A Novel Computational Package for DNA Enzyme Design

描述(由申请人提供)：在酶设计和工程领域，DNA限制性内切酶(RES)特别令人感兴趣，并提出了令人信服的挑战。限制性内切酶识别短定义的DNA序列，并以相当高的效率切割DNA的糖-磷酸骨架。这些酶已经被研究了半个多世纪，并在过去的几十年里催生了重组生物技术的时代。然而，它们的结构特征和倾向使它们具有识别基因组中短DNA序列的功能，这一点尚未在预测熟练程度上被理解。这项研究的总体目标是开发一种计算工具，使DNA限制性内切酶的研究和再工程成为可能。该软件包将包括以下组件：1)核酸识别位点扰动工具，它将允许对核酸识别位点进行序列识别、结构建模和可视化；2)生物聚焦算法，它将列举并关注那些具有设计潜力的支架和界面口袋(IP)，如进化上的有利特征所证明的那样；以及3)DNA内切酶文库集成和查询接口，将简化使用上述工具和算法进行的分析的编目、检索、使用和传播。这些计算工具一旦开发出来，将有助于启动对结构生物学基础和限制性内切酶工程的系统研究。该研究小组在高性能分子建模和优化以及高通量基因合成、蛋白质表达和筛选技术方面的实力将推动此类创新生物医学计算技术的发展。这项研究最终将转化为定制设计的内切酶，用于序列特异的生物分子探针，或在进一步的研究或治疗中用于临床治疗。

DESCRIPTION (provided by applicant): In the area of enzyme design and engineering, DNA restriction endonucleases (REs) are of particular interest and present compelling challenges. Restriction enzymes recognize short defined DNA sequences and cleave the DNA sugar-phosphate backbone with considerable efficiency. These enzymes have been studied for over half a century and have given rise to the era of recombinant biotechnology in the past few decades. Yet, their structural features and propensities that lend their functional ability to recognize short DNA sequences in the genome have yet to be understood at predictive proficiency. The general goal of this research is to develop a computational tool to enable study and reengineering of DNA restriction enzymes. The package will include the following components: 1) nucleic acid recognition site perturbation tools, which will allow sequence recognition, structural modeling and visualization of the nucleic acid recognition site; 2) a biological focusing algorithm which will enumerate and focus on those scaffolds and interfacial pockets (IPs) that have potential for design, as demonstrated by evolutionarily favorable features; and 3) a DNA endonuclease library integration and querying interface which will streamline the cataloging, retrieval, use, and dissemination of analyses performed using the above tools and algorithm. These computational tools, once developed, will help launch systemic research into the fundamentals of structural biology and engineering of restriction endonucleases. The development of such innovative biomedical computing technologies will be facilitated by the research group's strength in high-performance molecular modeling and optimization as well as high-throughput gene synthesis, protein expression, and screening technologies. This research will eventually translate into custom-designed endonucleases for sequence-specific biomolecular probes or clinical therapeutic in further investigations or treatments.