| This thesis describes work with a set of nonpolar nucleoside isosteres of the DNA bases. These analogs are the closest possible shape and size mimics of the natural nucleobases, but have nonpolar groups substituted on the Watson-Crick face and do not exhibit hydrogen-bonding ability. Here the isosteres of cytosine (named D) and guanine (named H and J) were characterized for their properties in naked DNA and in replication studies with two high-fidelity A-family polymerases. We found that these analogs are nonselective for pairing against natural DNA bases in a 12-mer duplex, and destabilize the duplex overall, similar to the previous results obtained with isosteres. In contrast to earlier results with adenine and thymine analogs, we found that these new isosteres do not code for their natural counterparts efficiently and selectively in steady-state kinetics reactions for single-nucleotide insertions. H and J were nonselective among the natural bases, while D acted as a thymine mimic, coding for A, with the polymerases studied. Notably, nonpolar base pairs were efficiently replicated, with small differences in efficiency due to varying sizes. We also undertook studies in other systems to determine whether our isosteres were substrates for new and unique enzymes such as telomerase and low-fidelity polymerases. The isosteres tested were replicated by Y-family polymerases with low efficiency and selectivity, indicating a possible dependence on hydrogen bonds for replication by those enzymes. Studies in living bacteria demonstrated high fidelity replication without hydrogen bonds in vivo for adenine and thymine mimics. We found that our nonpolar nucleoside isosteres are quite useful tools for probing DNA polymerase mechanisms and show promise for investigating other protein-DNA interactions. |
