Specific and Efficient Binding of Xeroderma Pigmentosum Complementation Group A to Double-Strand/Single-Strand DNA Junctions with 3‘- and/or 5‘-ssDNA Branches
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Human XPA is an important DNA damage recognition protein in nucleotide excision repair (NER). We previously observed that XPA binds to the DNA lesion as a homodimer [Liu, Y., Liu, Y., Yang, Z., Utzat, C., Wang, G., Basu, A. K., and Zou, Y. (2005) Biochemistry 44, 7361-7368]. Herein we report that XPA recognized undamaged DNA double-strand/single-strand (ds-ssDNA) junctions containing ssDNA branches with binding affinity (Kd = 49.1 +/- 5.1 nM) much higher than its ability to bind to DNA damage. The recognized DNA junction structures include the Y-shape junction (with both 3'- and 5'-ssDNA branches), 3'-overhang junction (with a 3'-ssDNA branch), and 5'-overhang junction (with a 5'-ssDNA branch). Using gel filtration chromatography and gel mobility shift assays, we showed that the highly efficient binding appeared to be carried out by the XPA monomer and that the binding was largely independent of RPA. Furthermore, XPA efficiently bound to six-nucleotide mismatched DNA bubble substrates with or without DNA adducts including C8 guanine adducts of AF, AAF, and AP and the T[6,4]T photoproducts. Using a set of defined DNA substrates with varying degrees of DNA bending, we also found that the XPC-HR23B complex recognized DNA bending, whereas neither XPA nor the XPA-RPA complex could bind to bent DNA. We propose that, besides DNA damage recognition, XPA may also play a novel role in stabilizing, via its high affinity to ds-ssDNA junctions, the DNA strand opening surrounding the lesion for stable formation of preincision NER intermediates. Our results provide a plausible mechanistic interpretation for the indispensable requirement of XPA for both global genome and transcription-coupled repairs. Since ds-ssDNA junctions are common intermediates in many DNA metabolic pathways, the additional potential role of XPA in cellular processes is discussed.
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XPA binds ds-ssDNA junctions with a higher affinity (Kd = 49.1 ± 5.1 nM) than it binds bulky DNA lesions (Kd = 200 nM).
“In addition, XPA binds to ds-ssDNA junctions with a significantly higher affinity (Kd = 49.1 ± 5.1 nM) 100 than it’s specific binding to bulky DNA lesions (Kd = 200 nM) 101.”
From Xeroderma Pigmentosa Group A (XPA), Nucleotide Excision Repair and Regulation by ATR in Response to Ultraviolet Irradiation (2017) · cites this paper as [100]
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Kong, M. (2017) · D-Scholarship@Pitt (University of Pittsburgh) · Cited by 1 · see citing works
Progeria and Genome Instability
Meng, F., Liu, B., & Zhou, Z. (2015) · Springer eBooks · doi:10.1007/978-4-431-55763-0_3
Biochemical and Structural Domain Analysis of Xeroderma Pigmentosum Complementation Group C Protein
Shell, S. M., & Chazin, W. (2010) · ACS symposium series · doi:10.1021/bk-2010-1041.ch005
Self-citationMechanisms of Repeat Instability in Fragile X Syndrome
Usdin, K., Gazy, I., & Zhao, X.-N. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-804461-2.00005-6
Structural and Biophysical Characterization of the Nucleotide Excision Repair Factor XPA
Sugitani, N. (2017) · ProQuest Demo Repository
Visualization of stepwise derepression of TFIIH in global genome nucleotide excision repair
Garrido, N. D. M., Haste, C. A. F., Feng, J., Cronin, N. B., & Greber, B. J. (2026) · Science Advances · doi:10.1126/sciadv.aeb3506
- Authors
- Yang, Z., Roginskaya, M., Colis, L. C., Basu, A. K., Shell, S. M., Liu, Y., Musich, P. R., Harris, C. M., Harris, T. M., & Zou, Y.
- Affiliations
- East Tennessee State University (US)
- Corresponding author
- Zou, Yue
- ORCID
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-12-01
- Volume
- 45
- Issue
- 51
- Pages
- 15921-15930
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- PMC
- PMC2528077
- OpenAlex
- W2400984959
- Cited by
- 65
- References
- 41
- Citations by year
- 2026: 1 · 2025: 1 · 2022: 3 · 2021: 2 · 2020: 4 · 2019: 3 · 2018: 4 · 2017: 9 · 2016: 3 · 2015: 3 · 2014: 2 · 2013: 2 · 2012: 6
- FWCI
- 1.63
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Commons - East Tennessee State University (East Tennessee State University) (submittedVersion)
- Funders
- East Tennessee State University
- National Cancer Institute (R56CA086927, R01CA086927, CA-86927)
- National Institute of Environmental Health Sciences (ES09127, ES-013324, R01ES013324, R56ES009127, R01ES009127)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Keywords
- XPA, nucleotide excision repair, DNA damage recognition, DNA bending, photoproducts, transcription-coupled repair, global genome repair
- MeSH terms
- Animals, Base Sequence, Cell Line, DNA Damage, DNA Repair, DNA-Binding Proteins, DNA, Single-Stranded, Humans, Molecular Sequence Data, Nucleic Acid Conformation, Protein Binding, Baculoviridae, Spodoptera, DNA Adducts, Xeroderma Pigmentosum Group A Protein
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