Structural Effects of Secondary DNA Damage Products

Abstract

DNA, a crucial biomolecule, can undergo damage from both exogenous and endogenous sources. Examples of common DNA damage products include abasic sites (AP sites), thymine glycol, and 8-oxoguanine. These DNA damage products can undergo further chemical reactions to yield secondary DNA damage products. Here, the structural effects of secondary DNA products were studied by NMR spectroscopy. Urea lesions result from the hydrolysis of thymine glycol and 8-oxoguanine. The chemistry of the urea lesion in single stranded DNA was studied by NMR spectroscopy. The presence of the α and β anomers were present. Spectroscopic studies of the urea lesion in single stranded DNA provided the foundation for studies in duplex DNA.

AP sites are one of the most common DNA damage products that results from spontaneous depurination, an intermediate in the Base Excision Repair (BER) pathway, and deglycosylation from exposure to alkylating agents. AP sites can form secondary DNA damage products due to the reactive ring-opened intermediate that results from the anomerization of the α and β anomers. These secondary DNA damage products include interstrand crosslinks (ICLs) with nucleobases adenine, guanine, and the non-natural cytosine as well as DNA-drug conjugates. The structure of adenine crosslinked with an AP site (dA-AP ICL) was studied by restrained Molecular Dynamics with restraints generated by NMR spectroscopy. The structural effects of AP conjugates with mitoxantrone (MTX-AP) and pixantrone (PIX-AP) were studied by NMR spectroscopy. Both MTX-AP and PIX-AP conjugates increase the thermal stability compared to duplex DNA with solely AP sites, and intercalates between G18 and C19 on the complementary strand. The data generated from NMR experiments will be utilized for future restrained Molecular Dynamics experiments with both conjugates.