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，目的是了解这些联系背后的驱动力。有了这些信息，就有可能开发出一套规则来设计能够与其他目标分子(受体)特定结合的分子(配体)。长期以来，DNA一直被视为小分子配体结合的重要大分子靶标，确实有许多天然和设计的分子与DNA的小凹槽有关。然而，目前还不存在用于设计主要沟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的主要沟槽有关，因此非常需要开发直接影响DNA结合启动的细胞事件的主要沟槽配体。利用荧光光谱和等温滴定量热法，这项研究有助于揭示一套从简单碳水化合物和芳香族起始原料制备此类配体的设计原则。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学方面的实践培训，包括那些在科学界传统上代表性较低的群体。此外，预计该项目可能导致新的程序和方案，可用于北岭大学本科化学实验室课程，预计将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-糖苷是自然产生的分子楔形分子，可用作刚性嵌入支架，在DNA主槽中A/T和G/C碱基对的区别边缘附近定位官能团。这种配体的独特结构使人们能够研究碳水化合物单元的C.2和C.4处的碱基互补官能团对序列特异性DNA结合的效用。该研究项目包括：(1)合成一系列含有碳酸盐、氨基甲酸酯、胍和氨基甲酸酯识别元件的双(巴林酮-C，O-糖苷)，分别与4个碱基对序列5‘-CGCG-3’，5‘-CATG-3’，5‘-CAAC-3’和5‘-CGTG-3’互补，(2)用荧光插层置换法评价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)用等温滴定量热法测量最紧密的配体-DNA组合的热力学参数(deltaH和deltas)，以优化配体的结构；(4)用EMSA法评估这些配体抑制转录因子AP-1与其共同位点结合的能力，这可能有助于揭示这类化合物在调节细胞过程方面的潜在用途。

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.