Modified nucleosides present in DNA have been implicated in such diverse areas as mutagenesis, carcinogenesis, protein-DNA recognition, and transcription. In addition, it is now known that DNA is conformationally flexible, and that conformational differences are critically important to DNA function. In order to begin to understand these effects it is necessary to have model systems - specifically modified oligonucleotides. However, such molecules have been largely unavailable due both to the lack of appropriate modified nucleosides and to the rigors of oligonucleotide synthesis and purification. The long term goals of this project are to develop and demonstrate the synthetic strategies and purification methodologies necessary for the synthesis and utilization of specifically modified oligonucleotides. The molecules that are proposed will have immediate impact on understanding of DNA base pairing, conformation, and structure/function relationships. In addition, the procedures developed will provide access to other modified oligonucleotides, designed to answer specific questions about DNA. The modified nucleosides to be incorporated will include: 06-methyl- and 06-ethyl deoxyguanosine, N6-methyl- and N6-methoxydeoxyadenosine, 2-aminopurine deoxyriboside, and 15N labelled deoxyadenosine, deoxyguanosine and 06-alkyldeoxyguanosine. In all cases the routes devised will be amenable to large scale synthesis so that the modified nucleosides produced will be usable for oligonucleotide synthesis. In order to incorporate these modified nucleosides into oligonucleotides we will devise synthetic strategies that are more nucleoside efficient than are present approaches. The modified oligonucleotides will then be """"""""paired"""""""" with a set of complementary oligonucleotides, so that all possible combinations with the modified nucleoside and its nearest neighbors will be present. In addition, we will rigorously examine these synthetic oligonucleotides to attempt to isolate and identify the minor side reactions which accompany oligonucleotide synthesis. Side reactions have been a particular problem with certain modified nucleosides, and also accompany standard oligonucleotide synthesis.
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