Parametric design software for nanostructured CRISPR payloads

用于纳米结构 CRISPR 有效负载的参数化设计软件

• 批准号: 10602823
• 负责人: Steven L Armentrout
• 金额: $ 30万
• 依托单位: PARABON NANOLABS, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-02-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10602823
• 关键词: 3-Dimensional; Acceleration; Affect; Atomic Force Microscopy; Automation; Base Pairing; Biological Sciences; Biomedical Research; CRISPR/Cas technology; Capital; Cell Line; Cells; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Computer software; DNA; Development; Effectiveness; Engineering; Face; Flow Cytometry; Genetic; Genetic Diseases; Genetic Engineering; Genetic Template; Genome; Genomics; Geometry; Goals; Health; Hour; Human; Human Genome; In Vitro; Knock-in; Legal patent; Licensing; Marketing; Measures; Medical; Medical Research; Methods; Mission; Modification; Nanostructures; Nanotechnology; National Institute of General Medical Sciences; Nucleic Acids; Oligonucleotides; Performance; Persons; Phase; Phase III Clinical Trials; Positioning Attribute; Process; Protocols documentation; Research; Research Personnel; Science; Services; Shapes; Single-Stranded DNA; Small Business Innovation Research Grant; Software Design; Software Tools; Specific qualifier value; Specificity; Structure; System; Techniques; Testing; Therapeutic Studies; Tubular formation; Variant; Vendor; Writing; arm; bioinformatics tool; biomaterial compatibility; clinical application; combinatorial; commercial application; commercialization; design; design,build,test; gene therapy; genetic payload; genome editing; improved; in silico; inhibitor; iterative design; manufacture; molecular modeling; nanocarrier; nanomaterials; nanomedicine; nanosensors; novel; operation; personalized medicine; repaired; scale up; self assembly; software development; therapeutic DNA; therapeutic genome editing; 3-Dimensional; Acceleration; Affect; Atomic Force Microscopy; Automation; Base Pairing; Biological Sciences; Biomedical Research; CRISPR/Cas technology; Capital; Cell Line; Cells; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Computer software; DNA; Development; Effectiveness; Engineering; Face; Flow Cytometry; Genetic; Genetic Diseases; Genetic Engineering; Genetic Template; Genome; Genomics; Geometry; Goals; Health; Hour; Human; Human Genome; In Vitro; Knock-in; Legal patent; Licensing; Marketing; Measures; Medical; Medical Research; Methods; Mission; Modification; Nanostructures; Nanotechnology; National Institute of General Medical Sciences; Nucleic Acids; Oligonucleotides; Performance; Persons; Phase; Phase III Clinical Trials; Positioning Attribute; Process; Protocols documentation; Research; Research Personnel; Science; Services; Shapes; Single-Stranded DNA; Small Business Innovation Research Grant; Software Design; Software Tools; Specific qualifier value; Specificity; Structure; System; Techniques; Testing; Therapeutic Studies; Tubular formation; Variant; Vendor; Writing; arm; bioinformatics tool; biomaterial compatibility; clinical application; combinatorial; commercial application; commercialization; design; design,build,test; gene therapy; genetic payload; genome editing; improved; in silico; inhibitor; iterative design; manufacture; molecular modeling; nanocarrier; nanomaterials; nanomedicine; nanosensors; novel; operation; personalized medicine; repaired; scale up; self assembly; software development; therapeutic DNA; therapeutic genome editing

