High-throughput, Label-free Promoter Sequence Discovery

高通量、无标记启动子序列发现

• 批准号: 7268015
• 负责人: M SELIM UNLU
• 金额: $ 19.72万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2009-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7268015
• 关键词: Binding; Biological Assay; Biosensor; Boston; Cells; Condition; DNA; DNA Microarray Chip; DNA Microarray format; Detection; Devices; Dyes; Enabling Factors; Gene Expression; Genes; Genome; Hand; Histocompatibility Testing; Housing; Human; Image; Industry; Label; Legal patent; Measures; Methods; Monitor; Nucleic Acid Regulatory Sequences; Oligonucleotide Microarrays; Optical Methods; Optics; Pattern; Profilometer; Protein Binding; Proteins; Proteomics; Purpose; Reading; Research Personnel; Rest; Reverse Transcription; Sampling; Semiconductors; Sensitivity and Specificity; Silicon; Streptavidin; Structure; Surface; Techniques; Technology; TimeLine; Universities; Work; base; cost effective; design; improved; innovation; instrumentation; interest; monolayer; new technology; novel; programs; promoter; protein expression; response; size; transcription factor

DESCRIPTION (provided by applicant): The proposed work is aimed at demonstrating a high throughput, cost effective, and label-free microarray- based method for detecting macromolecular interactions. In particular, we propose a novel technology that involves the use of microarrays and a new label-free optical detection method based on the Resonant Cavity Imaging Biosensor (RCIB). While the use of optical resonators for sensing applications has been studied for many years, the unique capabilities of RCIB described in this proposal have been enabled by recent innovations developed at Boston University as well as advancements in optical instrumentation. One of the primary enabling factors is the invention of high-quality multi-layer dielectric reflectors developed at Boston University for the study of optoelectronic devices on silicon. This is accompanied by new techniques to sense small changes in material on layered structures. Resonant Cavity Imaging Biosensor (RCIB) promises to open the way to high throughput array based methods for profiling protein expression and for discovering intergenic regulatory regions. This proposal will focus on demonstrating and adapting RCIB detection techniques for protein oligonucleotides arrays, and assessing the sensitivity and specificity of the technology. Promoter sequences and potential promoter sequence regions will be photolithographically synthesized on a DNA microarray. Unlabeled TFs will be introduced to the microarray surface and allowed to bind to their corresponding promoter sequences. The presence of TFs will be detected and quantified using the label-free RCIB method. This work will achieve the following specific aims: 1. Demonstrate RCIB sensing and imaging of 0.1 nm high artificial structures patterned on SiO2; 2. Detect monolayer of streptavidin bound to biotinylated DNA patterned in an array format with 64 features each 50 mu m x 50 mu m in size; 3. Demonstrate specificity and sensitivity of different transcription factors (TFs) binding to their corresponding promoter sequences on a 100-feature microarray.

描述(由申请人提供)：拟议的工作旨在展示一种基于高通量、成本效益和无标记的微阵列检测大分子相互作用的方法。特别是，我们提出了一种新的技术，包括使用微阵列和一种新的基于共振腔成像生物传感器(RCIB)的无标记光学检测方法。虽然使用光学谐振器进行传感应用的研究已有多年，但本提案中描述的RCIB的独特功能是由波士顿大学最近开发的创新以及光学仪器的进步实现的。主要的促成因素之一是波士顿大学为研究硅上的光电子器件而开发的高质量多层介质反射器的发明。伴随而来的是感知分层结构上材料微小变化的新技术。共振腔成像生物传感器(RCIB)有望为基于高通量阵列的蛋白质表达谱和发现基因间调控区的方法开辟道路。该提案将侧重于展示和采用蛋白质寡核苷酸阵列的RCIB检测技术，并评估该技术的敏感性和特异性。启动子序列和潜在的启动子序列区域将在DNA微阵列上进行光刻合成。未标记的转录因子将被引入微阵列表面，并允许与其相应的启动子序列结合。将使用无标记的RCIB方法来检测和定量TF的存在。这项工作将实现以下具体目标：1.展示基于二氧化硅的0.1 nm高人工结构的RCIB传感和成像；2.以阵列的形式检测与生物素化的DNA结合的链霉亲和素单层，每个大小为50微米×50微米；3.在100个特征微阵列上展示不同转录因子(TF)与其相应启动子序列结合的特异性和敏感性。

项目成果

Applications of optical resonance to biological imaging and label-free protein microarrays.

光学共振在生物成像和无标记蛋白质微阵列中的应用。

• DOI: 10.1109/iembs.2008.4649744
• 发表时间: 2008
• 期刊: Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
• 作者: Unlü,MSelim;Ozkumur,IE;Needham,J;Bergstein,DA;Goldberg,BB;Yalcin,A;Spuhler,P;Irani,R;DeLisi,C
• 通讯作者: DeLisi,C

Label-free multiplexed virus detection using spectral reflectance imaging.

• DOI: 10.1016/j.bios.2011.01.019
• 发表时间: 2011-04-15
• 期刊: Biosensors & bioelectronics
• 影响因子: 12.6
• 作者: Lopez CA;Daaboul GG;Vedula RS;Ozkumur E;Bergstein DA;Geisbert TW;Fawcett HE;Goldberg BB;Connor JH;Unlü MS
• 通讯作者: Unlü MS

Quantification of DNA and protein adsorption by optical phase shift.

• DOI: 10.1016/j.bios.2009.06.033
• 发表时间: 2009-09-15
• 期刊: Biosensors & bioelectronics
• 影响因子: 12.6
• 作者: Ozkumur E;Yalçin A;Cretich M;Lopez CA;Bergstein DA;Goldberg BB;Chiari M;Unlü MS
• 通讯作者: Unlü MS

Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.

• DOI: 10.1016/j.bios.2009.12.032
• 发表时间: 2010-03-15
• 期刊: Biosensors & bioelectronics
• 影响因子: 12.6
• 作者: Ozkumur E;Ahn S;Yalçin A;Lopez CA;Cevik E;Irani RJ;DeLisi C;Chiari M;Unlü MS
• 通讯作者: Unlü MS

Direct observation of conformation of a polymeric coating with implications in microarray applications.

直接观察聚合物涂层的构象对微阵列应用的影响。

• DOI: 10.1021/ac801954x
• 发表时间: 2009
• 期刊: Analytical chemistry
• 影响因子: 7.4
• 作者: Yalçin,Ayça;Damin,Francesco;Ozkumur,Emre;diCarlo,Gabriele;Goldberg,BennettB;Chiari,Marcella;Unlü,MSelim
• 通讯作者: Unlü,MSelim