一种用于基因芯片可靠的RNA线性扩增技术

基因芯片是大规模表达谱分析的有力工具 ,有助于阐明疾病发生的分子机制及发现新的诊治靶标。但常规方法需要大量RNA ,每张芯片需要 5 0～ 2 0 0 μg总RNA ,2～ 5 μgmRNA。许多珍贵难得样本都不能满足这一要求 ,成为限制芯片广泛应用的瓶颈。结合模板转移效应 ,优化了基于T7的RNA线性扩增技术 ,可从 3μg以下总RNA得到足量的反义RNA ,克服了这一难题。同一RNA样本的自身比较试验结果显示反义RNA标记的芯片与总RNA、mRNA标记的芯片假阳性率相似。同一对RNA样本的表达谱分析也显示反义RNA标记的芯片与总RNA、mRNA标记的芯片无明显差异。     

鼻咽癌组织的显微切割及其 RNA 线性扩增

从微小体积鼻咽癌活检标本中获取纯净癌细胞一直是鼻咽癌分子生物学研究中的难题 . 为了寻找一种能从鼻咽癌活检组织中获得高纯度、高质量 RNA 来完成 cDNA 微阵列 (cDNA Microarray) 实验的简便实用方法,采用 RNAlater 技术保存鼻咽癌活检组织,显微切割技术来获得高纯度鼻咽癌细胞,利用 RNA 线性扩增技术得到 cDNA 微阵列实验所需 RNA. 结果表明：利用 RNAlater 技术可以很好地保持组织 RNA 的稳定,通过优化显微切割和 RNA 线性扩增的条件获得了 cDNA 微阵列实验所需的高纯度、高质量 RNA.     

一种新型细胞微阵列的制作和应用

为了高通量地检测大量培养细胞中基因原位表达, 发明了一种制作细胞微阵列的新方法,成功地制作含20种细胞系共100个供体细胞石蜡混合物点阵的细胞微阵列.免疫组化检测P53, P21, PTEN、P16基因在细胞微阵列中的蛋白质表达.原位杂交检测BRD7、NGX6 基因在细胞微阵列中mRNA原位表达.建立了P53、P21、PTEN、P16蛋白和BRD7、NGX6 mRNA 在不同培养细胞中的原位表达谱.细胞微阵列为基因功能研究提供一种新的高通量工具.细胞微阵列可广泛用于DNA、RNA和蛋白质水平上的基因原位表达研究.细胞微阵列还可用于筛选药物作用靶标的研究.     

HSV-IgM人-鼠嵌合抗体制备及稳定细胞株构建工艺开发

为实现体外大规模制备单纯疱疹病毒HSV-IgM(HSV1,HSV2)人鼠嵌合抗体,本研究通过RNA连接酶介导的cDNA末端快速扩增(RNA ligase-mediated rapid amplification of cDNA ends,RLM-RACE)技术获取其对应杂交瘤细胞基因序列,构建嵌合抗体至真核表达载体,在CHO-S细胞中稳定表达所需目的蛋白。同时优化稳定细胞株筛选工艺,对细胞池构建阶段和单克隆筛选阶段的加压条件进行摸索与探究,最后目的抗体采用蛋白L亲和纯化法进行纯化并进行生物活性检测;最终成功制备899 kDa和909 kDa的稳定高表达重组IgM抗体(HSV1,HSV2)细胞株。结果表明,最适筛选压力为20P200M(一轮加压)和50P1000M(二轮加压);使用加压培养基进行单克隆筛选抗体表达量较高,HSV1-IgM和HSV2-IgM单克隆最终表达量分别为1620 mg/L和623 mg/L。本研究为HSV1和HSV2的IgM系列重组抗体质控品开发以及体外高表达分泌IgM亚型抗体提供理论与实践基础。     

基于核酶技术的人线粒体色氨酸tRNA的高效转录及其活性鉴定

利用T7RNA聚合酶(T7 RNA polymerase,T7 RNAP)的体外转录方法因其简便、高效而在RNA制备中得到广泛应用,但该法由于T7RNAP的启动子跨越转录起始位点而会导致转录产物多出附加序列;如果去掉T7启动子的转录起始位点,则会严重降低T7RNAP的转录活性。本实验很好地消除了以上弊端,将T7RNAP的高效转录系统与核酶高度专一的自剪切技术相结合,成功构建了一种不影响转录效率的体外转录方法,而且转录后核酶能够在设计的特定位点进行自剪切并释放出目的RNA,得到了活性达113.6pmol/μg的人线粒体色氨酸tRNA(HmtRNATrp(UCA))。该方法转录效率高、重复性好,适合RNA的大量精确制备。     

