This proposal is aimed at expanding or contracting the diameter of the DNA helix, and studying the effects on its pairing properties. The normal C1'-C1' distance in B-form DNA is ca. 10.7 Angstrom units. It is proposed that DNA bases of varying length be synthesized and their base pairing thermodynamics tested in helices consisting entirely of such """"""""stretched"""""""" or """"""""compressed"""""""" base pairs. Taking inspiration from an extended adenine compound originally synthesized by Leonard, we will accomplish the length variation of the nucleobases by addition or removal of the width of one benzene ring. Thus, the dimensions will be varied in 2.4 Angstrom units increments. This work will address some important basic scientific questions, by providing new insight into the physical origins of DNA helix stability, and the role that electrostatics and base stacking play in it. It will also provide useful data regarding the effects of steric size and shape of the nucleobase on polymerase replication of DNA. Finally, the project will explore the viability of an alternative genetic system, giving insight into how our natural genetic system evolved. For sequence-generalizable hybridization, designs of four 2.4 Angstrom units extended DNA bases are proposed. It is hypothesized that DNA strands completely comprised of such analogues will be competent in hybridizing to natural RNA or DNA complements. Moreover, it is predicted that because of greatly enhanced base stacking, the binding will exhibit higher affinity and pairing specificity than natural DNA does. Further, a number of these extended bases are expected to be fluorescent, allowing for the possibility that they can act as self-reporters of helix formation. These enhanced properties are likely to be of significant utility in many nucleic acid hybridization applications, such as in synthetic DNA microarrays. In the term covered by this proposal, the aims are to (1) evaluate two compressed thymine analogues in 8.4 Angstrom units helices; (2) study an expanded deoxyadenosine analogue in 10.7 and 13.0 Angstrom units helices, and evaluate polymerase enzyme activity; (3) test generalizability of pairing with analogues of four expanded bases in 10.7, 13.0 and 15.4 Angstrom units helices; and (4) study the structure and fluorescence properties of single nucleosides and of helices comprised of these modified- sized bases.
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