DNA microarray surface analysis to optimize detection

DNA 微阵列表面分析以优化检测

基本信息

批准号：
8058811
负责人：
DAVID W GRAINGER
金额：
$ 35.09万
依托单位：
UNIVERSITY OF UTAH
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-07-15 至 2013-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8058811
关键词：
Address Adoption Affect Bacteria Base Pairing Biocompatible Materials Biological Assay Biomedical Engineering Biomedical Research Biosensing Techniques Biotechnology Bromine Cells Charge Chemicals Chemistry Clinical Communities Complementary DNA Complex Contracts Critical Pathways Custom DNA DNA Microarray Chip DNA Probes Data Detection Development Diagnosis Diagnostic Diagnostic radiologic examination Disease Elements Environment Enzymes FDA approved Fluorescence Food Frequencies Funding Future Gambling Generations Glass Goals Gold Growth Head Health behavior Heterogeneity Image Immobilization In Situ Kinetics Knowledge Learning Medical Medicine Methods Microarray Analysis Modeling Molecular Molecular Analysis Monitor Nucleic Acid Probes Nucleic Acids Oligonucleotides Peptide Nucleic Acids Performance Pharmaceutical Preparations Pharmacology Polymers Preclinical Drug Evaluation Printing Productivity Progress Reports Protein Array Proteins Proteome Public Health Publishing Radiolabeled Reagent Reporting Reproducibility Research Research Personnel Research Project Grants Resolution Resources Roentgen Rays Sampling Science Screening procedure Serum Slide Source Spectrometry, Mass, Secondary Ion Spectrum Analysis Spottings Sum Surface Surface Plasmon Resonance Surface Properties System Techniques Technology Testing Time Toxicology Translations Uncertainty United States National Institutes of Health Washington Work Yeasts absorption analytical method aptamer base biosecurity clinical application clinically relevant density design disease diagnosis experience fluorescence imaging improved innovation insight instrumentation interfacial nanoscale prevent radiotracer small molecule tool

项目摘要

DESCRIPTION (provided by applicant): This Bioengineering Research Group R01 competing continuation proposal aims to continue the productivity and impact of the preceding funded period in elucidating key surface properties of commercial and model nucleic acid microarray diagnostic assays. Despite immense potential clinical and environmental applications for these multiplexed diagnostic formats, only two microarray assays are FDA-approved for clinical diagnostic use. Array surface-capture problems preclude assay reliability, sensitivity, and reproducibility, occurring across all commercial platforms, within batches in a single platform, between different clinical labs, and even within microarray elements on a single slide. This is also the most significant problem for a substantial fraction of assays under commercial development: custom printed arrays involving different printing technologies and assay reagents. Hence, clinical impact of microarrays is currently very limiting. Significance is derived from this proposal's focus on obtaining new information necessary for understanding and resolving the issues of assay reliability, sensitivity and reproducibility. Wide adoption of microarray technology for recent FDA, EPA and NIH Critical Path initiatives for disease, drug pharmacology and toxicitiy screening goals relies on improving assay performance and developing clear understanding of their limitations. This proposal responds directly to that need. The working hypothesis is that precise quantitation of surface immobilization and capture efficiencies in microarrays comprising nucleic acids using newly available high-resolution instrumentation will identify current assay limitations, and facilitate improved surface-capture assay performance necessary for clinical use of these diagnostics. Specific aims for the 3-year project include: Aim 1. Validate and correlate new surface analytical technology methods for molecular analysis of nucleic acids, specifically, to quantify printed and captured nucleic acid density on microarrayed surfaces. Aim 2. Compare DNA and PNA microarray printed spot uniformity as it relates to printed substrate conditions and chemistry, and address spot-to-spot variability at high chemical resolution as common sources of microarray assay variance and uncertainty observed on commercial microarray substrates. Aim 3. Improve standard microarray assay performance requirements and capture assay detection limits by direct quantitation and detection of small amounts of target DNA in complex media without pre-purification. This proposal focuses on improving the current capabilities in nucleic acid microarray bioassay. A suite of complementary state-of-the-art surface analytical methods will be exploited to assess variables affecting DNA surface immobilization and target hybridization in model and commercial assay formats. The strategy proposed addresses important bio-analytical problems in these assays to identify improvements that impact high-priority science and technology involved in monitoring public health and disease, pharmacology and personalized medicine, and toxicology. Developing reliable bio- assays capable of detecting DNA hybridization from real-world samples at an attomole level would allow rapid clinical diagnostic applications beyond current research use. Facilitating translation of these widely used microarray assay formats from current research to true clinical future use is a major aim of this research.