琉球病毒、索尔韦齐病毒、苏里斯病毒等三种沙粒病毒实时荧光RT-PCR检测方法研究

建立可检测琉球病毒(Ryukyu virus,RYKV),索尔韦齐病毒(Solwezi virus,SOLV)以及苏里斯病毒(Souris virus,SOUV)等三种沙粒病毒的实时荧光定量RT-PCR检测方法.分析三种病毒流行病学分布特征,从国际公共数据库搜索下载基因组序列,进行比对分析,确定检测靶标,借助primer premier 6.0生物信息学软件,设计引物和探针,建立实时荧光定量RT-PCR检测方法,利用化学合成和体外转录方法制备模拟样本,比较评价三种方法的检测限、特异性、重复性特征.所建实时荧光定量RT-PCR检测方法均可有效扩增检测病毒RNA靶标,检测限分别为40拷贝/μL、7拷贝/μL和15拷贝/μL,检测汉城病毒、汉滩病毒、登革病毒Ⅰ～Ⅳ型分离株、发热伴血小板减少综合病毒及30份健康人血清样本无非特异性扩增,三种病毒相互间以及其他8种出血热相关沙粒病毒RNA间无交叉反应,重复性比较分析显示变异系数均在2％以内.本研究建立的检测RYKV、SOLV和SOUV三种沙粒病毒的实时荧光RT-PCR方法具备用于相关疑似感染者临床样本、宿主动物标本以及进出口物品的筛查检测的潜力,但因未经基于实际病毒感染样本的比较评价,检测结果的解释仍具有一定的局限性.     

siRNA制备技术的研究进展

近年来,siRNA(small interfering RNA)被广泛用于诱导哺乳动物体系中的RNA干扰。目前有五种siRNA制备方法：化学合成法、体外转录法、RNase Ⅲ家族体外消化法、表达载体法和表达框架法。在这些方法中siRNA序列的选择至关重要。随着药物研究和基因组研究的进展,siRNA的制备技术需要在高通量筛选、稳定性、基因导入和调控等方面进一步发展与完善。作者综述了siRNA序列的选择原则和哺乳动物系统中的siRNA产生方法,并简要讨论了其发展前景。     

基于多重置换扩增技术的RNA病毒基因组扩增方法研究

为了便于新发或罕见病毒性传染病的筛查检测,本研究利用多重置换扩增技术,以负链RNA病毒—发热伴血小板减少综合征病毒和正链RNA病毒—登革病毒为模拟样本探索临床样本中RNA病毒基因组非特异性扩增方法。研究中通过梯度稀释的RNA病毒模拟样本中可能存在的不同丰度的病原体,样本核酸依次加工成单链cDNA、双链cDNA、T4DNA连接酶处理后的双链cDNA以及添加外源辅助RNA后合成并连接的双链cDNA形式,然后进行Phi29DNA聚合酶等温扩增,使用荧光定量PCR方法比较各种方法对RNA病毒核酸扩增的影响。结果显示,对于不同类型的RNA病毒模拟标本,多重置换扩增对于单链及双链cDNA的扩增效果有限,而双链cDNA经DNA连接酶处理后的扩增能达到6×103倍;在cDNA合成过程中加入外源辅助RNA,模拟样本中病毒基因组的扩增可达2×105倍,尤其是对含有低丰度病原体的模拟样本扩增效果的改善更为明显。本研究摸索建立了基于多重置换扩增技术的RNA病毒基因组扩增方法,能够对样本中低丰度RNA病毒基因组实现有效扩增,可满足开展多种病原体筛查检测的需求。     

安捷伦推出小鼠cDNA微阵列试剂盒

安捷伦日前宣布 ,推出小鼠ｃＤＮＡ微阵列试剂盒 (Ｇ410 4) ,其中ｃＤＮＡ克隆序列由ＩｎｃｙｔｅＧｅｎｏｍｉｃｓ认证。通过这套微阵列试剂盒 ,研究人员可以在一次微阵列实验中 ,对 85 0 0多个小鼠基因进行大规模的基因差异表达筛选。安捷伦的小鼠ｃＤＮＡ微阵列采用双色标记 ,方便研究人员在一次实验中对“疾病”样本和“对照”样本上同时进行基因差异表达分析。传统的单色标记技术需两次分别的微阵列标记、杂交及后继分析步骤 ,而新的方法则减少了传统单色标记技术中固有的偏差。此外 ,所有安捷伦ｃＤＮＡ微阵列都以方便使用的试剂盒形…     

标准品制备方法对FQ-PCR定量基因表达水平的影响

实时荧光定量PCR (FQ-PCR)标准曲线法准确定量基因表达的关键在于标准品与待检样本的扩增效率是否一致. 为检测DNA标准品与样本cDNA扩增效率的一致性,探讨定量用标准品的最佳制备方法,本研究以脂肪酸结合蛋白5(Fabp5)、过氧化物酶体增殖活化受体α (Ppar-α)及β肌动蛋白（β-Actin）的3个基因为对象,分别采用质粒纯化法、PCR产物直接纯化法、PCR产物凝胶回收法制备DNA标准品,10倍梯度稀释后用FQ PCR制作标准曲线. 并以10倍梯度稀释的样本cDNA标准曲线的参数为对照,进行比较分析. 结果表明,不同方法制备的DNA标准品的扩增效率差异较大,并且与cDNA的扩增效率不一致,不能对cDNA样本进行准确定量. 另外,虽然目的基因在cDNA样本中的拷贝未知,不能对基因表达水平进行绝对定量,但因不同cDNA样本的同一基因的扩增效率一致, 可对基因的表达进行准确的相对定量.     

