DNA enzyme generated by a novel single-stranded DNA expression vector inhibits expression of the essential bacterial cell division gene ftsZ

Rapid emergence of antibiotic-resistant bacterial pathogens has created urgent demand for the discovery and development of new antibacterial agents directed toward novel targets. Antisense oligodeoxynucleotides (AS-ODN) and their modified forms have been utilized to block gene expression in bacterial cells, showing potential for developing highly specific and efficacious antibacterial agents. In this study, a tetracycline-regulated expression vector was developed for generating single-stranded DNA (ssDNA) of a desired target sequence in bacterial cells. This inducible ssDNA expression vector was tested for producing a DNA enzyme designed to specifically cleave ftsZ mRNA. Our results indicate that the expressed DNA enzyme molecules not only repress ftsZ gene expression and but also inhibit bacterial cell proliferation. Although we believe that the cleavage of ftsZ mRNA by the expressed DNA enzyme molecules is responsible for the inhibitory effects on ftsZ gene expression and bacterial cell proliferation, the antisense mechanism could also be responsible for the biological effects. The ability of this ssDNA expression system to selectively modulate gene expression may provide a powerful strategy in determining the contribution of a given gene product to bacterial growth or pathogenesis and opens a new venue for developing antibacterial agents.     

Expression of ssDNA in mammalian cells

Antisense therapy involves the use of antisense oligonucleotides for altering targeted gene function. However, the low efficiency of cell delivery of antisense oligonucleotides has limited the efficacy of antisense therapeutic approaches. RNA-based antisense or ribozyme oligonucleotides can be either synthesized endogenously (e.g., by a viral vector) or delivered exogenously. However, there is presently no vector delivery system available for DNA-based oligonucleotides. Recently, a novel ssDNA expression vector that can generate intracellularly any ssDNA molecule, such as antisense oligonucleotide or DNA enzyme, has been developed in our laboratory. Here we describe an improved expression vector based on the first-generation two-vector system. To test this new expression vector, we chose to express a single-stranded "10-23" DNA enzyme targeting c-raf mRNA in the human lung carcinoma A549 cell line. After introduction into cells by transient transfection, c-raf-cleaving DNA enzymes produced by this expression vector can significantly suppress the expression of c-raf mRNA. Furthermore, the expressed c-raf DNA enzymes induced cell apoptosis, as indicated by genomic DNA fragmentation assay. Our study further demonstrates the feasibility of using this novel ssDNA expression technology to produce intracellularly any sequence of interest, including antisense oligonucleotides and DNA enzyme molecules.     

In vitro excision of adeno-associated virus DNA from recombinant plasmids: isolation of an enzyme fraction from HeLa cells that cleaves DNA at poly(G) sequences.

When circular recombinant plasmids containing adeno-associated virus (AAV) DNA sequences are transfected into human cells, the AAV provirus is rescued. Using these circular AAV plasmids as substrates, we isolated an enzyme fraction from HeLa cell nuclear extracts that excises intact AAV DNA in vitro from vector DNA and produces linear DNA products. The recognition signal for the enzyme is a polypurine-polypyrimidine sequence which is at least 9 residues long and rich in G.C base pairs. Such sequences are present in AAV recombinant plasmids as part of the first 15 base pairs of the AAV terminal repeat and in some cases as the result of cloning the AAV genome by G.C tailing. The isolated enzyme fraction does not have significant endonucleolytic activity on single-stranded or double-stranded DNA. Plasmid DNA that is transfected into tissue culture cells is cleaved in vivo to produce a pattern of DNA fragments similar to that seen with purified enzyme in vitro. The activity has been called endo R for rescue, and its behavior suggests that it may have a role in recombination of cellular chromosomes.     

Intracellular generation of single-stranded DNA for chromosomal triplex formation and induced recombination

Synthetic triple helix-forming oligodeoxyribonucleotides (TFOs) have been used to alter gene expression and to induce targeted genome modification in cells and animals. However, the efficacy of such oligodeoxyribonucleotides (ODNs) depends on efficient intracellular delivery. A novel vector system was tested for the production of single-stranded DNA (ssDNA) to serve as a TFO in mouse cells. Mouse cells carrying a substrate that can report triplex-stimulated intrachromosomal recombination were transfected with a series of ssDNA vectors, and induced recombination was assayed. Transfection with a vector set designed to generate a 34 nt G-rich ssDNA capable of triplex formation at a 30 bp polypurine target site within the reporter substrate yielded recombinants at a frequency of 196 × 10^–6, versus a background frequency of 45 × 10^–6 in mock transfected cells. No induction was seen when a vector set lacking the TFO sequence insert was tested or when the component vectors were transfected individually. Vectors engineered to express a C-rich 34 nt sequence (not expected to form triplex under physiological conditions) had no effect over background. Primer extension analyses on lysates from transfected cells confirmed the production of the intended ssDNAs. These results suggest that ssDNA molecules of a defined sequence can be generated intracellularly using a novel vector system and that such molecules are active in mediating triplex-dependent chromosomal events. The ability to produce active TFOs within cells may provide a new foundation for triplex-based gene targeting strategies.     

