cDNA微阵列与寡核苷酸芯片的制备方法

cDNA微阵列和寡核苷酸芯片是常见的合成后点样的DNA微阵列。点样方法主要是通过物理吸附或共价结合的方式将探针固定于载体上,本总结了近年来国内外献报道的cDNA微阵列制备方法;在多聚赖氨酸包被的玻璃基片表面制备cDNA微阵列;用琼脂糖包被的玻璃基片制备cDNA微阵列;在氨基或醛基修饰的玻璃基片表面制备cDNA微阵列;寡核苷酸芯片的制备方法;氨基修饰的玻片与5′末端带氨基的寡核苷酸探针通过不同的linker连接;硅烷化寡核苷酸直接点样于玻片上制成寡核苷酸微阵列;硫代寡核苷酸通过二硫键与巯基修饰的玻片连接;水凝胶芯片固定寡核苷酸。丙烯酰胺硅烷化的基片与5′丙烯酰胺修饰的寡核苷酸连接。并展望了基因芯片的应用前景。     

人白细胞介素－2基因在人骨肉瘤细胞系内表达

从pHIG53质粒内切下人白细胞介素-2(IL-2)cDNA基因, 并经中间质粒pSP72转换成与pDOR-neo载体相匹配的酶切位点, 然后将IL-2cDNA定向连接入pDOR-neo载体, 构建成功人IL-2逆转录病毒载体, 经脂质体导入人骨肉瘤细胞系Ma中, 经G418筛选后测转基因肿瘤细胞培养上清中IL-2表达量, 每1×10⁵细胞24hIL-2表达量为50～800U, 为骨肉瘤的基因治疗创造条件.     

乳腺癌中VEGF和MMP9的免疫组织化学表达及其与肿瘤转移复发的关系

目的探讨血管内皮生长因子(vascular endothelial growth factor,VEGF)及基质金属蛋白酶9(matrix metalloproteinases 9,MMP9)的表达与乳腺癌临床病理因素及肿瘤转移复发的关系。方法通过免疫组织化学检测VEGF和MMP9在230例乳腺癌组织芯片中的表达,比较二者表达的相关性并分析二者表达与临床病理因素、肿瘤复发之间的关系。结果VEGF和MMP9在乳腺癌中的阳性率分别为68.3%和55.2%,显著高于癌旁组织;VEGF的表达与临床分期密切相关,Ⅰ期乳腺癌患者中的VEGF阳性率显著低于Ⅱ期+Ⅲ期;MMP9的表达与组织学分级、淋巴结转移密切相关,在淋巴结转移组中MMP9的阳性率显著高于未发生淋巴结转移组,且随着组织学分级的升高,其阳性率也逐渐升高;MMP9的表达与VEGF的表达呈显著正相关;MMP9与VEGF在复发组中的阳性率均显著高于未复发组,是乳腺癌复发的危险因素。结论乳腺癌组织中VEGF和MMP9的高表达是乳腺癌术后复发的危险因素,检测其表达对判断乳腺癌术后预后具有重要意义。     

重组人粒细胞集落刺激因子Cdna在哺乳动物细胞中高效表达的研究

利用PCR反应、DNA测序、基因重组等技术,构建了两个表达人粒细胞集落刺激因子cDNA的重组质粒pED－GCSF和pEF－GCSF,两质粒分别转染COS7细胞作瞬时表达,转染CHO－dhfr－细胞作稳定表达。结果两质粒在COS7细胞和CHO细胞均获得了表达,pED－GCSF转染COS7细胞48h、72h的表达量分别为5.2×10⁴pg/ml和2.3×10⁵pg/ml,pEF－GCSF转染COS7细胞后48h、72h的表达量分别为2.8×10⁵pg/ml和1.4×10⁵pg/ml。转染CHO－dhfr－细胞,随着加入的氨甲喋呤(MTX)浓度升高,CHO－dhfr+克隆数减少,但平均每个克隆的rhG－CSF表达量升高,在0.5μmol/L MTX下最高表达rhG－CSF细胞株的量是4.46μg/ml/3d。且表达的rhG－CSF注射小鼠腹腔可提高小鼠外周血白细胞的数量。     