描述（由申请人提供）：这项生物工程研究小组 R01 竞争性延续提案旨在继续先前资助期间的生产力和影响力，阐明商业和模型核酸微阵列诊断测定的关键表面特性。尽管这些多重诊断格式具有巨大的临床和环境应用潜力，但只有两种微阵列检测获得 FDA 批准用于临床诊断。阵列表面捕获问题妨碍了测定的可靠性、灵敏度和重现性，这些问题发生在所有商业平台上、单个平台的批次内、不同的临床实验室之间，甚至在单个载玻片上的微阵列元件内。对于商业开发中的大部分检测来说，这也是最重要的问题：涉及不同打印技术和检测试剂的定制打印阵列。因此，微阵列的临床影响目前非常有限。该提案的意义在于获取理解和解决测定可靠性、灵敏度和重现性问题所需的新信息。 FDA、EPA 和 NIH 最近针对疾病、药物药理学和毒性筛选目标的关键路径计划广泛采用微阵列技术，这依赖于提高检测性能并清楚地了解其局限性。该提案直接响应了这一需求。工作假设是，使用新近可用的高分辨率仪器对包含核酸的微阵列中的表面固定和捕获效率进行精确定量将确定当前测定的局限性，并促进改善这些诊断的临床使用所需的表面捕获测定性能。该项目为期 3 年的具体目标包括：目标 1. 验证和关联用于核酸分子分析的新表面分析技术方法，特别是量化微阵列表面上打印和捕获的核酸密度。目标 2. 比较 DNA 和 PNA 微阵列印刷点的均匀性，因为它与印刷基质条件和化学有关，并解决高化学分辨率下点与点之间的变异性，这是在商业微阵列基质上观察到的微阵列测定差异和不确定性的常见来源。目标 3. 通过直接定量和检测复杂介质中的少量靶 DNA，无需预纯化，提高标准微阵列测定性能要求并捕获测定检测限。该提案的重点是提高目前核酸微阵列生物测定的能力。将利用一套互补的最先进的表面分析方法来评估影响模型和商业测定格式中 DNA 表面固定和目标杂交的变量。提出的策略解决了这些测定中的重要生物分析问题，以确定影响公共健康和疾病、药理学和个性化医疗以及毒理学的高优先级科学和技术的改进。开发能够在阿托摩尔水平上检测真实世界样品中 DNA 杂交的可靠生物测定方法将允许超越当前研究用途的快速临床诊断应用。促进这些广泛使用的微阵列测定格式从当前研究到未来真正的临床应用的转化是本研究的主要目标。

项目成果

期刊论文数量（26）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Surface Analysis of Photolithographic Patterns using ToF-SIMS and PCA.

使用 ToF-SIMS 和 PCA 进行光刻图案的表面分析。

DOI：
发表时间：
2009-03-18
期刊：
影响因子：
0
作者：
Dubey, Manish;Emoto, Kazunori;Cheng, Fang;Gamble, Lara J;Takahashi, Hironobu;Grainger, David W;Castner, David G
通讯作者：
Castner, David G

High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots.

单个 DNA 微阵列点的高分辨率落射荧光和飞行时间二次离子质谱化学成像比较。