小鼠白细胞介素33真核表达质粒的构建及表达

克隆小鼠IL-33基因构建其真核表达质粒,并转染COS-7细胞检测其表达。提取C57BL/6小鼠肺组织总RNA,经反转录聚合酶链式反应（RT-PCR）扩增小鼠IL-33基因,酶切后插入pcDNA^TM3.1/myc HisA构建其真核表达质粒pcDNA-3.1-IL-33,重组质粒转染COS-7细胞,RT-PCR和免疫印迹法（western blotting）检测目的基因表达。结果显示,pcDNA3.1-IL-33中插入的片段序列测定结果与小鼠IL-33cDNA序列一致,重组质粒转染COS-7细胞后检测到相应mRNA及蛋白表达。成功克隆了小鼠IL-33基因cDNA,并构建其真核表达质粒。     

核苷酸切除修复基因XPA反义RNA表达载体的构建及其抑瘤功能

采用RT PCR方法扩增出 4 2 6bp着色性干皮病A(xerodermapigmentosumgroupA ,XPA)cDNA片段 (2～ 4 2 7bp) ,反向插入pcDNA3 1质粒构建XPA反义RNA表达载体 .经测序证实 ,该片段序列与XPAmRNA对应片段完全互补 .通过脂质体Lipofectamine 2 0 0 0将重组质粒转染肺癌A5 4 9细胞 ,RT PCR检测表明转染XPA反义RNA重组质粒能够抑制肺癌细胞XPAmRNA表达 ;MTT实验表明转染XPA反义RNA的肺癌细胞对顺铂敏感性增强 .本研究为深入探讨NER途径基因功能及临床克服肿瘤耐药提出了一个新的思路     

乙酰肝素酶重组慢病毒转基因和siRNA干扰质粒的构建及鉴定

目的：构建乙酰肝素酶重组慢病毒转基因和siRNA干扰质粒,为探讨HPSE在在肿瘤浸润转移过程中的分子机理奠定基础。方法：乙酰肝素酶cDNA全长扩增和最佳siRNA干扰片段筛选分别采用PCR和Real-time PCR方法,慢病毒系统载体分别使用pWPI和siRNA pSico系统,采用限制性内切酶快速连接方法联接目的基因和最佳最佳siRNA干扰片段,表达载体鉴定均采用核苷酸序列测定,HPSE重组慢病毒表达质粒和siRNA片段细胞转染采用脂质体转染法。结果：成功扩增乙酰肝素酶全长并连接入pWPI载体构建成重组表达载体HPSE-pWPI,重组质粒测序结果显与HPSE基因的同源性达99%。转染293T后有HPSE基因的表达。筛选出最佳siRNA干扰片段为HPSE-1222并成功插入pSico载体,构建成重组表达载体HPSE-siRNA pSico,重组载体测序显示与构建的shRNA结构序列完全一致。结论：成功采用慢病毒载体系统构建了乙酰肝素酶重组慢病毒转基因和siRNA干扰质粒,为探讨HPSE在在肿瘤浸润转移过程中的分子机理奠定基础。     

