利用交错延伸剪接PCR技术扩增油菜花粉育性基因MS2Bnap全长cDNA序列

交错延伸剪接PCR是一种用于分子进化研究的DNA改组技术。本实验利用其原理,将已获得的油菜花粉育性MS2Bnap有部分序列重叠的三段PCR产物作为模板进行扩增,获得了花粉育性基因MS2Bnap的全长cDNA序列。     

四甲基氯化铵在PCR扩增小麦基因中的关键作用

利用高简并性引物,用PCR法从小麦DNA或cDNA中合成小麦几丁质酶基因、葡 聚糖酶基因和苯丙氨酸解氨酶基因片段。在PCR反应中添加四甲基氯化铵(TMACl)是合成这些特异基因片段的关键。合成的PCR片段都经末端补齐和磷酸化后用于克隆。核酸序列分析证实,这些PCR产物分别与用于设计PCR引物的基因具有高度的同源性。 Abstract:In the presence of tetramethy1 ammonium chloride(TMAC1),a chitinase gene sequence,a phenylalanine ammonia-lyase gene sequence and a glucanase cDNA sequence of wheat were amplified with highly degenerate primers by PCR.The inclusion of TMAC1 in the PCR reactions was essential for successful amplification of the desired sequences from genomic DNA or cDNA in wheat.The ends of the PCR fragments were made flush and phosphorylated prior to cloning.Sequence analyses of the above PCR fragments confirmed their identities,showing high sequence similarities to the genes used for the design of PCR primers.     

猪FGL2基因cDNA末端序列检测及结构分析

检测猪FGL2基因cDNA末端序列并对该基因结构初步分析。α-32P dCTP放射性同位素标记cDNA探针筛选猪基因组DNA文库;cDNA末端快速扩增(rapid amplification of cDNA end,RACE)。以猪正常小肠及心脏组织提取新鲜总RNA,反转录后作为模板,设计基因特异性引物,采用Advantage 2 聚合酶混合物进行PCR扩增;依据猪与人FGL2基因3′端已知同源序列设计PCR上游引物,以人FGL2基因3′末端序列设计下游引物,以猪基因组DNA为模板采用Advantage 2 聚合酶混合物进行PCR反应;PCR载体重组质粒DNA亚克隆扩增。同位素探针未能筛选到特异阳性克隆,RACE反应检测到特异性转录起始位置及第一个转录终止位置,但仍未检测到第二个转录终止位置。猪基因组DNA行PCR扩增成功检测到猪FGL2基因3′末端未知序列及第二个转录终止位置。     

一步PCR快速扩增辽宁碱蓬甜菜碱醛脱氢酶cDNA 3'末端序列

根据已获得的辽宁碱蓬甜菜碱醛脱氢酶cDNA的部分序列,设计一条基因特异性引物,与通用引物并用,一步PCR成功地克隆了辽宁碱蓬甜菜碱醛脱氢酶cDNA 3′末端。与常规的3′RACE法相比,一步PCR法具有快速、简便、经济等优点,是一种非常快捷的扩增cDNA 3′末端序列的方法。 Abstract:Based on part of a known cDNA sequence of Suaeda liaotungensis betaine aldehyde dehydrogenase,we successfully cloned the 3′cDNA end of S.lianotungensis betaine aldehyde dehydrogenase using one step PCR with a gene specific primer and universal primer.Compared with the typical 3′ RACE,one step PCR is rapid,simple and inexpensive.It is very rapid to amplify an unknown cDNA 3′end using this method.     

番茄1―氨基环丙烷羧酸(ACC)合成酶基因的反义RNA―核酶嵌合DNA序列的构建 The Construction of Antisense RNA-Ribozyme Chimeric DNA Sequence of Tomato ACC Synthase Gene

根据番茄ACC合成酶基因(LE-ACC2)DNA序列,以番茄(Lycopersicon esculentumMill)果实的总DNA为模板,利用PCR技术扩增得到预期大小的该基因编码区内部分DNA序列,插入到质粒载体pGEM-3zf(+)的BamHⅠ和HindⅢ位点之间后转化E. coliDH-5α,可选出重组子pRE,经酶切,PCR及DNA序列分析证明克隆成功;将pRE上的目的DNA序列以反义方式构建到我室已合成并克隆的含核酶DNA序列的重组质粒pRI的BamHⅠ和HindⅢ之间,构成含有反义RNA-核酶嵌合DNA序列的重组质粒pREI,经酶切及序列分析,结果与预期一致。 Abstract　According DNA sequence of Tomato ACC synthase gene(LE-ACC2)。5,Y#〗　Abstract　According DNA sequence of Tomato ACC synthase gene(LE-ACC2), and using total DNA of fruit of tomato (Lycopersicon esculentumMill) as template, the expected partial DNA Sequence in coding region of gene was obtainted by PCR amplification and inserted imto pGEM-3zf(+) digested with BamHⅠ and HindⅢ, then we transformcd the system into DH5-α and selected the postive recombinant (pRE). The digestion of enzyme, PCR amplification and sequence of DNA analysis demonstrated that the cloning was successiful; By the antisense way, the DNA sequence from pRE was combined to pRI between BamHⅠand HindⅢ to consturct pREI containing antisense RNA-Ribozyme chimeric DNA sequence (pRI was constructed in our Lab and contains Ribozyme DNA sequence). The restriction map of recombinants and sequence analysis were indentical to the expected results.     

