NONPOLAR NUCLEOSIDES AS PROBES OF NONCOVALENT BONDING

该项目的长期目标是合成和研究非极性， 作为生物物理探针的非氢键核苷和核苷酸 DNA-DNA、蛋白质-核苷酸和蛋白质-DNA中的非共价键 交互. 这些分子被设计成模仿 天然核苷的形状和大小，但没有极性 氢键N、N-H和C=O基团。几项初步研究 在过去的1.5年里，这些类似物显示出它们具有 许多不寻常的性质，无论是单独的，在DNA的背景下， 螺旋，他们已经导致了一些惊人的和有价值的 在研究双链体DNA中的堆积和配对以及 对E.大肠杆菌DNA聚合酶I。 叠加结果可能在设计中有实际用途。 用于基于阿昔肽的治疗剂的螺旋稳定剂， 聚合酶研究将有助于设计新的聚合酶抑制剂 (with潜在的抗病毒或抗病毒作用）。 从长远来看， 希望这些新的类似物将具有通用性， 非共价键的生物物理学研究。 所提出的研究旨在将这些新的类似物用于三种 单独的生物分子系统，既作为性能的测试， 的化合物的效用，也揭示了非共价键 这些系统中的互动。 实验计划用于研究 DNA中的碱基堆积，核苷酸中的非共价键合要求 通过DNA聚合酶的掺入，以及对DNA的能量贡献 通过TATA结合蛋白结合。 所涉期间的具体计划 主要内容包括：（1）深入研究六种电流类似物 (and它们的自然对应物）作为热动力学因素的探针， （2）合成了几种新的类似物， 堆积研究和聚合酶实验中的额外数据;（3） 深入研究了E. Coli Pol I和 （4）使用这些类似物来测试聚合酶的能量学。 酵母TATA结合蛋白与共有蛋白之间的特异性相互作用 TATA识别序列。

The long-term goals of this project are to synthesize and study nonpolar, non-hydrogen-bonding nucleosides and nucleotides as biophysical probes of noncovalent bonding in DNA-DNA, protein-nucleotide, and protein-DNA interactions. These molecules are designed to mimiC as closely as possible the shape and size of the natural nucleosides, but without polar hydrogen bonding N, N-H and C=O groups. Preliminary studies of several such analogs over the past 1.5 years have shown that they display a number of unusual properties both alone and in the context of DNA helices, and they have already led to a number of surprising and valuable findings in the study of stacking and pairing in duplex DNA and in the study of the fidelity of Klenow fragment of E. Coli DNA Polymerase I. The stacking results are likely to be of practical use in the design of helix-stabilizing agents for oligonucleotide-based therapeutics, and the polymerase studies will aid in the design of novel polymerase inhibitors (with potential antiviral or antineoplastic effects). In the long term, it is hoped that these new analogs will be of general utility in biophysical studies of noncovalent bonding. The proposed studies are aimed at the use of these novel analogs in three separate biomolecular systems, both as a test of the properties and utility of the compounds, and also to shed new light on noncovalent interactions in these systems. Experiments are planned for the study of base stacking in DNA, noncovalent bonding requirements in nucleotide incorporation by DNA polymerases, and energetic contributions to DNA binding by TATA-binding proteins. Specific plans for the term covered by this proposal include: (1) ln-depth study of the six current analogs (and their natural counterparts) as probes of thermodynamic factors of base stacking in DNA; (2) Synthesis of several new analogs to gain additional data in stacking studies and in polymerase experiments; (3) In-depth study of the processing of these analogs by E. Coli Pol I and three other polymerases; (4) Use of these analogs to test energetics of specific interactions between yeast TATA-binding protein and a consensus TATA recognition sequence.