Boston University Department of Biology

Faculty Profiles

Current Research

Carcinogens are cancer-causing substances and are active by causing mutations, which makes sense, since tumor cells have mutations in key genes involved in growth control. Benzo[a]pyrene (B[a]P) is a potent mutagen-carcinogen and a “polycyclic aromatic hydrocarbon,” which are substances found ubiquitously in the environment due to incomplete combustion (e.g., in car exhaust, power plant emissions, cigarette smoke, and charred foods). B[a]P is often the most important component of soot based on its prevalence and its potency. In cells, B[a]P reacts at N2-guanine to give “+BP” ([+ta]-B[a]P-N2-dG), which usually causes G->T mutations.

We investigate the DNA polymerases (DNAPs) involved in mutagenic and non-mutagenic bypass of +BP. In human cells this involves the Y-Family DNAPs eta and kappa, whose functional orthologs are DNAPs V and IV in E. coli, which is our model system since we can probe mechanism more readily.

We have shown that DNAP IV inserts dCTP correctly opposite +BP, while DNAP V inserts dATP in the G->T mutagenic pathway, and we are now determining why. Based on our models, we changed one amino acid in DNAP IV and made it work like DNAP V in one step (extension) with +BP. Taking this approach (i.e., assessing the minimal amino acid changes required to make DNAP IV function like DNAP V—and vice versa), we are determining structural features that define how Y-Family DNAPs work in other steps (insertion). Similar studies are planned for DNAPs eta and kappa, as well as the crystallization of IV and V for X-ray structural studies.

Courses Taught

• BI 552 Molecular Biology I

Selected Publications

• Chandani, S. and Loechler, EL. (submitted). Y-Family DNA Polymerases Use Two Different dNTP Shapes in Catalysis: A Hypothesis and Its Implications.
• Seo K -Y, Yin, J, Chandani S, Lee CH, Nagalingam A, Loechler EL. (Submitted). Amino Acid Architecture That Influences dNTP Insertion in Y-Family DNAP V of E coli.
• Chandani S, Lee CH, Loechler EL. (2007). Molecular Modeling Benzo[a]pyrene N2-dG Adducts in Two Partially Overlapping Active Sites of the Y-Family DNA Polymerase Dpo4. Journal of Molecular Graphics and Modelling.  25, 658-670.
• Lee CH, Chandani S, Loechler EL. (2006). Homology modeling of four lesion-bypass DNA polymerases: structure and lesion bypass findings suggest that E. coli pol IV and human Pol h are orthologs, and E. coli pol V and human Pol k are orthologs. Journal of Molecular Graphics and Modelling 25, 87-102.
• Seo K -Y, Nagalingam A, Miri S, Yin J, Kolbanovskiy A, Shastry A, Loechler EL. (2006). Mirror Image Stereoisomers of the Major Benzo[a]pyrene N2-dG Adduct Are Bypassed by Different Lesion-Bypass DNA Polymerases in E. coli DNA Repair 5, 515-527.
• Chandani S, Lee CH, Loechler EL. (2005). Free energy perturbation methods to study structure and energetics of DNA adducts: Results for the major N2-dG adduct of benzo[a]pyrene in two conformations and different sequence contexts. Chemical Research in Toxicology. 18, 1108-1123.
• Seo K -Y, Nagalingam A, Tiffany M, Loechler EL. (2005). Mutagenesis studies on four stereoisomeric N2-dG benzo[a]pyrene adducts in the identical 5'-CGC sequence used in NMR studies: Although adduct conformation differs, mutagenesis outcome does not as G->T mutations dominate in each case. Mutagenesis 20, 441-448.
• Yin J, Seo K –Y, Loechler EL. (2004). A role for DNA polymerase V in G->T mutagenesis from the major benzo[a]pyrene N2-dG adduct when studied in a 5'-TGT sequence in Escherichia coli. DNA Repair 3, 323-334.