DNA inside of living organisms is constantly subjected to a barrage of endogenous and exogenous agents that can damage it permanently. This damaged DNA must be restored to the native sequence and structure in order 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 have 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, a set of three complementary experiments will be performed on small pieces of DNA containing one known DNA base lesion.
The first aim i s to determine the rate of base pair opening at and around DNA lesions using Nuclear Magnetic Resonance (NMR). At and around base lesions the rate at which the base pairs breathe may be significantly larger than at normal sequences, signaling to base repair enzymes that a lesion is present.
The second aim i s to examine base pair accessibility and duplex destabilization around lesions using small, reactive chemical probes, to see if the DNA core is more open and accessible around base lesions.
The third aim i s to 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. DNA damage, repair (or the lack of repair), and mutation are often critical events in the processes of aging and carcinogenesis. Thus we must understand how damage to the DNA is detected and repaired in order to meaningfully assess the long-term effects of environmental contaminants, bioactive plant products, drug treatments, and other exogenous agents on the genome.
| Wenke, Belinda B; Huiting, Leah N; Frankel, Elisa B et al. (2013) Base pair opening in a deoxynucleotide duplex containing a cis-syn thymine cyclobutane dimer lesion. Biochemistry 52:9275-85 |
| Crenshaw, Charisse M; Wade, Jacqueline E; Arthanari, Haribabu et al. (2011) Hidden in plain sight: subtle effects of the 8-oxoguanine lesion on the structure, dynamics, and thermodynamics of a 15-base pair oligodeoxynucleotide duplex. Biochemistry 50:8463-77 |
| Rumora, Amy E; Kolodziejczak, Katarzyna M; Malhowski Wagner, Anne et al. (2008) Thymine Dimer-Induced Structural Changes to the DNA Duplex Examined with Reactive Probes. Biochemistry : |
