长距离反向PCR技术高效扩增已知DNA片断的侧翼序列

为解决传统反向PCR技术扩增片段短、假阳性多的不足,建立了长距离反向PCR(LD I-PCR)扩增技术:0.5μg DNA/mL的反应体系使DNA酶解片段充分自身环化连接,其产物用25 nt~30 nt的序列特异引物进行长距离PCR。结果表明该方法能特异地扩增出长达16 kb的序列,在已知DNA片段的侧翼序列克隆方面具有高效、简便、特异的优点。     

拟南芥光形态突变体的筛选与基因鉴定

以哥伦比亚(Columbia)野生型拟南芥(Arabidopsis thaliana)为实验材料,用含有激活标记双元质粒pCB260的农杆菌浸花进行转化,构建拟南芥T-DNA插入突变体库.通过突变体的筛选和表型分析,获得了两株光形态突变体,子叶下胚轴伸长的光抑制效应减弱.通过TAIL-PCR(thermal asymmetric interlaced-PCR)技术,成功扩增出突变植株T-DNA插入位点侧翼序列,经NCBI序列比对,T-DNA分别插在CRY1第一和第三外显子部位.突变体的表型分析及PCR鉴定结果表明,T-DNA插入CRY1并影响到突变植株的光形态建成.     

肺炎支原体P1蛋白羧基端基因片段在大肠杆菌中克隆的研究

在大肠杆菌中克隆肺炎支原体P1蛋白羧基端基因片段,为P1蛋白基因片段的扩增、表达及探讨羧基端基因片段功能打基础.采用PCR扩增方法获取P1结构基因.扩增产物用SalI和EcoRI酶切消化,回收1kb大小的DNA片段并与pUC19DNA连接,转入大肠杆菌JM109菌株.用X-gal平板及质粒图谱分析方法筛选重组克隆株,再用限制性核酸内切酶酶切图谱分析鉴定.经PCR扩增MPDNA获得1条5.0kbDNA片段.重组质粒限制性内切酶指纹图谱显示出2条带,1条为pUC19载体DNA带,另1条是1kb的插入片段.实验获得肺炎支原体P1蛋白结构基因及含P1蛋白羧基端DNA片段的重组克隆株.     

小麦6B染色体微切割及其不同片段的DNA文库构建

用Nd:YAG激光微束将处于丝分裂中期的小麦(Triticum aestivum L.)6B染色体微切割为四段,并用微细玻璃针将每个片段分别回收.将分离的染色体片段DNA用Sau3A接头介导的多聚酶链式反应(LA-PCR)分别扩增.Southem杂交证明4个特定区域的DNA确实来自于小麦基因组.用一系列(42对引物)位于6B染色体上的微卫星序列对微切割的染色体片段的PCR产物进行了验证.结果表明,获得的染色体片段的PCR产物来自于小麦6B染色体.将6B染色体4个片段的第二轮PCR产物克隆到pGET-vector中,建立了4个染色体特定区域的基因组文库,命名为R1、R2、R3和R4,分别包含2.1×105、2.74×105和2.93×105个重组子克隆.每个文库均随机挑选150个克隆进行质粒的小量制备和酶切验证.结果显示;插入片段大小在300～1800之间,平均大小为820～870bp,其中43%～48%的克隆为低/单拷贝序列,42%～47%为中/高拷贝序列.本研究为详细分析植物单染色体的不同片段的分子遗传学研究提供了基础.     

