| Propynyl groups on pyrimidines of DNA increase the affinity for complementary RNA by extended π stacking, and also activate RNase H. These features render propynyl groups as promising agents for preparing modified antisense oligonucleotides.; The introduction of C8-propynyl groups in the purines of DNA·DNA duplexes results in the destabilization of hybrid duplexes due to steric clash with the backbone. But the role of C8-propynyl modified purines in the RNA·DNA hybrid duplexes is not known. Propynyl and propargyl amine substitution have been reported in modified pyrimidines, which stabilize duplex as well as triplex formation. The effects of C8-propynyl and C8-propargylamino deoxyadenosine in RNA·DNA hybrid duplexes were investigated in this thesis.; This thesis work investigated the effects of C8-modified deoxyadenosines, regular DNA, d[GCGCAAAACGCG] (A4) and four base-modified DNA sequences, d[GCGCAA*A*ACGCG] (PP67), d[GCGCAA*AA*CGCG] (PP57), d[GCGCAA#A#ACGCG] (PPA67), and d[GCGCAA#AA#CGCG] (PPA57) were prepared (A* = C8-propynyl deoxyadenosine, A# = C8-propargylamino deoxyadenosine).; The C8-modified DNA thermally destabilized RNA·DNA hybrid duplexes. The extent of destabilization of RNA·DNA by C8-propynyl groups, however, is smaller than that for DNA·DNA duplexes. The C8-propargylamino groups do not enhance the affinity for the complementary RNA strand and show multiple transitions.; Both modifications confer resistance to DNase I endonuclease. PP57:U4 and PPA57:U4 are RNase H substrates, but the hydrolysis rates are slower than that of RNase H catalyzed hydrolysis. The position of modification seems to be responsible for the A4:U4, the unmodified hybrid duplex. PP67:U4 and PPA67:U4 are quite resistant to the different reaction rates, probably due to the interactions between the modified group and RNase H.; The solution structures of RNA·DNA (A4) and RNA·DNA (PP57) were determined by NMR spectroscopy. The syn conformation base of the C8-modified deoxyadenosine was observed, and seemed to be responsible for the differing destabilizing effects in the helix.; Since the elicitation of RNase H by the RNA·DNA duplex is related to the minor groove width of the helix, minor groove widths of A4:U4, PP57:U4, and backbone-modified hybrid duplexes (3'-thioformacetal, methylmethylene imino) were compared with one another. The minor groove width of PP57:U4 was not even, which might provide a unique insight regarding RNase H activation. |
