement can be attributed to the complex formation of UV-DDB and XPC-RAD23B (UX-complex), which increases the binding affinity of UV-DDB to undamaged DNA. We further show that UV-DDB finds CPDs through one-dimensional (1D) diffusion along DNA. Collectively, the UX-complex enhances UV-DDB loading to DNA to accelerate the search for CPD via 1D diffusion. Moreover, we find that UV-DDB and XPC-RAD23B can bind CPDs as a complex, which facilitates the transfer of CPD. Altogether, our results show that UV-DDB and XPC-RAD23B cooperatively interact for rapid CPD search, providing a new mechanism for lesion search in GG-NER.

Ultraviolet (UV) rays from sunlight can cause DNA damage that leads to skin aging and cancer. Fortunately, our bodies have a highly efficient repair system capable of swiftly identifying and repairing damaged DNA sites among approximately 3 billion base pairs. Recent research by a team at UNIST has shed new light on how this process operates at the molecular level.

A research team, led by Professor Ja Yil Lee in the Department of Biological Sciences at UNIST has revealed that, contrary to the previously understood sequential transfer model, two key proteins involved in nucleotide excision repair (NER) work together as a complex to locate UV-induced DNA lesions.

NER is a critical pathway that removes cyclobutane pyrimidine dimers (CPDs), a common form of UV-induced damage. Given the vast number of DNA base pairs, the speed and efficiency of damage detection are vital. The process involves the XPC protein, which detects structural distortions in DNA. However, because CPDs cause minimal distortion, XPC alone struggles to recognize these lesions. Instead, the UV-DDB protein is known to facilitate damage recognition.

Previously, it was believed that UV-DDB first binds to the damaged site and then hands it over to XPC in a sequential manner. However, this new study demonstrates that UV-DDB and XPC form a stable complex (referred to as the UX-complex), which cooperatively searches for damage along the DNA. Notably, XPC enhances UV-DDB's binding affinity and search efficiency for damaged DNA.

These findings were supported by experiments utilizing single-molecule DNA curtain imaging-a technique that visualizes individual protein-DNA interactions. The researchers observed that when UV-DDB and XPC form a complex, UV-DDB binds more effectively to DNA and moves along the strand in a sliding manner, efficiently locating damage sites.

Soyeong An, the study's first author, stated, "This is the first direct observation of molecular dynamics where damage sites are precisely targeted by these proteins working together."

Professor Lee explained, "We uncovered that UV-DDB and XPC cooperate more closely than previously thought, accelerating the DNA repair process." He further noted, "This discovery challenges the traditional textbook understanding of NER mechanisms and could have significant implications for preventing and treating UV-induced skin damage, aging, xeroderma pigmentosum, and skin cancers."

Meanwhile, xeroderma pigmentosum (XP) is a rare genetic disorder caused by mutations in the XPC gene, leading to a dramatically increased risk of skin cancer-sometimes hundreds to thousands of times higher than in the general population.

This research was supported by the National Research Foundation of Korea (NRF) through the Mid-Career Researcher Program and the Bio-Medical Technology Development Program. The findings were published online in the esteemed journal Nucleic Acids Research (Impact Factor: 16.6) on June 18, 2025.

Journal Reference

Soyeong An, Masayuki Kusakabe, Hyun-Suk Kim, et al., "XPC-RAD23B enhances UV-DDB binding to DNA to facilitate lesion search in nucleotide excision repair," Nucleic Acids Res. (2025).