DNA excision repair assays

Remarkable Enhancement of Nucleotide Excision Repair of a Bulky Guanine Lesion in a Covalently Closed Circular DNA Plasmid Relative to the Same Linearized Plasmid

The excision of DNA lesions by human nucleotide excision repair (NER) has been extensively studied in human cell extracts. Employing DNA duplexes with fewer than 200 bp containing a single bulky, benzo[a]pyrene-derived guanine lesion (B[a]P-dG), the NER yields are typically on the order of ∼5-10%, or less. Remarkably, the NER yield is enhanced by a factor of ∼6 when the B[a]P-dG lesion is embedded in a covalently closed circular pUC19NN plasmid (contour length of 2686 bp) rather than in the same plasmid linearized by a restriction enzyme with the B[a]P-dG adduct positioned at the 945th nucleotide counted from the 5'-end of the linearized DNA molecules. Furthermore, the NER yield in the circular pUC19NN plasmid is ∼9 times greater than in a short 147-mer DNA duplex with the B[a]P-dG adduct positioned in the middle. Although the NER factors responsible for these differences were not explicitly identified here, we hypothesize that the initial DNA damage sensor XPC-RAD23B is a likely candidate; it is known to search for DNA lesions by a constrained one-dimensional search mechanism [Cheon, N. Y., et al. (2019) Nucleic Acids Res. 47, 8337-8347], and our results are consistent with the notion that it dissociates more readily from the blunt ends than from the inner regions of linear DNA duplexes, thus accounting for the remarkable enhancement in NER yields associated with the single B[a]P-dG adduct embedded in covalently closed circular plasmids.

Purification and characterization of Escherichia coli and human nucleotide excision repair enzyme systems

Nucleotide excision repair is a multicomponent, multistep enzymatic system that removes a wide spectrum of DNA damage by dual incisions in the damaged strand on both sides of the lesion. The basic steps are damage recognition, dual incisions, resynthesis to replace the excised DNA, and ligation. Each step has been studied in vitro using cell extracts or highly purified repair factors and radiolabeled DNA of known sequence with DNA damage at a defined site. This chapter describes procedures for preparation of DNA substrates designed for analysis of damage recognition, either the 5' or the 3' incision event, excision (resulting from concerted dual incisions), and repair synthesis. Excision in Escherichia coli is accomplished by the three-subunit Uvr(A)BC excision nuclease and in humans by six repair factors: XPA, RPA, XPChR23B, TFIIH, XPFERCC1, and XPG. This chapter outlines methods for expression and purification of these essential repair factors and provides protocols for performing each of the in vitro repair assays with either the E. coli or the human excision nuclease.

Effect of the spectral range of a UV lamp on the production of cyclobutane pyrimidine dimers in human skin in situ

BACKGROUND

Ultraviolet (UV) irradiation has a broad spectrum of biological effects and a capacity to initiate skin carcinogenesis through DNA damage. The effect of different wave bands of UV light on the production of DNA damage in human skin in situ was studied with a broadband UV-B lamp TL-12 and a narrowband UV-B lamp TL-01.

METHODS

Eight psoriasis patients participated in the study. Their minimal erythema dose was assessed separately for the two UV-B wave band ranges. Test areas of buttock skin were irradiated with the two spectrally differing lamps using erythemally equivalent UV doses of 40 and 80 mJ/cm2 CIE (Commission International de I'Eclairage). Punch biopsies were taken from the irradiated areas, and UV-induced DNA lesions (cyclobutane pyrimidine dimers, CPDs) in the skin were analyzed with a 32P high-performance liquid chromatography postlabelling method.

RESULTS

No UV source-dependent differences in the induced levels of CPDs were detected in this study.

CONCLUSION

CPD production with broadband TL-12 and narrowband TL-01 UV-B lamps in situ did not differ when erythemally equivalent UV doses were used. The preliminary result needs to be confirmed in a larger study.

Evidence for epidermal growth factor receptor-enhanced chemosensitivity in combinations of cisplatin and the new irreversible tyrosine kinase inhibitor CI-1033

Irreversible inhibitors of the epidermal growth factor receptor (EGFR) are showing promise in clinical trials. This report is the first to show that inhibition of the EGFR tyrosine kinase by an irreversible binder synergizes with cisplatin, at least in EGFR-overexpressing tissue culture cell lines in vitro. Unlike previous synergies demonstrated between ErbB2 blockade and DNA-damaging drugs, the synergy between the irreversible EGFR inhibitor and cisplatin does not appear to involve the repair of DNA-cisplatin adducts. Given the current clinical data, this combination may be of more than theoretical interest.

Effect of age on the formation and repair of UV photoproducts in human skin in situ

Ultraviolet radiation (UVR)-induced photoproducts can be measured by a number of methods. The newly developed 32P-postlabelling method is feasible in molecular epidemiological studies due to its sensitivity, specificity and little amount DNA needed. We applied the 32P-postlabelling method to investigate the induction and repair of photoproducts (cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts) after UVR in human skin in situ and studied the effects of age, skin type and gender. The study included 30 subjects aged 32-78 years. The photoproduct induction levels varied 7- to 15-fold between the individuals tested. All four types of photoproducts were induced at a higher frequency in the older population (>/=50 years) than in the younger population (<50 years). Individuals with skin type I and II had a higher CPD induction frequency than individuals with skin type III and IV. In both cases, the differences in thymidylyl (3'-5') thymidylyl (3'-5')-2'-deoxycytidine induction reached statistical significant levels (p<0.05). Photoproduct repair rates 24 h and 48 h after UV irradiation showed a large inter-individual variation. No clear effects of age, skin type or gender on DNA repair could be detected. Our data suggest that UV-induced DNA photoproduct levels increase with age.

Characterization of reaction intermediates of human excision repair nuclease

Nucleotide excision repair in humans is a complex reaction involving 14 polypeptides in six repair factors for dual incisions on either sides of a DNA lesion. To identify the reaction intermediates that form by the human excision repair nuclease, we adopted three approaches: purification of functional DNA.protein complexes, permanganate footprinting, and the employment as substrate of presumptive DNA reaction intermediates containing unwound sequences 5' to, 3' to, or encompassing the DNA lesion. The first detectable reaction intermediate was formed by substrate binding of XPA, RPA, XPC.HHR23B plus TFIIH (preincision complex 1, PIC1). In this complex the DNA was unwound on either side of the lesion by no more than 10 bases. Independent of the XPG nuclease function, the XPG protein stabilized this complex, forming a long lived preincision complex 2 (PIC2). The XPF.ERCC1 complex bound to PIC2, forming PIC3, which led to dual incisions and the release of the excised oligomer. With partially unwound DNAs, thymine cyclobutane dimer was excised at a fast rate independent of XPC.HHR23B, indicating that a major function of this protein is to stabilize the unwound DNA or to aid lesion unwinding in preincision complexes.