Nucleotide excision repair (NER) removes lesions caused by environmental mutagens or UV light from DNA. A hallmark of NER is the extraordinarily wide substrate specificity, raising the question of how one set of proteins is able to recognize structurally diverse lesions. Two key features of good NER substrates are that they are bulky and thermodynamically destabilize DNA duplexes. To understand what the limiting step in damage recognition in NER is, we set out to test the hypothesis that there is a correlation of the degree of thermodynamic destabilization induced by a lesion, binding affinity to the damage recognition protein XPC-RAD23B and overall NER efficiency. We chose to use acetylaminofluorene (AAF) and aminofluorene (AF) adducts at the C8 position of guanine in different positions within the NarI (GGCGCC) sequence, as it is known that the structures of the duplexes depend on the position of the lesion in this context. We found that the efficiency of NER and the binding affinity of the damage recognition factor XPC-RAD23B correlated with the thermodynamic destabilization induced by the lesion. Our study is the first systematic analysis correlating these three parameters and supports the idea that initial damage recognition by XPC-RAD23B is a key rate-limiting step in NER.

A lattice chain model is extended to investigate the preferential position of a sticky sphere bound to a polymer chain, motivated by wrapping one nanosize core-histone with DNA to form a nucleosome structure. It was shown that the single bound histone is populated in DNA chain ends from the experiment by T. Sakaue et al. [Phys. Rev. Lett. 87, 078105 (2001)]. Here, the possible mechanisms are examined to elucidate such behavior. For neutral chains or ionic chains in high salt concentrations, spheres bound on the middle of chain may trigger conformational constraints to reduce conformational entropy. For ionic chains, the bound sphere can be driven to chain ends if its effective charge and the charge of chain monomers are of like charge. The two-dimensional chain is further studied to mimic the chromosome strongly adsorbed onto surfaces, of which behavior is similar to the three-dimensional case with minor difference due to surface confinement.

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