Ligand Binding and Catalysis in RNA Aptamers

点击翻译按钮获取中文摘要

Nucleic acids are frequently used as tools in chemistry, biochemistry and material sciences. DNA, RNA and their derivatives serve as recognition elements in biosensors, building blocks for nano-structures, and as pharmaceuticals. The long-term goals of the research outlined here are to improve our understanding of molecular recognition in RNA-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 for in vivo imaging of RNA in microscopy. Toward this end a detailed understanding of how ligand binding and catalysis in nucleic acids are 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 acids with an emphasis on RNA. Model systems we will use for these studies include RNA aptamers to organic dyes such as fluorescein or sulforhodamine B. In addition we will select aptamers in my laboratory that recognize the non-fluorescent fluorescein-diacetate (FDA) and pursue the selection of ribozymes that can catalyze its conversion to fluorescein. We will determine the three-dimensional structures of these molecules by high resolution NMR spectroscopy. 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. The experimental work will be supplemented by theoretical studies of both structure and interactions using molecular dynamics and ab initio calculations. Synthetic chemistry approaches will be employed for the production of ligand derivatives where needed. The combined application of these research objectives will provide an improved understanding of how RNA aptamers recognize and change the molecular properties of their ligands. This basic knowledge will then be employed to develop building blocks for nucleic acid based sensors that can be combined with existing recognition modules (DNA and RNA aptamers), ribozymes, or nanostructures.