Effects of Ring Functionalization in Anthracene‐Based Cyclophanes on the Binding Properties Toward Nucleotides and DNA

Supramolecular recognition of nucleobases and short sequences is an emerging research field focusing on possible applications to treat many diseases. Controlling the affinity and selectivity of synthetic receptors to target desired nucleotides or short sequences is a highly challenging task. Herein, we elucidate the effect of substituents in the phenyl ring of the anthracene‐benzene azacyclophane on the recognition of nucleoside triphosphates (NTPs) and double‐stranded DNA. We show that introducing phenyl rings increases the affinity for NTPs 10‐fold and implements groove and intercalation binding modes with double‐stranded DNA. NMR studies and molecular modeling calculations support the ability of cyclophanes to encapsulate nucleobases as part of nucleotides. Cyclophanes with different substitution patterns were prepared and studied for binding of nucleoside triphosphates and double‐stranded DNA. While the ortho‐phenyl derivative showed high affinity for nucleoside triphosphates, the meta‐derivative demonstrated GC‐selectivity and an intercalation binding mode with DNA.