Non-Technical Abstract: This award by the Biomaterials program in the Division of Materials Research to University of Chicago supports the investigation of nucleic acid structures by looking at the relationship between the topological structure of nucleic acid and its function. This researcher will construct nano-architectures encoded with different functionalities to probe the activity of the machinery of the cell. Furthermore, this support will be used for the development of assays to quantitatively measure the activity of the enzymes responsible for the modulation of these nucleic acid topologies within the cell. Detailed analyses of these interactions will offer researchers information relevant for targeted therapeutics, as well as for unlocking the role of these enzymes in cell cycle regulation. This project will provide resources and opportunities for high school, undergraduate, and graduate students in the fields of molecular biology and chemistry to explore interdisciplinary studies relating to biological topology and enzyme kinetics. By collaborating with the surrounding local schools, this investigator will encourage students from traditionally underrepresented demographics to participate in scientific exploration through scholastic workshops and summer research initiatives. As a member of the Seminar Committee, this researcher will organize weekly public seminars for visiting faculty members, serving the research community at the University of Chicago and other nearby academic institutions.
This project will advance the understanding of nucleic acid topology within the cell, and will help elucidate how these different 3-D structures interact with topoisomerases and polymerases for cell regulation and replication. The first research goal is to develop novel complex molecular topologies using the Four-Way-Junction and advance their applications in chemical and biological studies. The simplicity and flexibility of the proposed strategy allows for the construction of innovative nanostructures with diverse topologies to probe enzyme kinetics and biological processes. The synthesis of higher-order topologies encoded with various nucleic acid functionalities, on a cell-relevant size-scale, will represent a critical step in furthering the understanding of the relationship between DNA structure and function. The double stranded DNA knots will be tested as substrates for human topoisomerases, which will allow them to monitor the enzyme activity in real time. The significance of this lies in their ability to interrogate the effects on reaction rates of a range of topoisomerase drugs both in vitro and in vivo. Additionally, by measuring in real time activity of topoisomerases upon exposure to various small molecule inhibitors, information regarding the efficacy of certain therapeutics can be qualitatively measured both in vitro and in vivo. By interfacing with nucleic acid amplification technologies, the assay can be designed to operate in a wide variety of conditions in a method consistent with the goals of a high-throughput system. This project will provide resources and opportunities for high school, undergraduate, and graduate students in the fields of molecular biology and chemistry to explore interdisciplinary studies relating to nucleic acid topology, chemical biology, and enzyme kinetics.
