Optimization of interstrand hydrophobic packing interactions within unnatural base pairs

S. Matsuda, F.E. Romesberg, J. Am. Chem. Soc. (2004) 126:14419–14427.
pubpic2004matsudaWe 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.