Sequence specificity of hydrogen-bonded molecular duplexes

Hydrogen-bonded molecular duplexes, 1.3 and 1.4, each of which contains a m ismatched binding site (acceptor-to-acceptor in 1.3, and donor-to-donor in 1.4), were designed and synthesized based on duplex 1.2. One- and two-dimen sional NMR studies demonstrated that, despite their single mismatched bindi ng sites, the backbones of duplexes 1.3 and 1.4 still stayed in register th rough the formation of the remaining five H-bonds. The backbones of 1.3 and 1.4 adjusted to the presence of the mismatched binding sites by slightly t wisting around these sites, which alleviate any head-on repulsive interacti ons between two H-bond donors (amide O) or between two accepters (amide H). After 1 equiv of single strand 2, which forms a perfectly matched duplex 1 2 with single strand 1, was added into the solution of either 1.3 or 1.4, only 1 2 and single strand 3 or 4, were detected. Isothermal titration calo rimetry (ITC, in chloroform containing 5% DMSO) indicated that duplexes 1.3 and 1.4 were significantly (> 40 times) less stable than the corresponding perfectly hydrogen-bonded duplex 1 2. These NMR and ITC results indicate t hat the pairing of two complementary single strands is not affected by anot her very similar single strand that contains only one wrong H-bond donor or acceptor, which demonstrates that the self-assembly of this class of H-bon ded duplexes is a highly sequence-specific process. The role of these H-bon ded duplexes as predictable and programmable molecular recognition units fo r directing intermolecular interactions has thus been established.