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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）：本生物工程研究小组R01竞争性延续提案旨在继续前资助期在阐明商业和模型核酸微阵列诊断分析的关键表面特性方面的生产力和影响。尽管这些多路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方法被fda批准用于临床诊断。阵列表面捕获问题妨碍了检测的可靠性、灵敏度和可重复性，这些问题发生在所有商业平台、单个平台的批次内、不同临床实验室之间，甚至在单个载玻片上的微阵列元件中。这也是商业开发中相当一部分分析的最重要问题：涉及不同打印技术和分析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。重要的是，该提案的重点是获得理解和解决分析可靠性、灵敏度和可重复性问题所需的新信息。最近，微阵列技术被FDA、EPA和NIH广泛采用，用于疾病、药物药理学和毒性筛选目标的关键路径倡议，依赖于提高分析性能和对其局限性的清晰理解。这项建议直接回应了这一需要。工作假设是，使用最新可用的高分辨率仪器对包含核酸的微阵列的表面固定和捕获效率进行精确定量，将确定当前的分析局限性，并促进这些诊断临床使用所必需的表面捕获分析性能的改进。这个为期三年的项目的具体目标包括：验证和关联新的表面分析技术方法，用于核酸分子分析，特别是量化微阵列表面上印刷和捕获的核酸密度。目标2。比较DNA和PNA微阵列印刷点均匀性，因为它与印刷底物条件和化学有关，并在高化学分辨率下解决点对点的可变性，这是在商业微阵列底物上观察到的微阵列分析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少量目标DNA而无需预纯化，提高标准微阵列分析性能要求和捕获分析检测限。本提案的重点是提高当前核酸微阵列生物测定的能力。一套互补的最先进的表面分析方法将被利用来评估影响DNA表面固定和目标杂交模型和商业分析格式的变量。拟议的战略涉及这些分析中的重要生物分析问题，以确定影响监测公共卫生和疾病、药理学和个性化医疗以及毒理学方面的高度优先科学和技术的改进。开发可靠的生物分析方法，能够在原子水平上检测真实样品的DNA杂交，将使快速临床诊断应用超越当前的研究用途。促进这些广泛使用的微阵列检测格式从当前的研究到真正的临床应用是本研究的主要目的。

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）

Multivariate analysis of ToF-SIMS data from multicomponent systems: the why, when, and how.

DOI：
10.1007/s13758-012-0049-3
发表时间：
2012-12
期刊：
BIOINTERPHASES
影响因子：
2.1
作者：
Graham, Daniel J.;Castner, David G.
通讯作者：
Castner, David G.

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

DOI：
10.1002/sia.3056
发表时间：
2009-03-18
期刊：
SURFACE AND INTERFACE ANALYSIS
影响因子：
1.7
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.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.