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限制性内切核酸酶（RE）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的DNA序列，并以相当高的效率切割DNA糖-磷酸骨架。这些酶已经被研究了超过半个世纪，并且在过去的几十年中引起了重组生物技术的时代。然而，它们的结构特征和倾向，使它们能够识别基因组中的短DNA序列的功能能力，尚未被理解为预测能力。本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重组成为可能。该软件包将包括以下组件：1）核酸识别位点扰动工具，其将允许核酸识别位点的序列识别、结构建模和可视化; 2）生物聚焦算法，其将枚举并聚焦于具有设计潜力的那些支架和界面口袋（IP），如通过进化上有利的特征所证明的;和3）DNA内切核酸酶文库整合和查询界面，其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，将有助于对结构生物学和限制性核酸内切酶工程的基础进行系统研究。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优势将促进这种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核酸内切酶，用于序列特异性生物分子探针或进一步研究或治疗的临床治疗。

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.