A naphthyridine carbamate dimer (NCD) is a synthetic ligand for DNA containing a CGG/CGG sequence. Although NCD can bind selectively and tightly to a CGG/CGG sequence, the highly cooperative 2:1 binding mode has hampered precise analysis of the binding. We describe herein the synthesis of a series of naphthyridine tetramers consisting of two NCD molecules connected with various linkers to seek a ligand that binds to a CGG/CGG sequence exclusively with a 1:1 stoichiometry. Among the tested ligands, NCTB and Z -NCTS, which have linker moieties with restricted conformational flexibility [biphenyl and (Z) -stilbene linker, respectively], gave the exclusive formation of a 1:1 ligand–CGG/CGG complex. The (Z) -stilbene linker in Z -NCTS was designed to have pre-organized conformation appropriate for the binding and, in fact, resulted in the highest binding affinity. Thermodynamic parameters obtained by isothermal titration calorimetry indicated that the stronger binding of Z -NCTS was attributed to its lower entropic cost. The present study provides not only a novel 1:1 binding ligand, but also valuable feedback for subsequent molecular design of DNA and RNA binding ligands.
萘啶
氨基甲酸酯二聚体(NCD)是含有 CGG/CGG 序列的 DNA 的合成
配体。虽然 NCD 可以选择性地与 CGG/CGG 序列紧密结合,但其高度合作的 2:1 结合模式阻碍了对这种结合的精确分析。我们在本文中描述了一系列
萘啶四聚体的合成过程,这些四聚体由两个 NCD 分子与各种连接体连接而成,目的是寻找一种
配体,以 1:1 的
化学计量学比例完全与 CGG/CGG 序列结合。在测试的
配体中,NCTB 和 Z -NCTS 具有构象灵活性受限的连接分子[分别为
联苯和 (Z) -
二苯乙烯连接分子],这两种
配体都能形成 1:1 的
配体-CGG/CGG 复合物。在 Z -NCTS 中,(Z) -
二苯乙烯连接体被设计成具有适合结合的预组织构象,事实上,这种连接体具有最高的结合亲和力。通过等温滴定量热法获得的热力学参数表明,Z -NCTS 的较强结合力归因于其较低的熵成本。本研究不仅提供了一种新型的 1:1 结合
配体,还为后续 DNA 和 RNA 结合
配体的分子设计提供了宝贵的反馈信息。