Polycyclic aromatic hydrocarbons, PAH, are a class of chemical carcinogens, that generate mutations in DNA. In living systems the resulting mutations have been associated with the initiation of cancer. My objective is to investigate the structural perturbations caused by covalently adducting various PAH molecules to double-stranded DNA to the carcinogenic outcome of PAH-DNA adduction. Solution structures of PAH-covalently adducted DNA where obtained using multi-dimensional NMR spectroscopy in conjunction with molecular dynamics simulation routines. My second research objective is to investigate the effect of the observed DNA structural perturbations of PAH on DNA replication. I am currently studying the DNA-binding properties of a newly discovered DNA polymerase, polX. PolX is the smallest known DNA polymerase with a molecular weight of 20 kDa. This polymerase is thought to be mainly involved in excision repair of DNA. The crystal structure for many DNA polymerases has been determined, and all of the enzymes have been shown to share a common structural motif, which resembles a half-closed right hand with fingers, palm and a thumb. Primary structural comparisons of polX with previously characterized polymerases indicate similarities in the palm and thumb regions. However, polX lacks a sequence that is homologous to the finger region in these polymerases. Through a comparative analysis of polX and canonical DNA polymerases with regard to the thermodynamics and kinetics of DNA binding we hope to shed light on the function of the finger region of DNA polymerases on DNA binding affinity, DNA binding specificity, and processivity.
