Collaborative Research: Molecular engineering of Methylation-Specific Binding Agents for DNA Purification

Rensselaer Polytechnic Institute, Troy NY

Investigators

Abstract

DNA is a key building block of life and abnormal mutations or chemical modifications in DNA are associated with several diseases including cancer, diabetes, Alzheimer?s disease and rheumatoid arthritis. Recent advances in science and engineering have led to the emergence of exciting possibilities for DNA as therapeutics and diagnostics, particularly for cancer. However, biomanufacturing of DNA-based therapeutics and development of disease diagnostics that exploit chemical modifications in DNA are still in their infancy. Specifically, cost-effective materials that can enrich modified DNA at small and large scales, which are important for diagnostic and therapeutic applications, respectively, are lacking. The proposed research brings together state-of-the-art advances in computational chemistry, molecular engineering, and biotechnology in order to generate new functional materials for selectively binding and enriching modified DNA, leading to novel, cost-effective processes for disease diagnostics and biomanufacturing. This collaborative research project addresses a key gap in bioseparations involving methylated DNA by first generating a computational (in silico) library of ligands derived from chemotherapeutics that have inherent affinity to sites of DNA methylation. Novel computational representation of the electronic structure of DNA using DNA pixels, in concert with state-of-the-art methods for studying orientations of interacting molecules, will be employed to identify ligands that selectively bind methylated DNA over unmethylated analogs. These ligands will be conjugated onto microbeads in order to experimentally evaluate their efficacy for binding, enrichment, and elution of methylated vs. unmethylated DNA. Binding data of methylated and unmethylated DNA will be further used to develop computational structure-activity relationship models in order to elucidate physicochemical phenomena that govern ligand selectivity. These novel materials will be employed to enrich plasmid DNA for therapeutic applications and methylated genomic DNA from bladder cancer cells for diagnostic applications. The proposed small-molecule ligands are anticipated to be more stable and less expensive compared to protein-based ligands, which makes this approach attractive for bioseparations, biomanufacturing, diagnostics, and therapeutics. In addition to the training of two doctoral graduate students, we will mentor undergraduate students via the Fulton Undergraduate Research Initiative and high school students via the SCience and ENgineering Experience on research projects at Arizona State University. We will coordinate outreach to high schools via the Rensselaer Chemistry Society and will collaborate with the Education Through eXploration Center at ASU in order to develop online active learning modules for broader online dissemination and outreach to high-school students worldwide. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.