STRUCTURAL STUDY OF THE DNA DECAMER DUPLEXES CONTAINING DOUBLE T-G MISMATCHES

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Understanding the mechanism responsible for the DNA photodamage and the repair process would be a first step toward finding a solution to reduce the photodamage and enhance the repair. The cis-syn cyclobutane pyrimidine dimer (CPD) is one of the major classes of cytotoxic, mutagenic and carcinogenic DNA photoproducts induced by UV light. Though CPD formation due to the UV irradiation occurs quite frequently, CPD lesion is poorly recognized by repair enzyme XPC-hHR23B which is the primary damage recognition protein of the nucleotide excision repair (NER) pathway. Intriguingly, CPD/GG duplex represents unusually severe helical distortion due to the presence of double T-G mismatches, and XPC-hHR23B protein has a considerably higher binding affinity for CPD/GG duplex compared with the usual CPD lesion (CPD/TT). Therefore it is of importance to understand in which manner the target substrate for this protein is formed and how the T-G mismatches affect this process. Toward this goal we conducted wide-angle X-ray scattering (WAXS) measurement to investigate structural change of DNA duplex under CPD formation, double T-G mismatches and interaction with XPC-hHR23B protein in solution. Since X-ray solution scattering provides rich information about the structure, we expected to see the essential difference between damaged and undamaged DNA and between normal and mismatched DNA. We successfully obtained high-quality WAXS data from the DNA systems, with the experimental data in very good agreement with theoretical prediction. Further analysis to solve the nature of damaging and repairing process is still ongoing.