Single-stranded DNA intermediates in IS91 rolling-circle transposition

IS91 displays a number of characteristics unique among insertion sequence (IS) elements, suggesting that it transposes by a novel mechanism called rolling-circle (RC) transposition. We reported previously that IS91 transposase (TnpA) amino acid sequence shares a series of five conserved signatures with A proteins of RC replicating phages, including a pair of invariant tyrosines that catalyse two successive transesterification reactions during replication initiation and termination. To analyse their role in IS91 transposition, we constructed a series of TnpA derivatives in which the invariant Tyr-249 and/or Tyr-253 were mutated to either phenylalanine or serine. Mutation of either tyrosine resulted in complete loss of transposition activity in vivo. This result was taken as a first new line of evidence that TnpA is a functional analogue of phiX174 phage A protein. Secondly, RC replication plasmids and phages accumulate single-stranded DNA (ssDNA) intermediates as a result of uncoupled leading and lagging DNA strand synthesis. Using a plasmid carrying an IS91-derived IRLkan-IRR transposable cassette, in which the left (IRL)- and right (IRR)-terminal sequences of IS91 flank a kanamycin resistance gene (kan), we demonstrated the in vivo formation of two new DNA species after induction of transposase expression. The first was a circular ssDNA that contained the transposable cassette covalently joined at its exact termini, whereas the second was a double-stranded circle of the same element. When this experiment was repeated using the mutant transposases described above, the ssDNA and dsDNA intermediates could not be observed, indicating that the integrity of both Y249 and Y253 was essential for their appearance. The presence of ssDNA intermediate products is the first biochemical evidence for a RC mechanism of IS91 transposition.     

反义c-myc重组腺病毒载体的构建及其对大鼠胸腺淋巴细胞的增殖抑制作用

目的:观察反义c-myc重组腺病毒载体对大鼠胸腺淋巴细胞的增殖抑制作用.方法:构建大鼠反义及正义c-myc细菌质粒,并将所得细菌质粒与E1缺失腺病毒质粒导入293细胞系,经共转染得到正义及反义重组腺病毒载体.MTS法检测重组腺病毒载体对大鼠淋巴细胞增殖的抑制作用,RT-PCR检测重组腺病毒载体对c-myc mR-NA表达的影响.结果:反义c-myc重组腺病毒载体可抑制大鼠淋巴细胞增殖,降低淋巴细胞c-myc mRNA的表达.结论:反义c-myc重组腺病毒载体可抑制大鼠淋巴细胞增殖.     

Inhibition of the synthesis of proteins needed for Epstein-Barr virus replication by antisense RNA against the zta gene

Antisense RNA complementary to the Epstein-Barr virus (EBV) Zta gene, an immediate-early gene encoding a transactivator, was applied to inhibit EBV protein synthesis during its lytic cycle. A DNA fragment containing the Zta gene sequence was inserted into an expression vector, pMAMneo, in a sense and antisense direction under a dexamethasone-inducible murine mammary tumor virus LTR promoter, resulting in the construction of plasmids pZ(+) and pZ(–), respectively. Synthesis of Zta protein was reduced in pZ(–)-transfected cells upon dexamethasone induction. Because D-form early antigen and DNA polymerase are essential for viral DNA replication, the contents of these two viral proteins were examined. Amounts of the two lytic proteins were observed to be significantly repressed in pZ(–)-transfected cells. In contrast, both proteins were normally expressed in the sense plasmid pZ(+) or cells transfected with vector alone. Above results demonstrate that Zta antisense RNA can reduce the production of Zta protein and the other lytic proteins, possibly resulting in the inhibition of EBV replication.     

Delivery and long-term expression of a 135 kb LDLR genomic DNA locus in vivo by hydrodynamic tail vein injection

BACKGROUND: The delivery of a complete genomic DNA locus in vivo may prove advantageous for complementation gene therapy, especially when physiological regulation of gene expression is desirable. Hydrodynamic tail vein injection has been shown to be a highly efficient means of non-viral delivery of plasmid DNA to the liver. Here, we apply hydrodynamic tail vein injection to deliver and express large genomic DNA inserts > 100 kb in vivo. METHODS: Firstly, a size series (12-172 kb) of bacterial artificial chromosome (BAC) plasmids, carrying human genomic DNA inserts, episomal retention elements, and the enhanced green fluorescent protein (EGFP) reporter gene, was delivered to mice by hydrodynamic tail vein injection. Secondly, an episomal BAC vector carrying the whole genomic DNA locus of the human low-density lipoprotein receptor (LDLR) gene, and an expression cassette for the LacZ reporter gene, was delivered by the same method. RESULTS: We show that the efficiency of delivery is independent of vector size, when an equal number of plasmid molecules are used. We also show, by LacZ reporter gene analysis, that BAC delivery within the liver is widespread. Finally, BAC-end PCR, RT-PCR and immunohistochemistry demonstrate plasmid retention and long-term expression (4 months) of human LDLR in transfected hepatocytes. CONCLUSION: This is the first demonstration of somatic delivery and long-term expression of a genomic DNA transgene > 100 kb in vivo and shows that hydrodynamic tail vein injection can be used to deliver and express large genomic DNA transgenes in the liver.     

