This research project will determine the structures and dynamics of aptamer and telomere DNAs which have quadraplex base pairing. The structure of a DNA aptamer which binds to, and inhibits thrombin has been determined. This DNA aptamer exhibits a new structural motif which consists of a """"""""chair"""""""" like overall fold with tetrads of guanosine base pairs and three loops. The aptamer structure has led to a proposal for common secondary and tertiary structural features which telomere DNAs can adopt. The common secondary and tertiary structures are consistent with the known sequences of telomere DNAs. The structure of the telomere DNA of Oxytricha has been determined and been found to be consistent with the proposed common tertiary structure. This research plan will test the secondary and tertiary structure models by determining the structures of telomere DNAs in solution by NMR methods. This research also may have significant drug design implications for development of cancer therapeutics. Telomerase is known to be an important activity of tumor cells and intramolecular quartet structures are known to inhibit telomerase. Thus, the combination of the aptamer and telomere aspects of this project may provide important information for the discovery of leads for telomerase inhibition. The structures of two types of duplex-quadraplex junctions will also be investigated. It is proposed that there may be an equilibrium between duplex and duplex-quartet junction structures in telomere and other DNAs. Studies on the electrostatic potentials will be studied by use of the paramagnetic ion manganese. The dynamics of the samples will also be investigated. These studies will provide information about the properties of quadraplex based aptamers and help to guide the design and development of aptamers to targets other than thrombin, including telomerase. These studies will provide structural information on telomere DNAs, duplex-quadraplex junctions in telomere DNA and test the models for the common secondary and tertiary structures of telomere DNA. The information about these DNAs is relevant to the biological activities of telomere, centromere, immunoglobin switch regions and other DNAs.