侧翼序列获取技术研究进展

侧翼序列是指染色体中特定位点两侧的DNA序列,包含着候选基因、转录调控、染色体结构、生物安全等信息,在基因组学研究中具有重要的作用。侧翼序列获取技术主要应用于启动子和增强子等调控序列的克隆、鉴定T-DNA或转座子插入位点、染色体步移、全基因组空隙填补等,是结构基因组研究以及功能基因组研究的重要手段,在转基因动植物鉴定及安全管理等方面具有重要应用。随着分子生物学的发展,目前已经建立了许多侧翼序列的获取方法,依据技术原理可以分为质粒拯救法、反向PCR法、外源接头介导PCR法、半随机引物PCR法和基因组重测序法等5大类。本文系统总结了近年来侧翼序列获取技术的研究进展,并对这些技术的原理以及应用情况进行了较为系统的综述,为侧翼序列信息的获取提供参考。     

利用Gibson DNA组装技术构建人5型腺病毒感染性克隆

为了构建人5型腺病毒(HAdV-5)的感染性克隆,我们使用了Gibson DNA组装技术。设计1对引物用于扩增质粒骨架(包含卡那霉素抗性基因和质粒的复制起点,KAN-ORI),在引物的5'端添加HAdV-5基因组末端序列(约30NT)和Pac I位点,以携带卡那霉素抗性基因的pShuttle-CMV质粒为模板,PCR扩增得到KAN-ORI片段,该片段的两端均含有约30bp的HAdV-5基因组序列。将KAN-ORI片段与利用野毒扩增纯化的HAdV-5基因组混合,进行Gibson DNA组装反应;反应产物直接转化E.coli感受态细胞,涂布含卡那霉素的LB琼脂平板。挑取菌落,提取质粒,命名为pKAd5。限制性酶切鉴定的结果显示,所鉴定的质粒均含有完整的HAdV-5基因组。使用PacⅠ酶切线性化pKAd5,利用脂质体转染293细胞,转染4d后单层细胞出现病毒噬斑。拯救的病毒能够在HEp-2细胞扩增;电子显微镜观察呈现典型的腺病毒形态;提取病毒DNA,酶切鉴定的结果与预期的HAdV-5基因组相同,证实HAdV-5得到成功拯救。上述研究结果说明使用Gibson DNA组装技术构建HAdV-5感染性克隆简便易行,为其他DNA病毒基因组的克隆提供了新思路。     

小麦6B染色体微切割及其不同片段的DNA文库构建

用Nd∶YAG激光微束将处于有丝分裂中期的小麦(Triticum aestivum L.)6B染色体微切割为四段,并用微细玻璃针将每个片段分别回收。将分离的染色体片段DNA用Sau3A接头介导的多聚酶链式反应(LA-PCR)分别扩增。Southern杂交证明4个特定区域的DNA确实来自于小麦基因组。用一系列(42对引物)位于6B染色体和其他染色体上的微卫星序列对微切割的染色体片段的PCR产物进行了验证。结果表明,获得的染色体片段的PCR产物来自于小麦6B染色体。将6B染色体4个片段的第二轮PCR产物克隆到pGEMT-vector中,建立了4个染色体特定区域的基因组文库,命名为R1、R2、R3和R4,分别包含2.1×10~5、2.74×10~5、2.45×10~5和2.93×10~5个重组子克隆。每个文库均随机挑选150个克隆进行质粒的小量制备和酶切验证。结果显示:插入片段大小在300～1800 bp之间,平均大小为820～870 bp,其中43％～48％的克隆为低/单拷贝序列,42％～47％为中/高拷贝序列。本研究为详细分析植物单染色体的不同片段的分子遗传学研究提供了基础。     

巢式PCR克隆猪T细胞表面抑制性受体PD-1全长基因

为了获得猪T细胞表面抑制性受体PD-1的全长基因,本研究根据猪T细胞表面抑制性受体PD-1的c DNA序列,设计合成2对引物P1/P2、P3/P4,并在P1和P2的5'端分别引入Eco RⅠ和XhoⅠ酶切位点。应用巢式PCR技术从感染猪瘟病毒(CSFV)石门株的猪外周血单个核细胞中,扩增获得了大小为866 bp的基因片段。将扩增的目的基因回收、纯化,克隆至p MD-18 T克隆载体,转化宿主菌DH5α。菌液PCR和质粒PCR选择可疑阳性重克隆质粒,抽提质粒,然后用Eco RⅠ、XhoⅠ双酶切鉴定,最后进行基因序列测定。结果表明,成功构建猪PD-1全长基因的重组质粒(p MD-PD1)。     