siRNA表达载体的构建及其表达

本研究用限制性内切酶消化质粒pCMV-tag-2B,除去巨细胞病毒(Cytomegalovirus,CMV)启动子核苷酸序列,剩下的核苷酸序列作为构建表达siRNA(Small interfering RNA,siRNA)载体的前体。依据文献提供的扩增H1RNA启动子核苷酸序列的引物序列合成一对引物,以带有H1RNA启动子序列的质粒DNA为模板扩增HIRNA启动子序列,插入前体,构建SiRNA的表达载体pCH1。另外将H1RNA启动子插入pGEM．1lfz相应位点,构建瞬时表达载体pGHl。依据EGFP的有效SiRNA抑制位点,合成两条分别为64bp的核苷酸链,通过体外退火,形成双链,然后插入已构建的两个表达载体。将这两个载体分别与表达EGFP蛋白的质粒pEGFP．N3共转染Bel．7402细胞,观察siRNA对EGFP的抑制效应。研究结果表明构建的载体有效表达了siRNA,这些载体可以用于与siRNA相关抗病毒治疗性试验研究。     

结核分枝杆菌Rv3586结构域基因真核表达载体的构建及鉴定

目的:构建结核分枝杆菌(Mycobacterium tuberculosis,Mtb)环二腺苷酸(cyclic diadenosine monophosphate,c-di-AMP)合成酶Rv3586结构域基因的真核表达载体,并在COS-7细胞中表达。方法:以Mtb基因组为模板PCR扩增Rv3586三个结构域基因,分别克隆入pEGFP-N3真核表达质粒,用菌落PCR、质粒酶切和测序方法对插入序列进行鉴定。通过脂质体将重组质粒转染COS-7细胞,间接免疫荧光法检测目的基因在COS-7细胞内的表达。结果:PCR成功扩增出Rv3586三个结构域基因,菌落PCR、质粒酶切和质粒测序鉴定结果表明成功插入目的片段,包含Rv3586的三个结构域基因的真核表达载体构建成功。间接免疫荧光法结果显示,Rv3586三个结构域蛋白在COS-7细胞中表达成功。结论:成功构建Rv3586三个结构域基因的真核表达载体,并在COS-7细胞中表达成功,为后续Mtb Rv3586结构域的功能和应用研究奠定了基础。     

人IL-6受体胞外区真核表达载体的构建及体外表达

目的构建人IL-6受体（IL-6R）胞外区真核表达载体,检测其在体外培养细胞中的表达。方法利用PCR扩增IL-6R胞外区,克隆到pcDNA3．1（＋）中,用双酶切、测序鉴定。重组质粒通过脂质体转染HL-60细胞,用G418进行筛选,利用Western印迹检测IL-6R蛋白表达。结果PCR扩增出1218bp的目的片段,双酶切和测序结果显示重组质粒正确。Western印迹结果显示转染细胞能够表达目的蛋白。结论成功构建了人IL-6R胞外区真核表达载体,并且能够在真核细胞中表达。     

稳定携带山羊痘病毒DNA疫苗减毒沙门氏菌的构建

为构建质粒稳定型山羊痘DNA疫苗,采用PCR与限制性酶切技术去除真核表达质粒pcDNA3.1(+)的氨苄抗性bla基因启动子序列,构建改良质粒pmcDNA3.1(+),然后插入山羊痘病毒P32基因,获得重组表达质粒pmcDNA3.1-P32,通过TSS法将其转化至减毒沙门氏菌中,构建成功携带山羊痘DNA疫苗的重组减毒沙门氏菌SL7207(pmcDNA3.1-P32);体内和体外试验结果表明,重组质粒pmcDNA3.1-P32在沙门氏菌中的稳定性显著高于pcDNA3.1-P32。这为下一步减毒沙门氏菌介导的山羊痘DNA免疫研究奠定了基础。     

The location of the left-handedly curved DNA sequence affects exogenous DNA expression in vivo

The intranuclear disposition of a plasmid is extremely important for transgene expression. The effects of a left-handedly curved sequence with high histone affinity on plasmid expression were examined in vivo. A naked luciferase-plasmid was delivered into mouse liver by a hydrodynamics-based injection, and the luciferase activities were quantitated at various time points. The location of the left-handedly curved sequence determined the transgene expression, without affecting the amount of intranuclear exogenous DNA. The plasmid containing the curved sequence at the location that results in the exposure of the TATA box out of the nucleosome core showed the highest expression. These results suggest that sequences with high histone affinity could control transgene expression from plasmids in vivo.