乳腺癌肺转移过程中Th1/Th2型细胞因子的动态变化

探究乳腺癌肺转移模型鼠肺组织内Th1/Th2型细胞因子的动态变化。利用皮下接种或尾静脉注射乳腺癌细胞系-4T1细胞的方式,建立乳腺癌肺转移模型。在4T1细胞接种后第7、14、21天分离模型鼠肺组织,通过HE染色、墨汁染色确认模型建立成功后,提取肺组织总RNA,采用Real-time RT-PCR方法,检测肺组织内IFN-γ、IL-4、IL-5、IL-13表达水平的变化。结果显示,尾静脉注射4T1细胞的BALB/c鼠,肺组织内Th1型细胞因子水平呈现先升高后逐渐下降的趋势;而皮下接种4T1细胞的BALB/c鼠,其肺组织内Th1型细胞因子水平一致处于较低水平。与Th1型细胞因子不同,肺组织内Th2型细胞因子水平无论在皮下接种鼠亦或是尾静脉注射鼠均表现为逐渐升高趋势。结果表明,乳腺癌肺转移过程中出现Th1/Th2型细胞因子失衡,并且由刚开始的Th1优势应答逐渐转变为Th2优势应答。     

血管紧张素Ⅱ受体1、VEGF和MVD在乳腺癌中的表达及相关性研究

目的:研究AT1受体、VEGF和CD34在乳腺癌中的表达、并探讨其相关性及临床意义。方法:该实验采用免疫组化方法(SP法),对102例乳腺癌患者石蜡包埋切片中的AT1受体、VEGF和CD34进行检测。结果:AT1受体在乳腺癌中阳性表达率为48%,在乳腺癌中有腋淋巴结转移组为61．8%,无腋淋巴结转移组为31．9%,两者差别有统计学意义(P＜0．05)。VEGF在乳腺癌中表达率为40．2%,有腋淋巴结转移组44．4%,无腋淋巴结转移组为23．5%,两者差别有统计学意义(P＜0．01)。AT1R阴性表达组的VEGF阳性表达率为11．3%(6/53),AT1R阳性表达组的VEGF阳性表达为71．4%(35/49),两者差别有统计学意义(P＜0．05); AT1R阴性表达组的MVD值为17．35±5．67,AT1R阳性表达组的MVD值为20．37±7．30,两组差别有显著性(P＜0．05)。VEGF阴性表达组的MVD表达率为17．14±5．78,VEGF阳性表达组的MVD表达为21．27±7．14,两组差别有统计学意义(P＜0．05)。结论:乳腺癌组织中AT1受体的阳性表达率为48%(49/102)AT1受体表达与患者年龄、肿瘤大小、ER、PR无相关性,而与腋淋巴结转移成正相关;乳腺癌组织中VEGF的阳性表达率为40．2%(41/102),VEGF表达与患者年龄、肿瘤大小、ER、PR无相关性,而与腋淋巴结转移成正相关;AT1受体表达与VEGF表达成正相关。在乳腺癌组织中MVD和AT1R和VEGF表达均成正相关。     

VKC患儿与正常儿童泪液中细胞因子表达的比较

目的：比较VKC患儿与正常儿童泪液中细胞因子白细胞介素-4（IL-4）,白细胞介素-5（IL-5）和白细胞介素-13（IL-13）的表达量的变化,以及分析两组之间有无统计学差异。方法：收集10例春季角结膜炎（VKC）患儿与16例正常受试者（CT）的泪液;采用液体芯片技术测量两组泪液中IL-4,IL-5,IL-13的浓度,使用U检验来比较两组之间的差异有无统计学意义。结果：VKC组泪液中IL-4的浓度为1.09±0.73 pg/mL,IL-5的浓度为1.68±1.43 pg/mL,IL-13的浓度为1.90±1.59 pg/mL;与正常受试者（CT）相比,明显升高,两组之间比较差异均有统计学意义（P〈0.05）。结论：分析VKC患儿泪液中的细胞因子在了解VKC的发病机制中可能可以起到重要的作用,以及可以提供新的治疗方向。     

VKC患儿与正常儿童泪液中细胞因子表达的比较

目的:比较VKC患儿与正常儿童泪液中细胞因子白细胞介素-4(IL-4),白细胞介素-5(IL-5)和白细胞介素-13(IL-13)的表达量的变化,以及分析两组之间有无统计学差异。方法:收集10例春季角结膜炎(VKC)患儿与16例正常受试者(CT)的泪液;采用液体芯片技术测量两组泪液中IL-4,IL-5,IL-13的浓度,使用U检验来比较两组之间的差异有无统计学意义。结果:VKC组泪液中IL-4的浓度为1.09±0.73 pg/mL,IL-5的浓度为1.68±1.43 pg/mL,IL-13的浓度为1.90±1.59 pg/mL;与正常受试者(CT)相比,明显升高,两组之间比较差异均有统计学意义(P0.05)。结论:分析VKC患儿泪液中的细胞因子在了解VKC的发病机制中可能可以起到重要的作用,以及可以提供新的治疗方向。     

