In a groundbreaking study published this year, researchers have unveiled the intricate atomic mechanisms underlying nucleotide excision repair (NER), an essential DNA repair pathway that safeguards genomic integrity from bulky lesions. These lesions, often caused by ultraviolet radiation and various chemical agents, threaten cellular viability and contribute to severe human diseases, including xeroderma pigmentosum, cancer, and premature aging. By dissecting the functional steps and three-dimensional architecture of the complete NER machinery during DNA bubble formation and dual incision, the study fundamentally advances our understanding of how cells recognize and excise damaged DNA with extraordinary precision.
NER operates by first detecting distortions in the DNA helix, where bulky adducts compromise normal base pairing and helical structure. This initial recognition occurs via the XPC protein in global genome repair or through RNA polymerase stalling during transcription-coupled repair. However, lesion verification and removal require a cascade of carefully orchestrated molecular events, prominently featuring the helicase and ATPase activities of the TFIIH complex comprising XPB and XPD subunits. The study details how these ATPases collaborate to unwind approximately 27 base pairs surrounding the lesion, forming a characteristic DNA bubble that is a prerequisite for repair factor recruitment and incision.
A pivotal revelation of this research is the distinct roles of XPB and XPD helicases during unwinding. XPB acts predominantly as a double-strand DNA translocase, providing the mechanical force necessary to destabilize the DNA duplex. Complementary to this, XPB’s activity is spatially coordinated by subunits such as XPA and XPF, which function as duplex dividers that separate and stabilize the single-stranded DNA regions formed around the lesion. This cooperative action ensures the precise creation and maintenance of the repair bubble, enabling lesion accessibility and factor assembly at both the 5′ and 3′ borders of the damaged site.
Further structural insights reveal how XPD specifically binds to the lesion-containing strand, positioning it in concert with XPF at the 5′ double strand–single strand (ds-ss) junction. This assembly primes the lesion strand for incision, but intriguingly, cleavage by XPF is conditional on the accompanying binding of XPG to the 3′ ds-ss junction. The interplay between these endonucleases guarantees that dual incisions flank the lesion, excising a DNA oligonucleotide of defined length and preserving genomic stability.
The research also clarifies the multifunctional role of the ERCC1 subunit within the XPF complex. ERCC1 facilitates crucial DNA strand separation at the incision site, a process that not only assists in positioning XPF for precise cleavage but also promotes the recruitment of replication protein A (RPA) to the non-lesion strand. RPA binding stabilizes single-stranded DNA, preventing unwanted secondary structures and preparing the gap for downstream repair synthesis. This coordination exemplifies the intricate orchestration of protein-DNA interactions required for efficient lesion removal.
Advanced cryo-electron microscopy and biochemical analyses employed in the study allowed visualization of these key intermediate structures at near-atomic resolution, a feat that has eluded the field until now. These structural snapshots illuminate the conformational changes triggered by ATP hydrolysis and damage recognition, showcasing dynamic rearrangements that turn the disparate NER factors into a cohesive molecular machine. Such insights reveal how the DNA landscape is meticulously remodeled to allow incision only upon authentic lesion verification, thereby minimizing erroneous cleavages and maintaining genomic fidelity.
From a biomedical perspective, elucidating these mechanisms sheds light on the molecular basis of NER deficiencies seen in diseases such as xeroderma pigmentosum, where mutations in specific subunits can disrupt DNA binding or incision activities, leading to hypersensitivity to UV light and elevated cancer risk. Furthermore, understanding how NER factors modulate repair efficacy opens up avenues for therapeutic intervention. Modulating the activity of XPB, XPD, or the endonucleases may enhance the sensitivity of cancer cells to chemotherapeutic agents that induce bulky DNA lesions, potentially improving treatment outcomes.
This comprehensive model also challenges previous assumptions regarding lesion verification and opening, emphasizing that lesion unwinding and strand separation are mechanically driven rather than solely dependent on DNA affinity. The dual role of XPB as both a translocase and a mechanical force generator places it at the heart of DNA bubble formation, redefining functional hierarchies within the NER process. Such conceptual advances are poised to inspire further studies exploring related repair pathways and their integration with cellular stress responses.
The discovery is a testament to the power of integrating structural biology with biochemistry, providing a holistic view of the NER cascade from lesion detection to dual incision. It highlights the necessity for precise temporal and spatial coordination among proteins to execute complex molecular tasks on the genome. This knowledge not only deepens scientific understanding but also underscores the elegance of cellular machinery evolved to maintain life’s blueprint in the face of relentless environmental insults.
Beyond its immediate implications, the study sets a benchmark for future investigations aiming to manipulate DNA repair pathways artificially. For instance, targeted modulation of NER factors could potentially enhance genome editing technologies by controlling repair outcomes at DNA breaks or lesions. Moreover, the atomic-level details of protein-DNA interfaces revealed here might be exploited to design small molecules that selectively influence NER function, offering novel drug candidates with high specificity.
In summary, this groundbreaking research breathes new life into the study of nucleotide excision repair by unveiling the precise molecular choreography and structural underpinnings of DNA bubble formation and incision. It integrates key ATP-driven helicase activities with lesion recognition and endonuclease actions, providing a comprehensive blueprint of the NER machinery in action. These findings not only deepen our fundamental understanding of DNA repair but also illuminate potential therapeutic strategies for diseases linked to genomic instability, heralding a new era in molecular medicine and genomic maintenance.
Subject of Research: DNA nucleotide excision repair mechanisms and structural biology of NER factors.
Article Title: Pre-incision structures reveal principles of DNA nucleotide excision repair.
Article References:
Li, E.C.L., Kim, J., Brussee, S.J. et al. Pre-incision structures reveal principles of DNA nucleotide excision repair. Nature (2026). https://doi.org/10.1038/s41586-026-10122-5
DOI: https://doi.org/10.1038/s41586-026-10122-5
