Structure and Function of Aptamer based Biosensor Building Blocks

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In recent years, nucleic acid aptamers were increasingly employed as tools in chemistry, biochemistry and material sciences. DNA, RNA and their derivatives serve as recognition and reporter elements in biosensors, building blocks for nanostructures, and as pharmaceuticals. The long-term goals of the research program outlined here are to improve understanding of molecular recognition in aptamer - small molecule complexes and to develop a rational basis for the development of functional building blocks that can be used as part of biosensors or other nucleic acid applications. Toward this end a detailed understanding of how ligand binding in nucleic acids is related to sequence and structure must be obtained. In order to acquire this information, my research program focuses on structural and functional studies of nucleic acid aptamers. Model systems used for these studies include RNA and DNA aptamers to organic dyes such as Hoechst 33342 or its derivatives. In addition, my research group has identified a DNA aptamer by in vitro selection that recognizes the strongly fluorogenic molecular thiazole Orange with properties similar to its earlier selected and characterized RNA equivalent, the Mango Aptamer. We will determine the three-dimensional structures of these molecules by high resolution NMR spectroscopy. In addition, Isothermal titration calorimetry will be used to study binding thermodynamics. The kinetics of binding and folding will be studied using optical spectroscopy methods and surface plasmon resonance techniques. Differential Mobility Spectrometry techniques will be used to explore the interactions of the aptamers with ligands, ions, and solvents. Synthetic chemistry approaches will be employed for the production of ligand derivatives where needed. The combined application of these research tools will provide an improved understanding of how these aptamers recognize and change the molecular properties of their ligands. The basic knowledge gained by this research program will provide scientists and engineers with the tools to develop building blocks for nucleic acid based sensing and visualization applications using a more rational and systematic approach.