RUI: Functionalized bis (morindone-C, O-glycosides) for the molecular recognition of DNA in the major groove

Investigators in the field of molecular recognition study the non-covalent interactions between two (or more) molecules with the aim of understanding the driving forces behind these associations. With this information in hand, it is possible to develop a set of rules for the design of molecules (ligands) capable of specific binding interactions with other target molecules (receptors). DNA has long been viewed as an important macromolecular target for the binding of small molecule ligands, and indeed there are numerous examples of natural and designed molecules that associate with the minor groove of DNA. However, no general paradigm currently exists for the design of major groove-binding small molecules. Since most of the DNA-binding proteins that regulate cellular processes associate with the major groove of DNA, a great need exists for the development of major groove ligands that may directly influence DNA binding-initiated cellular events. Using the tools of fluorescence spectroscopy and isothermal titration calorimetry, this study helps uncover a set of design principles for crafting such ligands from simple carbohydrate and aromatic starting materials. The project also provides hands-on training in organic synthesis, molecular spectroscopy and microcalorimetry for undergraduate and graduate students, including those from groups traditionally underrepresented in science. Furthermore, it is anticipated that the project may lead to new procedures and protocols that can be adapted for use in the undergraduate chemistry laboratory curriculum at Northridge, which is expected to increase student interest in interface sciences such as chemical biology, bioorganic chemistry and medicinal chemistry.

Bicyclic aryl C,O-glycosides are naturally occurring molecular wedges that may be used as rigid intercalating scaffolds to position functional groups in proximity to the discriminatory edges of the A/T and G/C base pairs in the major groove of DNA. The unique architecture of this ligand allows an examination of the utility of base-complementary functional groups at C.2 and C.4 of the carbohydrate unit for sequence specific DNA binding. The research project involves: (1) the synthesis of a series of bis(morindone-C,O-glycosides) containing patterns of carbonate, carbamate, guanidine and carbamimidate recognition elements complementary to the 4 base-pair sequences 5'-CGCG-3', 5'-CATG-3', 5'-CGGC-3', 5'-CAAC-3', and 5'-CGTG-3', respectively, (2) the assessment of both the DNA binding affinity and sequence selectivity of the ligands for diverse nucleic acid polymers and DNA hairpins using fluorescent intercalator displacement assays, (3) the measurement of the thermodynamic parameters (deltaH and deltaS) for the tightest ligand-DNA combinations using isothermal titration calorimetry in order to optimize the structure of the ligands, and (4) the evaluation of the ability of these ligands to inhibit the binding of the transcription factor AP-1 to its consensus site by EMSA assay, which may shed light on the potential usefulness of this class of compounds for regulating cellular processes.