Molecular recognition of pyrimidine nucleobases by triplex DNA receptors

Triplex DNA receptors are known for their strong and specific binding of a variety of purine ligands. However, not many studies have been reported on their binding of pyrimidine ligands. Here we used fluorophore-labeled DNA receptors to study these binding interactions. The results suggest that in general, cytosine binds more strongly than thymine and uracil, although the selectivity between two pyrimidine ligands can be tuned by changing the surrounding nucleobases of the DNA receptor. In contrast, binding of pyrimidine nucleosides is much weaker, possibly due to lack of the N1 hydrogen bonding donor.