Single-molecule visualization reveals the damage search mechanism for the human NER protein XPC-RAD23B
| Autor: | Orlando D. Schärer, Hyun-Suk Kim, Jung-Eun Yeo, Na Young Cheon, Ja Yil Lee |
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| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular Protein Conformation alpha-Helical RAD23B DNA Repair Base pair DNA repair DNA damage NAR Breakthrough Article Pyrimidine dimer Biology Diffusion 03 medical and health sciences chemistry.chemical_compound Genetics Humans Protein Interaction Domains and Motifs 030304 developmental biology 0303 health sciences Binding Sites Osmolar Concentration 030302 biochemistry & molecular biology DNA Bacteriophage lambda Single Molecule Imaging Cell biology DNA-Binding Proteins Kinetics DNA Repair Enzymes Oligodeoxyribonucleotides chemistry Pyrimidine Dimers DNA Viral Nucleic Acid Conformation Protein Conformation beta-Strand Human genome DNA Damage Protein Binding Nucleotide excision repair |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkz629 |
| Popis: | DNA repair is critical for maintaining genomic integrity. Finding DNA lesions initiates the entire repair process. In human nucleotide excision repair (NER), XPC-RAD23B recognizes DNA lesions and recruits downstream factors. Although previous studies revealed the molecular features of damage identification by the yeast orthologs Rad4-Rad23, the dynamic mechanisms by which human XPC-RAD23B recognizes DNA defects have remained elusive. Here, we directly visualized the motion of XPC-RAD23B on undamaged and lesion-containing DNA using high-throughput single-molecule imaging. We observed three types of one-dimensional motion of XPC-RAD23B along DNA: diffusive, immobile and constrained. We found that consecutive AT-tracks led to increase in proteins with constrained motion. The diffusion coefficient dramatically increased according to ionic strength, suggesting that XPC-RAD23B diffuses along DNA via hopping, allowing XPC-RAD23B to bypass protein obstacles during the search for DNA damage. We also examined how XPC-RAD23B identifies cyclobutane pyrimidine dimers (CPDs) during diffusion. XPC-RAD23B makes futile attempts to bind to CPDs, consistent with low CPD recognition efficiency. Moreover, XPC-RAD23B binds CPDs in biphasic states, stable for lesion recognition and transient for lesion interrogation. Taken together, our results provide new insight into how XPC-RAD23B searches for DNA lesions in billions of base pairs in human genome. |
| Databáze: | OpenAIRE |
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