破伤风毒素C片段基因克隆、重组表达及免疫原性研究

应用PCR技术从破伤风梭状芽孢杆菌DNA中扩增出1．4kbDNA基因,将其克隆到pUC18质粒中,经测序证明该DNA片段为破伤风片段C的基因,并将此基因片段亚克隆到pGEX-4T-2,构建成表达质粒pGEX－TC在E．coli中进行表达。经聚丙烯酰胺凝胶电泳和免疫印迹鉴定,表达产物为76KD的特异性重组蛋白。动物实验显示：1μg重组蛋白免疫动物,可使动物产生1IU／ml的破伤风抗毒素单位,动物血清的抗体滴度可达1：800。     

拟南芥T-DNA插入突变体atsuc3的PCR鉴定

应用两种植物T-DNA插入突变体PCR鉴定方法,即“三引物法”和“双引物法”对拟南芥T-DNA插入突变体atsuc3（目的基因两条染色体均发生T-DNA插入的纯合突变体）进行鉴定和比较的结果表明,“三引物法”由于易产生非特异性扩增而无法得到PCR鉴定结果,从而导致鉴定失败;“双引物法”则可避免此种现象,得到可靠、有效的鉴定结果。     

稻瘟菌突变体T-DNA插入位点的精细定位和插入模式的研究

随机挑取已构建的37个稻瘟菌T-DNA突变株,利用TAIL-PCR技术扩增出T-DNA插入位点的侧翼序列,测序并进行比对分析。结果显示:成功获得扩增产物并测序的序列共有39条,T-DNA边界序列为稻瘟菌序列的有19条,其余20条为载体主干序列。在这有效扩增为稻瘟菌序列的19条中,有10条是T-DNA右侧翼序列与稻瘟菌序列,9条为左侧翼序列加稻瘟菌序列。分析T-DNA剪切位点,10条右侧翼序列中有9条的剪切位点相同,这与农杆菌介导T-DNA转化植物一样。而左边界的剪切位点就没有这种规律性。研究也精细确定了17个不同突变株的T-DNA插入位置,为后续的基因功能研究奠定基础。     

Supported PCR: an efficient procedure to amplify sequences flanking a known DNA segment

We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of genomic DNA on streptavidin-containing support. Subsequently, following ligation with a second universal linker primer, the selected fragments can be amplified to amounts suitable for further molecular studies. The procedure has been applied to recover T-DNA flanking sequences in transgenic tomato plants which could subsequently be used to assign the positions of T-DNA to the molecular map of tomato. The method called supported PCR (sPCR) is a simple and efficient alternative to techniques used in the isolation of specific sequences flanking a known DNA segment.     

转基因水稻T—DNA侧翼序列的扩增与分析

利用现有的转抗白叶枯病基因Xa21的水稻材料,通过TAIL－PCR技术扩增出携带Xa21基因的T－DNA的侧翼序列,对24个有效扩增片段的序列分析结果表明,其中14个侧翼序列是水稻DNA,9个含载体主干序列,1个是外源基因Xa21片段,14个T－DNA侧翼的水稻DNA序列与直接转化法外源基因整合位点的基因组序列具有不同的特点,这些T－DNA在水稻染色体上整合后其两端序列的特点类似于在转基因双子叶植物中观察到的现象,在含主干序列的侧翼序列（37．5％,9／24）,中,载体主干序列是以不同的类型出现的。     

Rapid discrimination of sequences flanking and within T‐DNA insertions in the Arabidopsis genome

