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

分子识别领域的研究人员研究两个（或更多）分子之间的非共价相互作用，目的是了解这些关联背后的驱动力。有了这些信息，就有可能开发出一套设计分子（配体）的规则，这些分子（配体）能够与其他靶分子（受体）进行特定的结合相互作用。长期以来，DNA一直被视为结合小分子配体的重要大分子靶标，确实有许多自然和设计的分子与DNA的小凹槽相关联的例子。然而，目前还没有设计主要凹槽结合小分子的通用范例。由于大多数调节细胞过程的DNA结合蛋白都与DNA的主要凹槽相关，因此迫切需要开发可能直接影响DNA结合引发的细胞事件的主要凹槽配体。利用荧光光谱和等温滴定量热法的工具，本研究有助于揭示一套设计原则，从简单的碳水化合物和芳香起始材料制作这种配体。该项目还为本科生和研究生提供有机合成、分子光谱学和微量热法的实践培训，包括那些来自传统上在科学领域代表性不足的群体的学生。此外，预计该项目可能会导致新的程序和协议，可以适用于北岭大学本科化学实验室课程，这有望增加学生对界面科学的兴趣，如化学生物学，生物有机化学和药物化学。双环芳基C， o -糖苷是天然存在的分子楔子，可以用作刚性插层支架，将功能基团定位在DNA主槽中A/T和G/C碱基对的区分边缘附近。该配体的独特结构允许检查碳水化合物单元C.2和C.4的碱基互补官能团对序列特异性DNA结合的效用。研究项目包括：(1)合成了一系列含碳酸盐、氨基甲酸酯、胍和氨基甲酸酯识别元件的双（morindo - c， o -糖苷），分别与4个碱基对序列5‘-CGGC-3’、5‘-CATG-3’、5‘-CGGC-3’、5‘-CAAC-3’和5‘-CGTG-3’互补；(2)利用荧光插层置换法评估了配体对不同核酸聚合物和DNA发夹的DNA结合亲和力和序列选择性；(3)使用等温滴定量热法测量最紧密配体- dna组合的热力学参数（δ tah和δ tas），以优化配体的结构；(4)通过EMSA分析评估这些配体抑制转录因子AP-1与其一致位点结合的能力，这可能揭示这类化合物在调节细胞过程中的潜在用途。

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.