Data-Rich Strategies for Programming Ligand-Responsive RNA Regulatory Systems

用于配体响应 RNA 调控系统编程的数据丰富策略

• 批准号: 10320468
• 负责人: DREW ENDY
• 金额: $ 33.17万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-01-02 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10320468
• 关键词: Automation; Biological Assay; Biological Process; Biosensor; Biotechnology; Catalytic RNA; Communities; Data; Data Set; Disease; Elements; Engineering; Environment; Evolution; Generations; Genes; Genetic; Goals; Libraries; Ligands; Measurement; Methods; Molecular; Monitor; Organism; Pharmaceutical Preparations; Process; RNA; RNA Sequences; Regulatory Element; Research; Structure; Structure-Activity Relationship; System; Technology; Untranslated RNA; Work; applied biomedical research; base; biological research; biological systems; complex biological systems; design; improved; innovation; insight; interest; molecular targeted therapies; novel; novel strategies; programs; tool

PROJECT SUMMARY Genetically-encoded technologies that enable the design of systems that receive, process, and transmit molecular information are essential to advancing basic biological research, applied biomedical research, and biotechnology. RNA switches are a class of ligand-responsive genetic controllers that are being implemented in diverse biological systems to transform our ability to monitor, interface with, and program the dynamic cellular state. While the application of synthetic regulatory RNAs has grown remarkably over the past decade, current approaches to the design of new RNA regulatory elements are inefficient, laborious, and typically do not yield insight into the sequence-structure-function relationships underlying the activities of these molecules in complex biological systems. The goal of the proposed project is to develop new strategies for approaching the design, measurement, and analysis of an important class of RNA switches that incorporate ribozymes as the gene-control element. The goal of the project will be achieved through three specific aims. The first specific aim will focus on developing and validating a multiplexed, automated evolution pipeline to enable the scalable discovery and characterization of new RNA switches. The second specific aim will focus on developing new quantitative methods to examine the secondary structures and tertiary interactions that are key to the activity of RNA switches. The third specific aim will apply the new evolution pipeline and analysis methods to generate new RNA switches and probe the diversity of mechanisms underlying the function of engineered switches. The successful execution of the project will transform our capacity to rapidly and reliably build these genetic tools for diverse biological systems. In addition, the rich datasets generated through the newly developed methods will be leveraged to uncover new insight into the sequence-activity landscapes underlying this important class of functional RNA molecules and answer long-standing questions in the field. These insights will more broadly advance our understanding of RNA sequence- structure-function relationships and ultimately dramatically improve our capacities to design functional RNA molecules tailored to biomedical applications. The pipelines and approaches developed through this project will change the paradigm by which the research community approaches functional RNA design, thereby having a substantially broader impact on the field.

项目摘要 遗传编码的技术，可实现接收，处理和 传输分子信息对于推进基本生物学研究至关重要 生物医学研究和生物技术。 RNA开关是一类配体响应遗传 在不同的生物系统中实施的控制器，以改变我们的能力 监视，与动态蜂窝状态进行监视，接口和编程。而合成的应用 在过去的十年中，监管RNA的增长非常明显，目前的设计方法 新的RNA调节元素效率低下，费力，通常不会深入了解 这些分子在复杂活动中的活性的序列结构函数关系 生物系统。 拟议项目的目的是制定新的策略来实现设计， 测量和分析重要的RNA开关，将核酶作为核酶 基因控制元件。该项目的目标将通过三个特定目标实现。第一个 具体目标将着重于开发和验证多路复用，自动化的进化管道 启用新RNA开关的可扩展发现和表征。第二个特定目标 将着重于开发新的定量方法来检查二级结构和第三级 相互作用是RNA开关活动的关键。第三个特定目标将适用新的 进化管道和分析方法生成新的RNA开关并探测的多样性 工程开关功能的基础机制。 该项目的成功执行将改变我们快速可靠地建造的能力 这些用于多种生物系统的遗传工具。另外，通过 新开发的方法将被利用以发现对序列活动的新洞察力 这一重要类别的功能性RNA分子的景观并回答长期存在 在现场的问题。这些见解将更广泛地提高我们对RNA序列的理解 - 结构功能关系，并最终显着提高我们设计功能的能力 针对生物医学应用量身定制的RNA分子。管道和方法通过 该项目将改变研究社区接近功能RNA的范式 设计，从而对该领域产生了更大的影响。