DNA is constantly under attack by agents that can chemically modify its structure. Some of these agents are exogenous, such as ultraviolet light, ionizing radiation, pharmaceuticals, and methylating agents, while others can be endogenous, like reactive oxygen species. When they react with the DNA base pairs, a variety of new and different bases can result:
8-oxoguanine and Fapy are formed by oxidation of guanine by various reactive oxygen species (ROS). Uracil is formed in double-stranded DNA by the spontaneous deamination of cytosine, while hypoxanthine is formed from the deamination of adenine. The cis-syn thymine dimer lesion is formed when two adjacent thymine bases become fused by UV light. 3-methyl-adenine is formed from the alkylation of adenine, and thymine glycol is formed by the oxidation of thymine. Chemical modifications to the base pairs such as these present a serious challenge to the integrity of the DNA, altering the way that the DNA is transcribed or regulated and potentially leading to mutations, cancer, and cell death.
My specific interest involves the formation and excision of small base lesions. Interestingly, though a lot is known about the substrate preference, structure, and mechanism of individual repair enzymes, it is still unclear how a relatively small number of base excision repair enzymes can patrol the entire genome. How are relatively small, thermodynamically-stable base lesions found, recognized, and excised? This question is often compared to a "needle in a haystack" search.
Using a variety of chemical and biochemical techniques, including selective chemical modification of DNA, gel electrophoresis, mass spectrometry, differential scanning calorimetry, atomic force microscopy, nuclear magnetic resonance, and DNA pulling with optical tweezers, we examine their thermodynamic, kinteic, and structural effects on the DNA helix.