An improvement to previous methods for recovering Arabidopsis thaliana genomic DNA flanking T-DNA insertions is presented that allows for the avoidance of some of the cloning difficulties caused by the concatameric nature of T-DNA inserts. The principle of the procedure is to categorize by size restriction fragments of mutant DNA, produced in separate digestions with NdeI and Bst1107I. Given that the sites for these two enzymes are contiguous within the pGV3850:1003 T-DNA construct, the restriction fragments obtained fall into two categories: those showing identical size in both digestions, which correspond to sequences internal to T-DNA concatamers; and those of different sizes, that contain the junctions between plant DNA and the T-DNA insert. Such a criterion makes it possible to easily distinguish the digestion products corresponding to internal T-DNA parts, which do not deserve further attention, and those which presumably include a segment of the locus of interest. Discrimination between restriction fragments of genomic mutant DNA can be made on rescued plasmids, inverse PCR amplification products or bands in a genomic blot.     

SNP discovery and genetic mapping of T-DNA insertional mutants in Fragaria vesca L.

As part of a program to develop forward and reverse genetics platforms in the diploid strawberry [Fragaria vesca L.; (2n = 2x = 14)] we have generated insertional mutant lines by T-DNA mutagenesis using pCAMBIA vectors. To characterize the T-DNA insertion sites of a population of 108 unique single copy mutants, we utilized thermal asymmetric interlaced PCR (hiTAIL-PCR) to amplify the flanking region surrounding either the left or right border of the T-DNA. Bioinformatics analysis of flanking sequences revealed little preference for insertion site with regard to G/C content; left borders tended to retain more of the plasmid backbone than right borders. Primers were developed from F. vesca flanking sequences to attempt to amplify products from both parents of the reference F. vesca 815 × F. bucharica 601 mapping population. Polymorphism occurred as: presence/absence of an amplification product for 16 primer pairs and different size products for 12 primer pairs, For 46 mutants, where polymorphism was not found by PCR, the amplification products were sequenced to reveal SNP polymorphism. A cleaved amplified polymorphic sequence/derived cleaved amplified polymorphism sequence (CAPS/dCAPS) strategy was then applied to find restriction endonuclease recognition sites in one of the parental lines to map the SNP position of 74 of the T-DNA insertion lines. BLAST search of flanking regions against GenBank revealed that 46 of 108 flanking sequences were close to presumed strawberry genes related to annotated genes from other plants.     

Transgene-specific and event-specific molecular markers for characterization of transgenic papaya lines resistant to Papaya ringspot virus

The commercially valuable transgenic papaya lines carrying the coat protein (CP) gene of Papaya ringspot virus (PRSV) and conferring virus resistance have been developed in Hawaii and Taiwan in the past decade. Prompt and sensitive protocols for transgene-specific and event-specific detections are essential for traceability of these lines to fulfill regulatory requirement in EU and some Asian countries. Here, based on polymerase chain reaction (PCR) approaches, we demonstrated different detection protocols for characterization of PRSV CP-transgenic papaya lines. Transgene-specific products were amplified using different specific primer pairs targeting the sequences of the promoter, the terminator, the selection marker, and the transgene, and the region across the promoter and transgene. Moreover, after cloning and sequencing the DNA fragments amplified by adaptor ligation-PCR, the junctions between plant genomic DNA and the T-DNA insert were elucidated. The event-specific method targeting the flanking sequences and the transgene was developed for identification of a specific transgenic line. The PCR patterns using primers designed from the left or the right flanking DNA sequence of the transgene insert in three selected transgenic papaya lines were specific and reproducible. Our results also verified that PRSV CP transgene is integrated into transgenic papaya genome in different loci. The copy number of inserted T-DNA was further confirmed by real-time PCR. The event-specific molecular markers developed in this investigation are crucial for regulatory requirement in some countries and intellectual protection. Also, these markers are helpful for prompt screening of a homozygote-transgenic progeny in the breeding program.     

