A molecular mechanism for DNA damage recognition by the xeroderma pigmentosum group C protein complex

Abstract

The XPC–HR23B complex is involved in DNA damage recognition and the initiation of global genomic nucleotide excision repair (GG-NER). Our previous studies demonstrate that XPC–HR23B recognizes and binds DNA containing a helix distortion, regardless of the presence or absence of damaged bases. Here, we describe an extended analysis of the DNA binding specificity of XPC–HR23B using various defined DNA substrates. Although XPC–HR23B showed significantly higher affinity for single-stranded DNA than double-stranded DNA, specific secondary structures of DNA, involving a single- and double-strand junction, were strongly preferred by the complex. This indicates that the presence of bases, which cannot form normal Watson–Crick base pairs in double-stranded DNA, is a critical factor in determining the specificity of XPC–HR23B binding. A DNase I footprint analysis, using a looped DNA substrate, revealed that a single XPC–HR23B complex protected a distorted site in an asymmetrical manner, consistent with the preferred secondary structure. The specific binding of XPC–HR23B is undoubtedly an important molecular process, based on which NER machinery detects a wide variety of lesions that vary in terms of chemical structure during DNA repair.