title: Human and yeast DNA damage recognition complexes bind with high affinity DNA structures mimicking in size transcription bubble.
abstract: The human XPC-RAD23B complex and its yeast ortholog, Rad4-Rad23, are the primary initiators of global genome nucleotide excision repair. In this study, two types of DNA binding assays were used for the detailed analysis of interaction of these proteins with damaged DNA. An electrophoretic mobility shift assay revealed that human and yeast orthologs behave similarly in DNA binding. Quantitative analyses of XPC/Rad4 binding to the model DNA structures were performed using fluorescent depolarization measurements. The XPC-RAD23B and the Rad4-Rad23 proteins bind to the damaged 15 nt bubble-DNA structure mimicking in size the "transcription bubble" DNA intermediate with the highest affinity (KD values ~10(-10)  M or less) that is reduced in the following order: damaged bubble > undamaged bubble > damaged duplex > undamaged duplex. The affinity of XPC/Rad4 for various DNAs was shown to correlate with DNA bending angle. The results obtained show clearly that more deviation from regular DNA structure leads to higher XPC/Rad4 affinity.
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
authors.forename: Yuliya S
authors.initials: YS
authors.lastname: Krasikova
authors.forename: Nadejda I
authors.initials: NI
authors.lastname: Rechkunova
authors.forename: Ekaterina A
authors.initials: EA
authors.lastname: Maltseva
authors.forename: Rashid O
authors.initials: RO
authors.lastname: Anarbaev
authors.forename: Pavel E
authors.initials: PE
authors.lastname: Pestryakov
authors.forename: Kaoru
authors.initials: K
authors.lastname: Sugasawa
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Min
authors.forename: Olga I
authors.initials: OI
authors.lastname: Lavrik
mesh_terms: D004247:DNA / Q000737:chemistry*; D004249:DNA Damage / Q000235:genetics*; D045643:DNA Repair Enzymes / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D024202:Electrophoretic Mobility Shift Assay; D005454:Fluorescence Polarization; D006801:Humans; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; C513287:RAD23B protein, human; C086984:XPC protein, human; D004247:DNA; D045643:DNA Repair Enzymes
keywords: Rad4-Rad23; XPC-RAD23B; fluorescence anisotropy; nucleotide excision repair