Research & Interests
Oxidative stress has been shown to contribute to aging and many disease etiologies, including diabetes, cancer, and atherosclerosis. The Davis Lab is interested in understanding how genomic and mitochondrial DNA is impacted by exogenous and endogenous oxidants. Our research encompasses questions ranging from: 1) What are the mechanisms of DNA damage initiation? 2) Which locations are susceptible to DNA damage? 3) What are the dynamics of DNA repair pathways in cellulo? 4) What are the consequences of DNA oxidative lesions on cellular processes like transcription and chromatin remodeling? Researchers in the Davis lab learn and apply techniques from Biochemistry, Biophysics, Microbiology, Molecular Biology, and Quantum Chemistry to tackle these questions. Our current research foci include:
1. DNA CHARGE TRANSPORT
Long-range DNA charge transport (CT) arises from either the addition or removal of excess charges from DNA. Once present, these excess charges become mobile through the stacked base pair environment of DNA and can migrate over considerable distances before becoming trapped to form mutagenic DNA lesions such as 8-oxoguanine, and oxazolone. While much is understood about CT in naked DNA, we are currently investigating how the DNA-protein complexes found in chromatin affect; i) the dynamics of hole transport in DNA, and ii) the observed distribution and types of oxidative damage observed. Thus far we have discovered that specific DNA-histone contacts in the nucleosome core particle significantly affect DNA CT. In addition to an altered guanine damage distribution, DNA CT in a NCP gives rise to DNA-protein cross-links (DPCs) between the packaged DNA and core histone proteins. Current studies in our laboratory focus on i) a molecular and structural understanding of the chemistry linking DNA CT to DPC formation in the NCP and other DNA-protein complexes, ii) in cellulo interrogation of DNA CT in eukaryotic cells and nuclei in the model eukaryote Saccharomyces cerevisiae (Baker’s yeast), and iii) the effects of DPC formation on fundamental cellular processes such as transcription, replication, and chromatin remodeling.
2. DNA REPAIR IN CHROMATIN
The proteins responsible for DNA repair in eukaryotes must recognize lesions, excise them, and restore the native DNA sequence within the confines of chromatin. Therefore, these direct repair processes are tightly coupled to cellular pathways responsible for disrupting chromatin structure and others that subsequently restore chromatin to complete repair. Currently, we are taking advantage of the powerful genomic tools available in the model eukaryote Saccharomyces cerevisiae to further our understanding of the roles different chromatin proteins play in regulating DNA repair pathways. Recently, we have discovered several novel residues in the core histone proteins that are important for yeast survival following UV-C irradiation. Using forward and reverse genetic approaches, along with biochemical analyses, we have shown that mutations in these regions of the histone proteins do not affect the biochemical reactions responsible for lesion removal, but instead are critical for the proper restoration of chromatin structure following DNA repair. We are currently working to delineate the molecular basis of these observations.
3. PAR AND ITS ROLES IN DNA REPAIR
A third project in the Davis lab focuses on Poly(ADP-ribose), a nucleic acid polymer whose roles in the cell are of intense current interest. The addition of polymeric forms of ADP-ribose to proteins by enzymes like PARP-1 is an event which has been shown to influence many intracellular events. We are interested in delineating the roles that ADP-ribosylation reactions play in DNA repair, and in particular their influence on BER. We have recently discovered that many of the BER glycosylases which repair oxidative lesions bind to PAR in vitro, and therefore they join a growing list of proteins including the core histones and P53 which possess the ability to bind to PAR. The consequences of the interaction between PAR and BER glycosylases on DNA repair reactions and other cellular processes are currently under investigation in our laboratory using a combination of in vitro and in vivo studies.
MBioS 499 (First year research seminar for STARS Students)
MBioS 413/513: General Biochemistry I
MBioS 414/514: General Biochemistry II