蛋氨酸脑啡肽单独或联合IL-2、IFN-γ对小鼠CD4+T细胞作用的研究

通过体内外MENK单独或联合IL-2、IFN-γ对C57BL/6小鼠CD4+T细胞数量,CD4+T细胞mRNA表达量以及细胞因子产生量的变化,来阐明MENK对CD4+T细胞的免疫效应.应用流式细胞术、酶联免疫吸附试验、RT-PCR方法检测C57 BL/6小鼠体内外单独应用MENK,或联合IL-2、IFN-γ后,CD4+T细胞数量,CD4+T细胞mRNA的表达量及上清中细胞因子含量.MENK单独或联合IL-2、IFN-γ,在体内能显著增加小鼠CD4+T细胞数量,CD4+T细胞mRNA表达量及细胞因子IL-2、IFN-γ含量;体外MENK单独应用可以显著增加小鼠CD4+T细胞数量,CD4+T细胞mRNA表达量及细胞因子IL-2、IFN-γ含量;而体外MENK联合IL-2或IFN-γ与MENK单独作用时相比无明显差异.MENK单独或联合IL-2、IFN-γ,在体内能上调CD4+T细胞的免疫效应.     

子宫内膜异位症患者细胞因子的表达与抗体反应

目的:探究细胞因子的表达与抗体反应在子宫内膜异位症(EMS)发生中的作用及其作为诊断指标的可能性。方法:选取子宫内膜异位症患者70例与对照组50例,检测并比较两组患者血清肿瘤坏死因子-α(TNF-α)、白细胞介素(IL-6)、单核细胞趋化因子-1(MCP-1)、血管内皮生长因子(VEGF)的表达以及抗子宫内膜抗体(EM-Ab)和转铁蛋白抗体(TRF-Ab)的阳性率。分析以上细胞因子及抗体的表达与子宫内膜异位症临床分期的关系。结果:子宫内膜异位症组TNF-α、IL-6、MCP-1与VEGF均显著高于对照组,差异具有统计学意义(P0.05);子宫内膜异位症组抗子宫内膜抗体阳性率、转铁蛋白抗体阳性率以及两种抗体均为阳性的比例均显著高于对照组,差异具有统计学意义(P0.05);TNF-α、IL-6、MCP-1与VEGF细胞因子与子宫内膜异位症分期呈正相关,分期越高、EMS病情越重则细胞因子表达水平越高(P0.05)。结论:细胞因子的表达与相关抗体反应均参与了子宫内膜异位症的发生及发展,通过检测到相关细胞因子水平的升高与自身抗体转阳可以筛选与诊断子宫内膜异位症,初步判断其临床分期和病情程度。     

Hybridization of DNA with oligonucleotides immobilized in a gel: a convenient method for recording single base replacements

In an attempt to develop a reliable system for DNA sequence analysis with multiple hybridization probes, oligonucleotides down to 8 bases long were covalently immobilized in a thin layer of polyacrylamide gel fixed on a glass plate. It was shown possible to detect single base changes in DNA by hybridization of the immobilized oligonucleotides with radioactively and fluorescently labeled DNA fragments. Moreover, it was found that dissociation temperatures of differently GC-rich duplexes could be equalized by appropriate choice of immobilized oligonucleotides concentrations. A model accounting for this phenomenon is presented. In order to make the system more compact, a rectangular matrix of 200 mm dots of immobilized oligonucleotides ("hybridization chip") was designed which offered the sensitivity of 20 attomoles per dot for fluorescent DNA fragment. The applications and perspectives of the approach are discussed.     

Fractionation, phosphorylation and ligation on oligonucleotide microchips to enhance sequencing by hybridization.

Oligonucleotide microchips are manufactured by immobilizing presynthesized oligonucleotides within 0.1 x 0.1 x 0.02 mm or 1 x 1 x 0.02 mm polyacrylamide gel pads arranged on the surface of a microscope slide. The gel pads are separated from each other by hydrophobic glass spacers and serve as a kind of 'microtest tube' of 200 pl or 20 nl volume, respectively. Fractionation of single-stranded DNAs is carried out by their hybridization with chip pads containing immobilized 10mers. DNA extracted separately from each pad is transferred onto a sequencing chip and analyzed thereon. The chip, containing a set of 10mers, was enzymatically phosphorylated, then hybridized with DNA and ligated in a site-directed manner with a contiguously stacked 5mer. Several cycles of successive hybridization-ligation of the chip-bound 10mers with different contiguously stacked 5mers and hybridized with DNA were carried out to sequence DNA containing tetranucleotide repeats. Combined use of these techniques show significant promise for sequence comparison of homologous regions in different genomes and for sequence analysis of comparatively long DNA fragments or DNA containing internal repeats.     

Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array.

Oligonucleotide microarrays, also called "DNA chips," are currently made by a light-directed chemistry that requires a large number of photolithographic masks for each chip. Here we describe a maskless array synthesizer (MAS) that replaces the chrome masks with virtual masks generated on a computer, which are relayed to a digital micromirror array. A 1:1 reflective imaging system forms an ultraviolet image of the virtual mask on the active surface of the glass substrate, which is mounted in a flow cell reaction chamber connected to a DNA synthesizer. Programmed chemical coupling cycles follow light exposure, and these steps are repeated with different virtual masks to grow desired oligonucleotides in a selected pattern. This instrument has been used to synthesize oligonucleotide microarrays containing more than 76,000 features measuring 16 microm 2. The oligonucleotides were synthesized at high repetitive yield and, after hybridization, could readily discriminate single-base pair mismatches. The MAS is adaptable to the fabrication of DNA chips containing probes for thousands of genes, as well as any other solid-phase combinatorial chemistry to be performed in high-density microarrays.     

Attachment of oligonucleotide probes to poly carbodiimide-coated glass for microarray applications

Oligonucleotide-based DNA microarrays are becoming increasingly useful tools for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Here, we present a method that permits the manufacture of microarrays from non-modified oligonucleotides on a poly carbodiimide-coated glass surface by UV-irradiation. The use of UV-irradiation facilitates an increase in the level of signal intensity, but it does not affect signal discrimination by the oligonucleotides immobilized on the surface. The signal intensity obtained for an array fabricated using non-modified oligonucleotides with UV-irradiation is ~7-fold greater than that without UV-irradiation. The detection of SNPs was tested to ascertain whether this technique could discriminate specific hybridization signals without causing significant UV-irradiation-induced damage to the immobilized oligonucleotides. We found that this immobilization method provides greater hybridization signals and a better match/mismatch ratio of SNPs than do the established aminosilane techniques. Application of this technology to manufacturing DNA microarrays for sequence analysis is discussed.     

Characterization of DNA chips by nanogold staining

DNA microarray is an important tool in biomedical research. Up to now, there are no chips that can allow both quality analysis and hybridization using the same chip. It is risky to draw conclusions from results of different chips if there is no knowledge of the quality of the chips before hybridization. In this article, we report a colorimetric method to do quality control on an array. The quality analysis of probe spots can be obtained by using gold nanoparticles with positive charges to label DNA through electrostatic attraction. The probe spots can also be detected by a simple personal computer scanner. Gold nanoparticles deposited on a glass surface can be dissolved in bromine-bromide solution. The same microarray treated with gold particles staining and destaining can still be used for hybridization with nearly the same efficiency. This approach makes quality control of a microarray chip feasible and should be a valuable tool for biomarker discovery in the future.     

Array-based mutation detection of BRCA1 using direct probe/target hybridization

We describe here an efficient microarray-based multiplex assay to detect Korean-specific mutations in breast cancer susceptibility gene BRCA1 using direct probe/target hybridization. Allele-specific oligonucleotides were covalently immobilized on an aldehyde-activated glass slide to prepare an oligonucleotide chip. From a wild-type sample, a two-step method was used to generate labeled multiplex polymerase chain reaction (PCR) amplification products of genomic regions containing the mutation sites. Amino allyl-dUTP, an amine-modified nucleotide, was incorporated during multiplex PCR amplifications and a monofunctional form of cyanine 3 dye was subsequently attached to the reactive amine group of the PCR products. Hybridization of the labeled PCR products to the oligonucleotide chip successfully identified all of the genotypes for the selected mutation sites. This work demonstrates that oligonucleotides chip-based analysis is a good candidate for efficient clinical testing for BRCA1 mutations when combined with the indirect strategy to prepare labeled target samples.     