利用RACE技术扩增大豆抗病基因同源cDNA 5′末端序列

利用抗病基因保守序列筛选大豆cDNA文库,获得一抗病基因同源cDNA片段,命名为KR3-1。根据KR3-1设计两个基因特异引物（GSP 和 NGSP）,分别与通用引物(UPM)和巢式通用引物（NUP）共同扩增,成功地克隆到了该基因的5′末端序列。该扩增片段长447 bp,与已知序列重叠部分为129 bp。 Abstract:Based on part of a known partial cDNA sequence of a disease resistance gene homolog,KR3-1,obtained by screening a cDNA library from soybean,5′-RACE-PCR was carried out with gene specific primers and universal primers.After the nested PCR reaction,an amplified fragment of 447 bp in length which overlapped the known KR3-1 sequence by 129 bp was obtained subsequently.Thus,a 5′ cDNA end of KR3 was successfully cloned.     

Preliminary study on the detection of the SARS-CoV specific target cDNA fragments by multiplex PCR

The multiplex polymerase chain reaction (PCR) technique was applied to detect the SARS-CoV (severe acute respiratory syndrome-associated coronavirus) specific target cDNA fragments in the present study. The target cDNA fragments of SARS-CoV were synthesized artificially according to the genome sequence of SARS-CoV in GenBank submitted by The Chinese University of Hong Kong, and were used as simulated positive samples. Five primers recommended by World Health Organization (WHO) were used to amplify the fragments by single PCR and multiplex PCR. Three target cDNA fragments (121, 182 and 302 bp), as well as the three different combinations of any two of these fragments, were amplified by single PCR. The combination of these three fragments was amplified by multiplex PCR. The re~sults indicated that the multiplex PCR technique could be applied to detect the SARS-CoV specific target cDNA fragments successfully.     

丙肝病毒融合抗原基因NS3-C定点整合入衣藻 叶绿体基因组的研究

用PCR方法从丙型肝炎病毒(HCV) cDNA文库中克隆了两段DNA片段,即HC基因组非结构NS3区抗原基因(约0.7 kb)和核心抗原C区抗原基因(约0.6 kb)的cDNA片段。在两段cDNA间加入连接肽Ser-Pro-Gly-Ser的密码子序列,构建成融合抗原基因NS3-C。将该融合基因与衣藻叶绿体基因atpA的启动子和rbcL基因的3'末端连接,得到丙肝病毒融合抗原基因NS3-C表达盒,再将该表达盒与选择标记基因aadA表达盒和衣藻叶绿体基因组同源片段连接,构建成衣藻叶绿体转化载体pSS6。基因枪法转化衣藻叶绿体,经壮观霉素筛选获得转化再生的单藻落,对转基因衣藻的PCR和Southern杂交分析表明,融合抗原基因NS3-C已整合到衣藻叶绿体基因组中。 Abstract:　Two DNA fragments encoding the nucleocapsid (C) region protein and the non-structural region 3 (NS3) protein of hepatitis C virus(HCV) were amplified from cDNA library by using PCR method. The 5' terminal of C cDNA fragment was linked up with the 3' terminal of NS3 cDNA fragment by a oligonucleotide linker Ser-Pro-Gly-Ser to form a chimeric gene NS3-C, which was placed under the control of the chloroplast atpA promoter and rbcL 3' region of Chlamydomonas reinhardtii to construct the chimeric gene NS3-C cassette. Then the NS3-C cassette was linked with selectable gene aadA cassette and the chloroplast homologous fragments of Chlamydomonas reinhardtii to generate transformation vector pSS6. Chloroplasts of Chlamydomonas reinhardtii were transformed by particle bombardment. Plastid transformants were selected by their resistance to 100 mg/L of spectinomycin. PCR and Southern hybridization analysis showed that the chimeric gene NS3-C had been integrated into chloroplast genome of Chlamydomonas reinhardtii.     

亚麻中雄性不育基因同源序列MS2-F的克隆和表达分析

用同源序列克隆法从亚麻中克隆了雄性不育基因同源序列MS2-F cDNA(登陆号:EU363493).该cDNA全长1 91lbp,包含一个1 608 bp的ORF,编码535个氨基酸.推导的蛋白质序列中包含2个雄性不育保守区:NAD结合区域和雄性不育C-末端区域.该基因与油菜和拟南芥雄性不育基因的一致性分别为59.65%和59.16%,为花蕾特异表达基因,推测在亚麻花粉发育过程中与脂酰辅酶A还原酶有相似功能.MS2-F cDNA对应的gDNA大小为2 696 bp(登陆号:EU365361),含有8个内含子和9个外显子.     

pepgrep: A Tool for Peptide MS/MS Pattern Matching

Typically, detection of protein sequences in collision-induced dissociation (CID) tandem MS (MS2) dataset is performed by mapping identified peptide ions back to protein sequence by using the protein database search (PDS) engine. Finding a particular peptide sequence of interest in CID MS2 records very often requires manual evaluation of the spectrum, regardless of whether the peptide-associated MS2 scan is identified by PDS algorithm or not. We have developed a compact cross-platform database-free command-line utility, pepgrep, which helps to find an MS2 fingerprint for a selected peptide sequence by pattern-matching of modelled MS2 data using Peptide-to-MS2 scoring algorithm. pepgrep can incorporate dozens of mass offsets corresponding to a variety of post-translational modifications (PTMs) into the algorithm. Decoy peptide sequences are used with the tested peptide sequence to reduce false-positive results. The engine is capable of screening an MS2 data file at a high rate when using a cluster computing environment. The matched MS2 spectrum can be displayed by using built-in graphical application programming interface (API) or optionally recorded to file. Using this algorithm, we were able to find extra peptide sequences in studied CID spectra that were missed by PDS identification. Also we found pepgrep especially useful for examining a CID of small fractions of peptides resulting from, for example, affinity purification techniques. The peptide sequences in such samples are less likely to be positively identified by using routine protein-centric algorithm implemented in PDS. The software is freely available at http://bsproteomics.essex.ac.uk:8080/data/download/pepgrep-1.4.tgz.