RomesbergLab | Publications

We synthesize two novel benzothiophene-based dNaM analogs, dPTMO and dMTMO, and characterize the corresponding UBPs with dTPT3. We demonstrate that these UBPs perform similarly to, or slightly worse than, dNaM-dTPT3 in vitro; but in the in vivo environment of a semi-synthetic organism, retention of dMTMO-dTPT3 and dPTMO-dTPT3 are significantly higher. The results demonstrate the importance of evaluating synthetic biology “parts” in their in vivo context

The continued optimization of a predominantly hydrophobic class of unnatural base pairs is reported. We find that minimizing the cost of nucleobase desolvation and optimizing packing interactions within the developing major groove of DNA is promising route toward optimization. While we identify an improved base pair, dNMO1-d5SICS, continued analysis of the previously reported dNaM-d5SICS pair reveals that it is replicated with an efficiency and fidelity approaching those of natural DNA.

We report the synthesis and analysis of the ribo- and deoxyribo-variants, (d)5SICS and (d)MMO2, modified with free or protected propargylamine linkers that allow for the site-specific modification of DNA or RNA during or after enzymatic synthesis. We also synthesized and evaluated the α-phosphorothioate variant of d5SICSTP, which provides a route to backbone thiolation and an additional strategy for the post-amplification site-specific labeling of DNA.

We report the synthesis and stability of unnatural base pairs formed between simple phenyl rings modified at different positions with methyl groups. Several are virtually as stable as a natural base pair in the same sequence context, showing that neither hydrogen-bonding nor large aromatic surface area are required for base pair stability within duplex DNA and that interstrand interactions between small aromatic rings may be optimized for both stability and selectivity.