Quantitating In Vitro Selection

Benner教授将领导一个结合有机合成，生物化学，体外进化（IVE）和单变量统计分析的项目，该项目将开发所需的物理有机化学工具，以量化添加化学功能（氨基，硫醇，咪唑，肽和金属螯合基团）通过共价连接到催化DNA分子的影响。这项工作将首先解决观察到的悖论，即赋予DNA和RNA文库额外的功能明显地提高了核酸的催化潜力，只有2到10倍，而不是有机化学中标准结构理论所预期的数量级。一组五个假设，解释了预期和观察之间的数量级差异将被测试，包括模型，认为（a）我们的观点在催化作用中的功能是天真的，（B）天然DNA的功能禀赋（磷酸酯和氢键给予和接受基团）通常足以用于催化，（c）由核酸从溶液中非共价募集的官能团（特别是，二价阳离子如Mg ++）阻碍了共价连接的官能团的贡献，（d）IVE实验失去了最好的催化剂，和（e）在看到官能性的预期大益处之前需要多于一种类型的官能团。这将需要仔细评估所选DNA分子影响的反应动力学顺序（一级，单分子，催化步骤速率决定？）。有了这个奖项，有机和大分子化学计划（OMC）和分子生物化学计划在分子和细胞生物科学（MCB）的部门将支持教授史蒂芬A的研究。佛罗里达大学的本纳说。 班纳教授的工作预计将产生广泛的影响。从实践的角度来看，我们可以学习如何真正从IVE实验中获得“按需催化”，对从生物医学到环境修复的一切都很有用。从科学的角度来看，我们将更深入地了解单一生物聚合物系统在生命起源中发挥作用的可能性。从方法论的角度来看，他将开发工具，允许IVE探索由DNA序列定义的“结构空间”中的化学性质的分布。而且，从理论的角度来看，这项工作最终可能会改变（也许是戏剧性的）我们对核酸功能性和反应性之间关系的整体看法。

Professor Benner will lead a project that combines organic synthesis, biological chemistry, in vitro evolution (lVE) and univariate statistical analysis that will develop the physical organic chemical tools needed to quantitate the impact of adding chemical functionality (amino, thiol, imidazole, peptides, and metal chelating groups) via covalent attachment to catalytic DNA molecules. This work will first address the paradox that arises from the observation that endowing DNA and RNA libraries with additional functionality evidently improves the catalytic potential of nucleic acids by only a factor of two to ten, not by the orders of magnitude expected from standard Structure Theory in Organic Chemistry. A set of five hypotheses that account for the orders-of-magnitude discrepancy between expectation and observation will be tested, including models that hold (a) that our view of the role of functionality in catalysis is naive, (b) that the functional endowment of natural DNA (phosphates and hydrogen bond donating and accepting groups) are sufficient for catalysis in general, (c) that the functionality recruited non-covalently by nucleic acids from solution (in particular, divalent cations such as Mg++) overwhelms the contribution of covalently linked functionality, (d) that lVE experiments lose the best catalysts, and (e) that more than one type of functional group is needed before the expected large benefit from functionality is seen. This will require careful assessment of the kinetic order of the reaction being effected by the selected DNA molecules (first order, unimolecular, with the catalytic step rate determining?).With this Award, the Organic and Macromolecular Chemistry Program (OMC) and the Molecular Biochemistry Program in the Division of Molecular and Cellular Biosciences (MCB) will support the research of Professor Steven A. Benner of the University of Florida. Professor Benner's work is expected to have broad impact. From a practical perspective, we may learn how to truly get "catalysis on demand" from IVE experiments, useful for everything from biomedicine to environmental remediation. From a scientific perspective, we will understand in greater depth the possibilities of single biopolymer systems playing a role in the origin of life. From a methodological perspective, he will develop tools that permit IVE to explore the distribution of chemical properties in "structure space" defined by a DNA sequence. And, from a theoretical perspective, the work may end up altering, perhaps dramatically, our global view of the relationship between functionality and reactivity in nucleic acids.