利用Inverse PCR快速筛选单个T—DNA拷贝转基因水稻植株的方法

In order to obtain single T-DNA copy transgenic rice, we have established a quick method to estimate the T-DNA copy number in transgenic rice using inverse PCR (IPCR). IPCR was used to amplify junction fragments, i.e. plant genomic DNA sequences flanking the known T-DNA sequences, which will help to estimate the T-DNA copy number in transgenic rice. We have analyzed 20 transgenic plants of 15 transgenic lines. Most plants (12) contain one integrated T-DNA copy per genome, 3 plants contain two and 1 plant contains 3 copies. In 4 transgenic plants no T-DNA copies could be detected using this method. The IPCR results were further tested by Southern analysis and sequence analysis.     

Revised selection criteria for candidate restriction enzymes in genome walking

A new method to improve the efficiency of flanking sequence identification by genome walking was developed based on an expanded, sequential list of criteria for selecting candidate enzymes, plus several other optimization steps. These criteria include: step (1) initially choosing the most appropriate restriction enzyme according to the average fragment size produced by each enzyme determined using in silico digestion of genomic DNA, step (2) evaluating the in silico frequency of fragment size distribution between individual chromosomes, step (3) selecting those enzymes that generate fragments with the majority between 100 bp and 3,000 bp, step (4) weighing the advantages and disadvantages of blunt-end sites vs. cohesive-end sites, step (5) elimination of methylation sensitive enzymes with methylation-insensitive isoschizomers, and step (6) elimination of enzymes with recognition sites within the binary vector sequence (T-DNA and plasmid backbone). Step (7) includes the selection of a second restriction enzyme with highest number of recognition sites within regions not covered by the first restriction enzyme. Step (8) considers primer and adapter sequence optimization, selecting the best adapter-primer pairs according to their hairpin/dimers and secondary structure. In step (9), the efficiency of genomic library development was improved by column-filtration of digested DNA to remove restriction enzyme and phosphatase enzyme, and most important, to remove small genomic fragments (<100 bp) lacking the T-DNA insertion, hence improving the chance of ligation between adapters and fragments harbouring a T-DNA. Two enzymes, NsiI and NdeI, fit these criteria for the Arabidopsis thaliana genome. Their efficiency was assessed using 54 T(3) lines from an Arabidopsis SK enhancer population. Over 70% success rate was achieved in amplifying the flanking sequences of these lines. This strategy was also tested with Brachypodium distachyon to demonstrate its applicability to other larger genomes.     

降低mRNA差异显示技术假阳性率的一种方法

为了探讨降低mRNA差异显示技术假阳性率的方法 ,进一步提高此技术的可靠性 ,提取了手术切除肝癌及非癌肝组织成对标本的总RNA ,逆转录获得cDNA片段 ,以mRNA差异显示方法筛选差异表达基因 ,选取较明显的一条差异表达条带 ,行进一步PCR扩增 .分别对PCR产物及其经TA克隆后随机挑选的 6个单克隆质粒DNA进行序列分析 ,并通过GenBank BLAST数据库进行序列的同源性比较 ,以Northern杂交予以来源确认 .自 72 0余条扩增条带中共选出 2 8条差异条带 .序列分析及同源性比较表明 ,所选择条带的PCR产物为一可能的新基因片段 ;而随机选择的 6个TA克隆质粒DNA中 ,有 4个为同一已知基因片段 ,一个为另一已知基因片段 ,一个为一可能的新基因片段 .同源性比较表明 ,PCR产物直接测序所得序列与TA克隆质粒DNA的 6个片段不具同源性 .结果表明 ,mRNA差异显示条带可能由 1条以上分子量相似的片段构成 ,直接对PCR产物行序列分析并以其为探针进行Northern杂交 ,是导致出现假阳性片段的原因之一 .将PCR产物进行TA克隆 ,对单克隆质粒DNA进行序列分析并以其为探针进行Northern杂交 ,可能是解决此问题的一种较好方法 .