Synthesis of a AT base pair model in DNA and determination of hydrogen bonding strength on the formation of base triplet T:AT in CDCl3

A molecular model has been synthesized to determine the hydrogen-bonding strength between AT and T in the base triplet, T:AT. A strong preference (>95%) of Watson-Crick mode along with 91% hydrogen-bonded conformation is observed in the model compound. The association constants of the AT model with 1-propyluracil and glutarimide are 15 M −1 and 5.2 M −1 , respectively, in CDCl 3 at 296 ± 0.5 K. Negative cooperativity by pre-existing hydrogen bonds might be involved in the intermolecular binding events.