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Human and yeast DNA damage recognition complexes bind with high affinity DNA structures mimicking in size transcription bubble
Author(s) -
Krasikova Yuliya S.,
Rechkunova Nadejda I.,
Maltseva Ekaterina A.,
Anarbaev Rashid O.,
Pestryakov Pavel E.,
Sugasawa Kaoru,
Min JungHyun,
Lavrik Olga I.
Publication year - 2013
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.2308
Subject(s) - dna , biology , yeast , dna damage , nucleotide excision repair , dna repair , microbiology and biotechnology , protein–dna interaction , electrophoretic mobility shift assay , dna binding protein , biophysics , gene , biochemistry , transcription factor
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 (K D 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. Copyright © 2013 John Wiley & Sons, Ltd.