Characterization of oligodeoxyribonucleotide synthesis on glass plates

Achieving high fidelity chemical synthesis on glass plates has become increasingly important, since glass plates are substrates widely used for miniaturized chemical and biochemical reactions and analyses. DNA chips can be directly prepared by synthesizing oligonucleotides on glass plates, but the characterization of these micro-syntheses has been limited by the sub-picomolar amount of material available. Most DNA chip syntheses have been assayed using in situ coupling of fluorescent molecules to the 5′-OH of the synthesized oligonucleotides. We herein report a systematic investigation of oligonucleotide synthesis on glass plates with the reactions carried out in an automated DNA synthesizer using standard phosphoramidite chemistry. The analyses were performed using ³²P gel electrophoresis of the oligonucleotides cleaved from glass plates to provide product distribution profiles according to chain length of oligonucleotides. 5′-Methoxythymidine was used as the chain terminator, which permits assay of coupling reaction yields as a function of chain length growth. The results of this work reveal that a major cause of lower fidelity synthesis on glass plates is particularly inefficient reactions of the various reagents with functional groups close to glass plate surfaces. These problems cannot be detected by previous in situ fluorescence assays. The identification of this origin of low fidelity synthesis on glass plates should help to achieve improved synthesis for high quality oligonucleotide microarrays.     

Hydrogel drop microchips with immobilized DNA: properties and methods for large-scale production

Although gel-based microchips offer significant advantages over two-dimensional arrays, their use has been impeded by the lack of an efficient manufacturing procedure. Here we describe two simple, fast, and reproducible methods of fabrication of DNA gel drop microchips. In the first, copolymerization method, unsaturated groups are chemically attached to immobilized molecules, which are then mixed with gel-forming monomers. In the second, simpler polymerization-mediated immobilization method, aminated DNA without prior modification is added to a polymerization mixture. Droplets of polymerization mixtures are spotted by a robot onto glass slides and the slides are illuminated with UV light to induce copolymerization of DNA with gel-forming monomers. This results in immobilization of DNA within the whole volume of semispherical gel drops. The first method can be better controlled while the second one is less expensive, faster, and better suited to large-scale production. The microchips manufactured by both methods are similar in properties. Gel elements of the chip are porous enough to allow penetration of DNA up to 500 nucleotides long and its hybridization with immobilized oligonucleotides. As shown with confocal microscope studies, DNA is hybridized uniformly in the whole volume of gel drops. The gels are mechanically and thermally stable and withstand 20 subsequent hybridizations or 30-40 PCR cycles without decrease in hybridization signal. A method for quality control of the chips by staining with fluorescence dye is proposed. Applications of hydrogel microchips in research and clinical diagnostics are summarized.     

Hydrogel-based protein microchips: manufacturing,properties, and applications

Here a simple, reproducible, and versatile method is described for manufacturing protein and ligand chips. The photo-induced copolymerization of acrylamide-based gel monomers with different probes (oligonucleotides, DNA, proteins, and low-molecular ligands) modified by the introduction of methacrylic groups takes place in drops on a glass or silicone surface. All probes are uniformly and chemically fixed with a high yield within the whole volume of hydrogel semispherical chip elements that are chemically attached to the surface. Purified enzymes, antibodies, antigens, and other proteins, as well as complex protein mixtures such as cell lysates, were immobilized on a chip. Avidin- and oligohistidine-tagged proteins can be immobilized within biotin- and Ni-nitrilotriacetic acid-modified gel elements. Most gel-immobilized proteins maintain their biological properties for at least six months. Fluorescence and chemiluminescence microscopy were used as efficient methods for the quantitative analysis of the microchips. Direct on-chip matrix-assisted laser desorption ionization-time of flight mass spectrometry was used for the qualitative identification of interacting molecules and to analyze tryptic peptides after the digestion of proteins in individual gel elements. We also demonstrate other useful properties of protein microchips and their application to proteomics and diagnostics.     

Microarray analysis of microbial virulence factors.

Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of Escherichia coli and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (eaeA, slt-I, slt-II, fliC, rfbE, and ipaH) encoding bacterial antigenic determinants and virulence factors of bacterial strains was monitored by multiplex PCR followed by hybridization of the denatured PCR product to the gene-specific oligonucleotides on the microchip. The assay was able to detect these virulence factors in 15 Salmonella, Shigella, and E. coli strains. The results of the chip analysis were confirmed by hybridization of radiolabeled gene-specific probes to genomic DNA from bacterial colonies. In contrast, gel electrophoretic analysis of the multiplex PCR products used for the microarray analysis produced ambiguous results due to the presence of unexpected and uncharacterized bands. Our results suggest that microarray analysis of microbial virulence factors might be very useful for automated identification and characterization of bacterial pathogens.