Model-guided design of RNA stabilizing elements for improved coronavirus diagnostics
用于改进冠状病毒诊断的 RNA 稳定元件的模型引导设计
基本信息
- 批准号:10280880
- 负责人:
- 金额:$ 117.37万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-09-17 至 2025-09-16
- 项目状态:未结题
- 来源:
- 关键词:5&apos Untranslated RegionsAcuteBindingBiological AssayCOVID detectionCOVID diagnosticCOVID-19COVID-19 detectionCOVID-19 diagnosticCharacteristicsClinicalClustered Regularly Interspaced Short Palindromic RepeatsCoronavirusDetectionDevelopmentDiagnosisDiagnosticDiagnostic testsElementsEngineeringEnzymesGuide RNAHalf-LifeHuman ResourcesIn VitroInfectionLeadLibrariesMessenger RNAMethodsModelingNorovirusNucleic Acid Amplification TestsNucleotidesOutcomePatientsPerformancePhaseProductionRNARNA DegradationRNA StabilityRNA amplificationRNA vaccineReagentReporterRepressionResistanceReverse Transcriptase Polymerase Chain ReactionRibonucleasesSamplingSchemeSensitivity and SpecificitySpecial EquipmentSpeedStructureTechnologyTestingTrainingTranscriptTranslationsViralaptamerbasedeep learningdesigndetection assaydetection sensitivitydiagnostic assaydiagnostic technologiesimprovedmRNA Stabilityportabilitypreservationprotein expressionrespiratoryrole modelscreeningsensorstemviral detection
项目摘要
Project Summary
Fast, inexpensive, and sensitive methods to detect the SARS-CoV-2 coronavirus are instrumental
in containing the spread of COVID-19. Currently, nucleic acid testing of respiratory samples using
RT-PCR is the primary and most commonly used method for diagnosing patients in the acute
phase of the infection. However, this standard approach suffers from the need for special
equipment and well-trained personnel and hence has become a bottleneck to meet the urgent
demand for large-scale screening. A range of new RNA-based technologies, including toehold
switches and CRISPR/Cas systems, are being actively developed with the aim to implement
diagnostic tests that are ultra-sensitive, easy to deploy, and make use of enzymes and reagents
separate from the traditional PCR pipeline. One common and critical component of these methods
is the engineering of RNA molecules to detect target viral sequences. Consequently, their
performance in terms of specificity and sensitivity have been significantly hindered by the fast
degradation of RNAs caused by the RNases ubiquitous in both clinical sample matrices and as
byproducts of biomolecular reagent production.
Here we propose to enhance coronavirus diagnostic performance by programming RNase
resistance into assay components, in turn increasing RNA stability and enhancing test
sensitivity and speed. We will rationally design RNA 5’ UTR sequences and the resulting
secondary structures of mRNA, toehold switch RNA, and CRISPR guide RNAs to modulate
their resistance to RNase activities and hence quantitatively tune their stability. Results
from the proposed forward engineering studies will increase our understanding and control of
RNA dynamics and provide a widely applicable strategy to improve coronavirus detection
efficiencies of many technologies under development. Impact: A comprehensively studied RNA
design scheme to improve RNA stability will be complementary to current technologies under
development to give them a boost in performance, and provide underlying design strategies with
potential broader applicability, such as overcoming the stability barrier for mRNA-based vaccines.
There are three specific aims in this proposal: Aim 1: Characterize and model the role of 5’
secondary structures in fine-tuning mRNA stability; Aim 2: Optimize sensing RNAs for detection
of COVID-19; Aim 3: Use dtRNAs to enhance sample and amplified RNA stability for improved
diagnostics.
项目摘要
快速、廉价和灵敏的方法检测SARS-CoV-2冠状病毒是有用的
遏制COVID-19的传播。目前,呼吸道样本的核酸检测使用
RT-PCR是诊断急性胰腺炎患者的主要和最常用的方法。
感染的阶段。然而,这种标准方法的缺点是需要特殊的
设备和训练有素的人员,因此已成为一个瓶颈,以满足迫切的
大规模筛选的需求。一系列基于RNA的新技术,包括立足点
交换机和CRISPR/Cas系统正在积极开发,旨在实现
超灵敏、易于部署并利用酶和试剂的诊断测试
与传统的PCR管道分离。这些方法的一个共同和关键组成部分
是设计RNA分子来检测目标病毒序列。因此,其
在特异性和灵敏度方面的性能已经被快速的
由临床样本基质和作为基质中普遍存在的RNA酶引起的RNA降解
生物分子试剂生产的副产品。
在这里,我们建议通过编程RNase来增强冠状病毒诊断性能
检测组分的抗性,进而增加RNA稳定性并增强检测
灵敏度和速度。我们将合理设计RNA 5' UTR序列,
mRNA、支点开关RNA和CRISPR引导RNA的二级结构来调节
它们对RNA酶活性的抗性,从而定量地调节它们的稳定性。结果
从拟议的前瞻性工程研究将增加我们的理解和控制,
RNA动力学,并提供了一个广泛适用的策略,以提高冠状病毒检测
许多技术正在开发中。影响:全面研究的RNA
提高RNA稳定性的设计方案将与现有技术互补,
开发,以提高性能,并提供底层设计策略,
潜在的更广泛的适用性,例如克服基于mRNA的疫苗的稳定性障碍。
本建议有三个具体目标:目标1:描述和模拟5'的作用
二级结构的微调mRNA的稳定性;目的2:优化传感RNA检测
目的3:使用dtRNA增强样品和扩增RNA的稳定性,以改善
诊断
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Alexander Arthur Green的其他文献
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{{ truncateString('Alexander Arthur Green', 18)}}的其他基金
Model-guided design of RNA stabilizing elements for improved coronavirus diagnostics
用于改进冠状病毒诊断的 RNA 稳定元件的模型引导设计
- 批准号:
10562816 - 财政年份:2022
- 资助金额:
$ 117.37万 - 项目类别:
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