Probing the structure and function of nucleic acids with nonpolar isosteric nucleoside analogs

Recently the Kool group has designed nonpolar, isosteric, analogues to the natural DNA bases. Due to their isosteric nature, hydrogen bonding can be studied in the absence of significant steric effects.' Herein we describe several studies which utilize these analogues to probe the stability, structure, and function of nucleic acids.;In the first study we use a series of nucleoside analogues to evaluate the role of base stacking in DNA duplex formation. In general we find surface area excluded upon stacking to be the physical property which correlates best with stacking ability.;In the second set of studies we sought to provide evidence that these analogues are indeed nonpolar, isosteric, mimics of the natural DNA bases. To achieve this goal we have undertaken structural studies on both the thymidine and adenine mimics. We find that both the thymidine and adenine analogues imitate their natural counterparts well.;In the third study we attempt to design a new base pair that can be replicated by DNA polymerases without the use of hydrogen bonds. Previous work in the group has shown that hydrogen bonds are not necessary for DNA replication. This led to the proposal of a steric matching model for DNA replication. Using this model as a base we have designed a new base pair that does not have the ability to hydrogen bond at the Watson-Crick interface, and is instead intended to replicate based on the steric complementarity of the two bases within the pair. This pair is ultimately found to replicate with poor efficiency and fidelity, but its study has led to several possible second generation base pairs.;The final study was undertaken to evaluate the importance of shape matching in transcription. Transcription is thought to be driven primarily by hydrogen bonding between the bases of the replicating pair. In an effort to examine the importance of hydrogen bonding to the transcription process several isosteric, nonpolar, analogues of the natural DNA bases are used in conjunction with a nonpolar, isosteric, uridine mimic. Although preliminary, these studies seem to indicate that shape matching does play a role in transcription.