Fluorescence-based nucleic acid detection and microarrays

Recent analytical innovations for nucleic acid detection have revolutionized the biological sciences. Single nucleic acid sequence detection methods have been expanded to incorporate multiplexed detection strategies. A variety of nucleic acid detection formats are now available that can address high throughput genomic interrogation. Many of these parallel detection platforms or arrays, employ fluorescence as the signaling method. Fluorescence-based assays offer many advantages, including increased sensitivity, safety and multiplexing capabilities, as well as the ability to measure multiple fluorescence properties. Multiplexed microarray platforms provide parallel detection capabilities capable of measuring thousands of simultaneous responses. This review will discuss both single target detection and microarray applications with a focus on gene expression and pathogenic microorganism (PM) detection.     

Comparison of a pump-around, a diffusion-driven, and a shear-driven system for the hybridization of mouse lung and testis total RNA on microarrays

In the present study, we demonstrate the benefits of a shear-driven rotating microchamber system for the enhancement of microarray hybridizations, by comparing the system with two commonly used hybridization techniques: purely diffusion-driven hybridization under coverslip and hybridization using a fully automated hybridization station, in which the sample is pumped in an oscillating manner. Starting from the same amount of DNA for the three different methods, a series of hybridization experiments using mouse lung and testis DNA is presented to demonstrate these benefits. The gain observed using the rotating microchamber is large: both in terms of analysis speed (up to tenfold increase) and in final spot intensity (up to sixfold increase). The gain is due to the combined effect of the hybridization chamber miniaturization (leading to a sample concentration increase if comparing iso-mass conditions) and the transport enhancement originating from the rotational shear-driven flow induced by the rotation of the chamber bottom wall.     

Fluorescence Analysis in Microarray Technology

Fluorescence has been the preferred choice for data quantification in biomedical microarray formats since their earliest days. As much as the formats have grown and evolved over the years, the methods in optical analysis have become ever more sophisticated and complex in order to produce more and better output. This review will provide an insight into the most common methods and the state-of-the-art of all areas in microarray fluorescence analysis. Starting with an overview on microarray formats with a focus on their demands on the readout, the most common and useful organic fluorescent stains are discussed before proceeding on to other approaches; the use of semiconductor nanocrystals (quantum dots), polymer and silica nanoparticles and fluorescent proteins. Ways to enhance the intrinsically low signal on biochips have become increasingly important as they offer a sound approach towards the detection of low concentration sample content. The three main categories are presented: amplification using DNA, enzymes, and dendrimers. As much diversity as on the microarrays themselves can be found at the detection device. Standard optical microarray detectors, and non-standard methods using fluorescence anisotropy, fluorescence lifetime imaging (FLIM) and fluorescence resonance energy transfer (FRET), and their advantages and disadvantages are discussed.     

聚氨酯分子印章的制备和表征

“软平板印刷”微结构制备技术为微米和亚微米器件的制备提供了一条新的途径 [1] ,已被电子学家和材料学家所应用 ,近年来进入了生物学领域[2 ] .本实验室将这一方法与生物分子电子学相结合 ,提出了用于 DNA芯片在片合成的分子印章法 [3,4 ] .分子印章法的实质是接触压印与组合化学相结合的固相界面反应 .聚二甲氧基硅氧烷 ( PDMS)是一种软印刷的优良材料 [5] ,但是由于其疏水性和较差的机械性能 ,必须对其进行改性才能用来制备 DNA分子印章 [6 ] .　　聚氨酯作为一种功能材料 ,由于分子中交替的软、硬链段及其不同的热动力学性能而形成…     

Protein microarrays enhanced performance using nanobeads arraying and polymer coating

A nanosize material composed of 330 nm glass beads coated with a copolymer of N,N-dimethylacrylamide (DMA), N,N-acryloyloxysuccinimide (NAS) and [3-(methacryloyl-oxy)propyl]trimethoxysilane (MAPS) was developed to improve the protein immobilization on biochips. The developed material, bearing rabbit-IgG proteins, was arrayed as 150 μm spots trapped at the surface of a poly(dimethylsiloxane) elastomer (PDMS), and compared to copoly(DMA-NAS-MAPS)-coated glass slides and latex beads based biochips. Evidences were made through scanning electron microscopy that the newly developed material based microarray exhibited surface irregularities at the submicron level leading to high specific area.The combination of such large immobilization area with the highly efficient protein immobilization of the copoly(DMA-NAS-MAPS) polymer, enabled the achievement of microarrays exhibiting good performances both in pure media and complex samples (human sera). Indeed, high specific/non-specific signal ratio was found using this optimized immobilization procedure.Chemiluminescent detection of anti-rabbit-IgG was obtained through peroxidase labeled antibodies in the 5 μg/l to 10 mg/l range. Application of the developed system to real samples was achieved for the detection of rheumatoid factor (RF) through a capture assay. Interesting results were obtained, with a RF detection over the 5.3-485 IU/ml range and without measurable matrix effect or non-specific signal.     

High throughput drug screening by direct RNA profiling on DNA sensors

The feasibility of DNA microarray sensor technology as a routine technique of molecular pharmacology to perform high throughput drug screening and the advantages of directly labeled RNA for a high throughput experiment are presented in this paper. A novel, single-step direct chemical labeling method for DNA microarray target samples has been developed to reduce the sample amount, cost, time and error of the experiment by eliminating the need for enzyme mediated labeling. Reproducibility of the data for high throughput drug screening is demonstrated by monitoring differential gene expression of a set of 45 gene targets involved in the genotoxic stress response pathways.     

