The relationships between XPC binding to conformationally diverse DNA adducts and their excision by the human NER system: Is there a correlation?

Abstract

The first eukaryotic NER factor that recognizes NER substrates is the heterodimeric XPC-RAD23B protein. The currently accepted hypothesis is that this protein recognizes the distortions/destabilization caused by DNA lesions rather than the lesions themselves. The resulting XPC-RAD23B -DNA complexes serve as scaffolds for the recruitment of subsequent NER factors that lead to the excision of the oligonucleotide sequences containing the lesions. Based on several well-known examples of DNA lesions like the UV radiation-induced CPD and 6-4 photodimers, as well as cisplatin-derived intrastrand cross-linked lesions, it is generally believed that the differences in excision activities in human cell extracts is correlated with the binding affinities of XPC-RAD23B to these DNA lesions. However, using electrophoretic mobility shift assays, we have found that XPC-RAD23B binding affinities of certain bulky lesions derived from metabolically activated polycyclic aromatic hydrocarbon compounds such as benzo[a]pyrene and dibenzo[a,l]pyrene, are not directly, or necessarily correlated with NER excision activities observed in cell-free extracts. These findings point to features of XPC-RAD23B-bulky DNA adduct complexes that may involve the formation of NER-productive or unproductive forms of binding that depend on the structural and stereochemical properties of the DNA adducts studied. The pronounced differences in NER cleavage efficiencies observed in cell-free extracts may be due to differences in the successful recruitment of subsequent NER factors by the XPC-RAD23B-DNA adduct complexes, and/or in the verification step. These phenomena appear to depend on the structural and conformational properties of the class of bulky DNA adducts studied.

Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway

“…Repair resistant lesions have been observed to bind XPC, and we have hypothesized that such binding modes are nonproductive ones. 60 …”

Transcription-coupled repair: an update

“…DDB1 and DDB2 are part of the CUL4-ROC1 ubiquitin ligase complex that ubiquitinates DDB2, XPC and histones when DNA is damaged. XPC binds the DNA strand opposite the lesion; this explains the ability of NER to recognize a wide array of lesions, adducts and abnormal structures in DNA (Lee et al 2014). The XPC/hRAD23b/Cen2 complex melts the DNA around the lesion and recruits the transcription/repair factor TFIIH.…”

Base and Nucleotide Excision Repair of Oxidatively Generated Guanine Lesions in DNA

“…Mouse monoclonal antibody (5F12) against human XPA (ab65963, Abcam, Cambridge, MA) was used to inhibit the NER activities. The full-length (amino acid residues 1-940) and truncated forms of XPC-RAD23B (the latter missing residues 1-155 only but active in binding to DNA (45)) were expressed in SF-9 insect cells as described (46). Another sample of fulllength XPC-RAD23B was kindly provided by Dr. Orlando Schärer (Stony Brook University, Stony Brook, NY).…”