DNA microarrays have revolutionized the way that biological research is done, enabling the analysis of thousands of genes in a single experiment. Microarrays are being used in gene profiling, toxicogenomics, drug discovery, pathway biochemistry, and legal identification. Even though this powerful technique has been enthusiastically adopted by the scientific community, it is far from mature. Considerable uncertainty exists about how to design microarrays for maximum sensitivity and specificity. A fundamental understanding of the interplay between the various factors that affect microarray performance is needed.
The proposed research has two basic objectives. The first objective is to develop guidelines for designing microarrays with maximum sensitivity and specificity. This will be accomplished by performing Monte Carlo simulations of the adsorption and molecular recognition of lattice model DNA target molecules by lattice model probe molecules tethered to a microarray surface. DNA is basically at the nano-scale. The factors that affect the sensitivity and specificity of microarrays will be systematically explored including: the probe sequence, length and concentration; the target sequence, length and concentration; the nucleotide compositions of the probe and target, the spacer length, and the temperature. Results from this study will be compared to those of our experimental collaborator, Professor Stefan Franzen and to data in the literature. The second objective is to develop a new computational tool that can be used to improve accuracy in interpreting microarray data. This will be accomplished by building a new intermediate resolution model of DNA molecules and then performing implicit-solvent discontinuous molecular dynamics simulations of the adsorption of target model DNA molecules (both perfect match and mismatch) on microarray surfaces containing probe model DNA molecules. A multiscale modeling approach will be used to extract the energetic and geometrical parameters in the model from potentials of mean force calculated during explicit-solvent CHARMM simulations. A sub-objective here is to quantify the difference between hybridization on surfaces and hybridization in bulk, and then to use this information to modify and improve the bulk-based theoretical models currently used to correlate microarray data on perfect matches and mismatches. Results from this part of the project will be compared to experimental results of our collaborator Professor Erdogan Gulari. Taken together these two projects should give us a good
physical picture of molecular recognition in DNA microarrays. The broader impacts of the proposed research are the following. The proposed research could have an impact on the world of medical research. DNA microarrays are heavily used in cancer research today as researchers struggle to identify genes that are expressed in tumors, or to identify genetic markers (oncogenes) that could serve as potential targets for chemotherapy. In addition to training two graduate students, research and education will be fostered by the following two activities. (1) Hybridization of DNA on microarrays will be used as the basis for a number of examples that will be developed for the PI's undergraduate chemical engineering thermodynamics course, and inserted into an undergraduate chemical engineering thermodynamics textbook that she is writing. (2) A power point presentation describing the basics of genomics and culminating in a description of DNA microarrays will be prepared for dissemination via the web. The PI will continue her considerable but informal activities to broaden the opportunities for women. Since she was one of the first women to be appointed to a chemical engineering faculty in the US, the PI is now viewed as a role model by younger members of the academic community, and hence serves as an informal mentor to many women students (undergraduate and graduate) at NCSU, as well as to women faculty and prospective women faculty across the US. The PI attracts a disproportionate number of women graduate students to her research group; of the 16 graduate students that she has advised over the past five years, 9 have been women.