Clinicopathological value and underlying molecular mechanism of annexin A2 in 992 cases of thyroid carcinoma

BackgroundThyroid carcinoma (THCA) is one of the most frequent endocrine cancers and has increasing morbidity. Annexin A2 (ANXA2) has been found to be highly expressed in various cancers; however, its expression level and potential mechanism in THCA remain unknown. This study investigated the clinicopathological value and primary molecular machinery of ANXA2 in THCA.Material and MethodsPublic RNA-sequencing and microarray data were obtained and analyzed with ANXA2 expression in THCA and corresponding non-cancerous thyroid tissue. A Pearson correlation coefficient calculation was used for the acquisition of ANXA2 coexpressed genes, while edgR, limma, and Robust Rank Aggregation were employed for differentially expressed gene (DEG) in THCA. The probable mechanism of ANXA2 in THCA was predicted by gene ontology and pathway enrichment. A dual-luciferase reporter assay was employed to confirm the targeting relationships between ANXA2 and its predicted microRNA (miRNA).ResultsExpression of ANXA2 was significantly upregulated in THCA tissues with a summarized standardized mean difference of 1.09 (P < 0.0001) based on 992 THCA cases and 589 cases of normal thyroid tissue. Expression of ANXA2 was related to pathologic stage. Subsequently, 1442 genes were obtained when overlapping 4542 ANXA2 coexpressed genes with 2248 DEGs in THCA; these genes were mostly enriched in pathways of extracellular matrix-receptor interaction, cell adhesion molecules, and complement and coagulation cascades. MiR-23b-3p was confirmed to target ANXA2 by dual-luciferase reporter assay.ConclusionsUpregulated expression of ANXA2 may promote the malignant biological behavior of THCA by affecting the involving pathways or being targeted by miR-23b-3p.     

lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis

BackgroundColorectal cancer (CRC) is one of the most frequent and diagnosed diseases. Accumulating evidences showed that mRNAs and noncoding RNAs play important regulatory roles in tumorigenesis. Identification and determining the relationship between them can help diagnosis and treatment of cancer.MethodsHere we analyzed three microarray datasets; GSE110715, GSE32323 and GSE21510, to identify differentially expressed lncRNAs and mRNAs in CRC. The adjusted p-value ≤0.05 was considered statistically significant. Gene set enrichment analysis was carried out using DAVID tool. The miRCancer database was searched to obtain differentially expressed miRNAs in colorectal cancer, and the miRDB database was used to attain the targets of the obtained miRNAs. To predict the lncRNA-miRNA interactions we used DIANA-LncBase v2 and RegRNA 2.0. Finally the lncRNA-miRNA-mRNA-signaling pathway network was constructed using Cytoscape v3.1.ResultsBy analyzing the three datasets, a total of 21 mRNAs (15 up- and 6 down-regulated) and 24 lncRNAs (18 up- and 6 down-regulated) were identified as common differentially expressed genes between CRC tumor and marginal tissues. Nevertheless, the constructed lncRNA-miRNA-mRNA-signaling pathway network revealed a convergence on 6 lncRNAs (3 up- and 3 downregulated), 7 mRNAs (2 up- and 5 downregulated) and 6 miRNAs (3 up- and 3 downregulated). We found that dysregulation of lncRNAs such as PCBP1-AS1, UCA1 and SNHG16 could sequester several miRNAs such as hsa-miR-582-5p and hsa-miR-198 and promote the proliferation, invasion and drug resistance of colorectal cancer cells.ConclusionsWe introduced a set of lncRNAs, mRNAs and miRNAs differentially expressed in CRC which might be considered for further experimental research as potential biomarkers of CRC development.     

基于压电振荡原理的微阵列点样系统的研制

针对基于电磁微阀原理的非接触点样方式存在操作过程复杂、点样量偏大,以及压电喷墨原理的非接触点样方式存在点样针不易清洗、造价昂贵等不足,研制了一种基于压电振荡原理的新型非接触点样装置,实现了微量液体点样.在本装置中,毛细管点样针与压电驱动装置为两个独立单元,可以单独对毛细管点样针进行更换和清洗.采用激光拉制法制备的玻璃毛细管点样针具有内径可调、成本低等优点.此点样方式通过改变压电陶瓷的振幅和频率,可在10Symbolm@@_10～10Symbolm@@_9 L之间调控点样体积.以此为基础,结合三维精密位移控制技术,研制了一种基于压电振荡原理的微阵列生物芯片点样系统.对点样系统的点样体积、点样密度、点样精度等参数进行了测试,结果表明,此点样系统的最小点样体积可达320 pL,点样密度可达4000 点/cm2,并能够实现界面图案化制备.     

Assembly of sugars on polystyrene plates: a new facile microarray fabrication technique

The work presented herein is a new noncovalent glycoarray assembly method for microplates created by simply mixing together an isocyanate-containing C₁₄-hydrocarbon and an amine-containing carbohydrate. 2-Aminoethyl-β-d-galactopyranoside (1) was utilized in model studies and product formation was detected by both ESI-MS and lectin binding. The method has been further extended to array complex carbohydrates.