Book of Abstracts: Albany 2007
June 19-23 2007
Effect of Base Lesions on Duplex DNA
DNA inside of living organisms is constantly subjected to a barrage of endogenous and exogenous agents that can damage it permanently. This covalently damaged DNA must be restored to the native sequence and structure to prevent permanent mutations from persisting in the genetic code, leading to cancer, aging, or cell death. Damage to the DNA base pairs is particularly insidious as this part of the DNA carries the genetic information. Because modification of the DNA can be deadly, all organisms use multiple mechanisms to detect and correct damaged DNA. However, it is not clear how these cellular repair machineries selectively recognize modified base lesions since many are small, rare, and similar to the unmodified DNA bases. To determine what sets base lesions apart from normal DNA bases and makes them recognizable, we are performing a set of three complementary experiments on small pieces of DNA containing one known DNA base lesion. First, we examine base pair accessibility and duplex destabilization around lesions using small, reactive chemical probes. Secondly, we measure the thermodynamics of DNA stability with and without lesions to determine the extent to which the lesion weakens the integrity of the double helix itself. Finally, we are examining DNA dynamics around DNA lesions using Nuclear Magnetic Resonance (NMR). At and around base lesions the rate at which the DNA "breathes" may be significantly larger than at normal sequences, signaling to base repair enzymes that a lesion is present. The combination of these different sources of information generates a more complete and complex picture of the changes induced by DNA base lesions within normal DNA structure and may provide some insight into the way that small base lesions are detected and repaired in DNA.
Department of Chemistry