PROJECT SUMMARY More than 300 million people worldwide are affected by a genetic health condition. Over 4,400 genetic diseases have been identified; nearly all of which are considered rare, which limits the amount of research each receives. Gene therapy is an attractive approach for treatment of genetic disease because of its broad applicability. CRISPR-Cas9 genome editing systems (CRISPR) have revolutionized gene therapy research and other fields of life science, however, no CRISPR-based treatments have reached the market and clinical application still faces important challenges. In this project, we aim to develop design automation software to help improve how genetic donor templates are packaged for genomic integration via CRISPR, thereby increasing CRISPR editing efficiency. Whereas such templates are usually delivered as unstructured (linear) single-stranded DNA, recent studies indicate genome integration efficiency is significantly improved when templates are folded into compact shapes using techniques from DNA nanotechnology. Such nanostructured genetic payloads (NGPs) for CRISPR have the potential to become an essential component of genetic therapy and personalized medicine. The long-term goal of the project is to provide researchers with software for designing more effective CRISPR treatments to improve the lives of people with genetic health problems. Our solution will also advance other application domains where DNA nanotechnology is being employed, such as nanomedicine, nanosensing and biocompatible nanomaterials, thereby supporting the mission of the National Institute of General Medical Sciences (NIGMS): improving the effectiveness of computational approaches in biomedical research. Academic software exists to facilitate design of DNA nanostructures, however, these applications either require extensive expertise or are limited to 3D wireframe designs. Design of a novel DNA nanostructure of modest complexity that is not among a small set of simple designs can require hundreds of hours of expert labor. Moreover, because NGPs are new to science, no software currently exists to automatically generate DNA nanostructures for a given set of NGP design parameters. In Aim 1 of this project, we will employ an iterative design-build-test development cycle we have used to bring other software products to market to develop novel parametric design software (PDS) able to create NGPs automatically for a given genetic template and set of design parameters. In Aim 2, we will simulate and synthesize eight NGPs and characterize them via molecular modeling and atomic force microscopy to confirm they meet design specifications. We will then test these NGPs for CRISPR editing efficiency against unstructured payload controls in vitro. In Phase II, we will enhance the PDS and use it to explore the vast space of NGP designs for those that optimize CRISPR performance via combinatorial testing across multiple cell lines, templates and insertion targets. Ultimately, we aim to commercialize NGP software and design services to accelerate CRISPR research.

项目摘要 全球超过3亿人受到遗传健康状况的影响。超过4,400个遗传 已经确定了疾病；几乎所有这些都被认为是罕见的，这限制了研究的数量 每个收到。基因疗法是治疗遗传疾病的一种有吸引力的方法 适用性。 CRISPR-CAS9基因组编辑系统（CRISPR）彻底改变了基因治疗研究和 但是，其他生命科学领域，没有基于CRISPR的疗法进入市场和临床领域 应用程序仍然面临重要的挑战。 在这个项目中，我们旨在开发设计自动化软件，以帮助改善遗传供体模板的方式 通过CRISPR包装进行基因组整合，从而提高了CRISPR编辑效率。而这样 模板通常作为非结构化（线性）单链DNA传递，最近的研究表明基因组 当模板折叠成紧凑的形状时，集成效率得到显着提高 DNA纳米技术的技术。这种纳米结构的基因有效载荷（NGP）的CRISPR具有 成为基因疗法和个性化医学的重要组成部分的潜力。长期目标 该项目的内容是为研究人员提供设计更有效的CRISPR处理的软件 改善患有遗传健康问题的人的生活。我们的解决方案还将推进其他应用 使用DNA纳米技术的域，例如纳米医学，纳米传感和 生物相容性的纳米材料，从而支持美国国家一般医学研究所的任务 科学（NIGMS）：提高计算方法在生物医学研究中的有效性。 存在学术软件以促进DNA纳米结构的设计，但是，这些应用都需要 广泛的专业知识或仅限于3D线框设计。新颖的DNA纳米结构的设计 不属于一小部分简单设计的复杂性可能需要数百小时的专家劳动力。 此外，由于NGP是科学的新手，因此目前尚无软件可以自动生成DNA 一组NGP设计参数的纳米结构。在该项目的目标1中，我们将采用迭代 设计建造测试开发周期我们用来将其他软件产品推向市场以开发新颖 能够自动为给定遗传模板和一组一组创建NGP的参数设计软件（PDS） 设计参数。在AIM 2中，我们将模拟和合成八个NGP，并通过分子进行表征 建模和原子力显微镜确认它们符合设计规范。然后我们将测试这些 NGPS用于CRISPR编辑效率，以防止在体外进行非结构化有效载荷控制。在第二阶段，我们将增强 PDS并使用它来探索NGP设计的广阔空间，以优化CRISPR性能的人 跨多个细胞系，模板和插入靶标的组合测试。最终，我们的目标是 将NGP软件和设计服务商业化，以加速CRISPR研究。