A Novel Computational Package for DNA Enzyme Design

用于 DNA 酶设计的新型计算包

• 批准号: 7661170
• 负责人: Jingdong Tian
• 金额: $ 23.4万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-03 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7661170
• 关键词: Activities of Daily Living; Address; Algorithms; Amino Acids; Area; Arts; Back; Biological; Biological Models; Biomedical Computing; Biotechnology; Cataloging; Catalogs; Classification; Cleaved cell; Clinical; Codon Nucleotides; Complex; Computer software; Custom; DNA; DNA Packaging; DNA Restriction Enzymes; DNA Sequence; DNA-Protein Interaction; Databases; Deoxyribonuclease I; Development; Engineering; Enzyme Interaction; Enzymes; Exhibits; Future; Generations; Genome; Goals; Human Genome; Imagery; Investigation; Libraries; Life; Maintenance; Molecular Conformation; Molecular Models; Mutation; Nucleic Acids; Nucleotides; Organism; Outcome; Partner in relationship; Performance; Positioning Attribute; Process; Recombinants; Research; Retrieval; Scheme; Screening procedure; Side; Site; Site-Directed Mutagenesis; Specificity; Structural Models; Structure; Sugar Phosphates; Technology; Therapeutic; Time; Translating; Translational Research; Validation; Vertebral column; base; computerized tools; cost; design; endonuclease; engineering design; gene synthesis; improved; innovation; insight; interest; interfacial; molecular modeling; nanomedicine; novel; protein expression; restriction enzyme; scaffold; structural biology; tool; web-enabled

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.

描述（由申请人提供）：在酶设计和工程领域，DNA限制性核酸内切酶（RES）尤其令人感兴趣，并且出现了令人信服的挑战。限制性酶识别短定义的DNA序列，并以相当大的效率裂解DNA糖磷酸主链。这些酶已经进行了半个多世纪的研究，并在过去几十年中引起了重组生物技术的时代。然而，它们在识别基因组中短DNA序列的功能能力的结构特征和倾向尚未在预测能力上理解。这项研究的一般目标是开发一种计算工具，以实现DNA限制酶的研究和重新设计。该软件包将包括以下组件：1）核酸识别位点扰动工具，该工具将允许对核酸识别位点的序列识别，结构建模和可视化； 2）一种生物焦点算法，该算法将列举并专注于那些具有设计潜力的脚手架和界面口袋（IPS），如进化上有利的特征所证明的那样； 3）DNA核酸内切酶库的集成和查询接口，该界面将简化使用上述工具和算法进行的分析，检索，检索，使用和传播分析。这些计算工具曾经开发，将有助于启动系统研究，以介绍结构生物学和限制性核酸内切核酸酶的工程基础。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强度将促进这种创新的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叶酶，用于进一步研究或治疗中的序列特异性生物分子探针或临床治疗。