DNA/RNA Quadruplexes: Structure, Stability, Interactions

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DESCRIPTION (provided by applicant): This project focuses on the unusual nucleic acid conformation of quadruplexes, built upon the guanine quartet. Evidence for the presence of these structures in biological systems, and their functional roles, has been mounting over the past five years: for example, quadruplex structures have been proposed to play a role in regulating telomerase activity, in initiation of transcription, in translational repression, and in binding specifically to a substantial number of proteins. Furthermore, applications have been described for quadruplexes as a folding motif for protein recognition, and as diagnostic agents, in addition to antiviral and anticancer chemotherapeutic agents. Structures based on guanine quartets are unique among nucleic acids in their dependence on specific binding of certain stabilizing cations. Our long term goal is an enhanced understanding of the thermodynamics, structure and interactions of this class of nucleic acids, in particular, in terms of the specific nature of cation binding, the properties of folded RNA quadruplexes and their differences with respect to DNA quadruplexes, and their interactions with other molecules of biological interest. In particular, we propose thermodynamic analyses of a series of biologically significant guanine-rich sequences, both in DNA and RNA forms, structural analyses of these sequences, development of methods to assess the molecularity of quadruplex forms and a detailed investigation of a catalytic DNA construct and its interactions with hemin. Experimental techniques to be employed in this goal include UV/CD spectroscopy, isothermal titration calorimetry, NMR, and fluorescence, and equilibrium sedimentation. This combination of approaches will afford a detailed examination of the conformation and interaction properties of the very important nucleic acid species.