Linear amplification of catalyzed reporter deposition technology on nylon membrane microarray

The application of microarray analysis to gene expression from limited tissue samples has not been very successful because of the poor signal qualityfrom the genes expressed at low levels. Here we discussed the use of catalyzed reporter deposition (CARD) technology to amplify signals from limited RNA samples on nylon membrane cDNA microarray. When the input RNA level was greater than 10 microg, the genes expressed at high levels did not amplify in proportion to those expressed at low levels. Compared to conventional colorimetric detection, the CARD method requires less than 10% of the total RNA used for amplification of signal displayed onto a nylon membrane cDNA microarray. Total RNA (5-10 microg), as one can extract from a limited amount of specimen, was determined to produce a linear correlation between the colorimetric detection and CARD methods. Beyond this range, it can cause a nonlinear amplification of highly expressed and low-abundance genes. These results suggest that when amplification is needed for any applications using the CARD method, including DNA microarray experiments, precaution has to be taken in the amount of RNA used to avoid skew amplification and thus misleading conclusions.     

cRNA target preparation for microarrays: comparison of gene expression profiles generated with different amplification procedures

Microarray technology has become a standard tool for generation of gene expression profiles to explore human disease processes. Being able to start from minute amounts of RNA extends the fields of application to core needle biopsies, laser capture microdissected cells, and flow-sorted cells. Several RNA amplification methods have been developed, but no extensive comparability and concordance studies of gene expression profiles are available. Different amplification methods may produce differences in gene expression patterns. Therefore, we compared profiles processed by a standard microarray protocol with three different types of RNA amplification: (i) two rounds of linear target amplification, (ii) random amplification, and (iii) amplification based on a template switching mechanism. The latter two methods accomplish target amplification in a nonlinear way using PCR technology. Starting from as little as 50 ng of total RNA, the yield of labeled cRNA was sufficient for hybridization to Affymetrix HG-U133A GeneChip array using the respective methods. Replicate experiments were highly reproducible for each method. In comparison with the standard protocol, all three approaches are less sensitive and introduced a minor but clearly detectable bias of the detection call. In conclusion, the three amplification protocols used are applicable for GeneChip analysis of small tissue samples.     

Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis

We describe here a protocol for the representative amplification of global mRNAs from typical single mammalian cells to provide a template for high-density oligonucleotide microarray analysis. A single cell is lysed in a tube without purification and first-strand cDNAs are synthesized using a poly(dT)-tailed primer. Unreacted primer is specifically eliminated by exonuclease treatment and second strands are generated with a second poly(dT)-tailed primer after poly(dA) tailing of the first-strand cDNAs. The cDNAs are split into four tubes, which are independently directionally amplified by PCR, and then recombined. The amplified products (approximately 100 ng) show superior representation and reproducibility of original gene expression, especially for genes expressed in more than 20 copies per cell, compared with those obtained by a conventional PCR protocol, and can effectively be used for quantitative PCR and EST analyses. The cDNAs are then subjected to another PCR amplification with primers bearing the T7 promoter sequence. The resultant cDNA products are gel purified, amplified by one final cycle and used for isothermal linear amplification by T7 RNA polymerase to synthesize cRNAs for microarray hybridization. This protocol yields cDNA templates sufficient for more than 80 microarray hybridizations from a single cell, and can be completed in 5-6 days.     

Comparative analysis of amplified and nonamplified RNA for hybridization in cDNA microarray

Limiting amounts of RNA is a major issue in cDNA microarray, especially when one is dealing with fresh tissue samples. Here we describe a protocol based on template switch and T7 amplification that led to efficient and linear amplification of 1300x. Using a glass-array containing 368 genes printed in three or six replicas covering a wide range of expression levels and ratios, we determined quality and reproducibility of the data obtained from one nonamplified and two independently amplified RNAs (aRNA) derived from normal and tumor samples using replicas with dye exchange (dye-swap measurements). Overall, signal-to-noise ratio improved when we used aRNA (1.45-fold for channel 1 and 2.02-fold for channel 2), increasing by 6% the number of spots with meaningful data. Measurements arising from independent aRNA samples showed strong correlation among themselves (r(2)=0.962) and with those from the nonamplified sample (r(2)=0.975), indicating the reproducibility and fidelity of the amplification procedure. Measurement differences, i.e, spots with poor correlation between amplified and nonamplified measurements, did not show association with gene sequence, expression intensity, or expression ratio and can, therefore, be compensated with replication. In conclusion, aRNA can be used routinely in cDNA microarray analysis, leading to improved quality of data with high fidelity and reproducibility.