Towards sequence-selective DNA recognition with designed major groove binders
This thesis is mainly focused on the design, synthesis and DNA binding studies of aminobenzyl and guanidinium calixarene dimers. The work consists of two parts. The first part of my Ph.D. work was focused on the synthesis and DNA binding studies of Dimer A and Dimer B. In order to broaden the scope of the investigation, the corresponding monomeric calixarenes (Monomer A and Monomer B) were also synthesized. Compared with anilino-calixarenas (R. Zadmard, T. Schrader, Angew. Chem. Int. Ed. 2006, 45, 2703 –2706), these dimers and monomers are water-soluble, and bind to DNA with much higher affinity (binding constants: 1000000–100000000 M-1 in 2 mM Hepes buffer with 150 mM NaCl). When investigating the properties of new DNA binding molecules, one initial goal is to establish their mode of binding to DNA. Because direct structure information from a crystal or NMR structure was not yet available in my work, several other biophysical experiments have been designed and performed between calixarenes and different nucleic acids with varying base composition and conformation. The following results from established binding assays strongly support a major groove binding mode: (1). The DAPI displacement assay indicates that the calixarene dimers and DAPI can simultaneously bind to poly (dAdT) – poly (dAdT). Because DAPI occupies the minor groove, the dimeric calixarenes should reside in the major groove. (2). Ethidium bromide displacement assays, fluorescence titrations, and circular dichroism measurements indicate that calixarene dimers strongly prefer nucleic acids with a wide, shallow or even major groove; while low affinities are observed for nucleic acids with a narrow, deep or rugged major groove, which must be widened before complexation occurs. This characteristic also implies that the accessible area for our ligands is on the major groove side, contrary to the well-known slim oligoamide binders, which target the minor groove. In line with these observations, it was noticed that changes in shape and width of the minor groove had no influence on the ligands’ affinities.
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