抗HPV11／E2基因Ribozyme对靶RNA的体外剪切研究

为了寻找HPV11型引起的生死系统感染的治疗途径和探讨HPV的致病机理,本实验以HPV11病毒质粒为模板,扩增出HPV11型E2区644bp片段,采用pEGM-T-Easy Vector为载体,构建pTV-644克隆载体,经筛选得到克隆株,取质粒测序鉴定,采用上海生化所陈农安教授编制的锤头状Ribozyme设计软件进行计算机分析,选择Ribozyme对靶基因的最佳剪切位点,及进行基因同源性分析和生物学功能分析,选择出针对HPV11 E2靶基因的RZ2777,在最适条件下进行体外剪切反应,发现人工合成和体外转录得到的Ribozyme分子均能在相应位点准确切割靶RNA分子,选择合适的反应条件切割效率达60％以上,Km和Kcat值分别为0.63μmol／L、0.12μmol／L、RibozymeL两端的5′c－is－ribozyme和3′－cis－ribozyme自我剪切释放并未影响切割活性,但靶RNA侧翼序列影响了Ribozyme的剪切活性。实验研究表明,Ribozyme可能成为治疗HPV11型引起的尖锐湿疣的有效手段,并有望在分子水平上开辟出基因治疗HPV11病毒感染的另一新天地。     

pRNA导入型Ribozyme的设计和体外转录制备

目的:枯草杆菌的包装RNA分子pRNA是新型纳米分子载体,将其同锤头型核酶Ribozyme重组可以构建结构稳定、能进入细胞、主动识别结合和剪切基因RNA的pRNA-Ribozyme.由于目前100 nt以上的RNA分子采用化学合成制备较为困难,实验采用基因重组构建并体外转录制备170 nt的pRNA-Ribozyme....     

抗HPV11E2核酸的计算机设计

借助计算机软件分析,设计出能特异性切割HPV11型644nt型644ntE2mNA的核酶。遵循Symons锤头状核酶结构和GUX剪切位点原则,靶序列存在32个剪切位点,通过计算机软件分析核酶的最佳剪切位点,并对底物及核酶的二级结构进行预测及进行相应基因生物学功能和基因同源性分析,筛选出2个锤头结构核酶。针对这两位点设计的核酶分别命名为RZ277和RZ3281。计算机分析显示,两核酶与底物切点两翼碱基形成锤头状结构,切点所在基因序列具有相对松驰的二级结构,位于该基因重要生物功能区内,是核酶的理想攻击区域,通过基因库检索,在已知人类基因中排除了与上述两核酶切点两翼碱基有基因同源性序列的可能性。并非所有的GUX位点（X：C、U、A）或CUX均可作为核酶的最佳剪切切割反应,为下一步将核酶用于细胞内和体内试验打下基础。     

抗HPV16 E7-ribozyme在CV-1细胞中的稳定表达

构建了由RSV—LTR启动子带动并能在细胞内稳定复制的Ribozyme的自身修剪表达质粒pRSV—Rz523、Ribozyme反义对照质粒pRSV—AE7及人增殖细胞核抗原基因(PCNA)启动子带动的HPVl6 E7片段(+554～+686)的真核表达质粒pPCNA—E7。经G418抗性筛选获得了稳定表达Ribozyme的CV-1细胞克隆,其表达水平约为9．Opmol／lO6个细胞,其中活性Ribozyme的量大于50fmol／lO6个细胞,分离得到的Ribozyme可在体外特异切割E7靶RNA片段。通过共转染Ribozyme(或反义对照)和底物表达质粒并筛选出细胞克隆．研究了Ribozyme在细胞中对底物表达水平的影响。初步结果显示．Rihozyme的导人可使细胞内底物E7的RNA表达水平降低了90％(反义对照使E7 RNA表达降低20％)。上述结果提示：在CV-1细胞中表达的Ribozyme不仅在体外,同时在细胞内具有一定的生物学活性,有可能应用于逆转官颈癌细胞的恶性表型。     

抗HPV11 E2核酶的计算机设计

 借助计算机软件分析 ,设计出能特异性切割HPV11型 6 4 4ntE2mRNA的核酶 (ribozyme) .遵循Symon′s锤头状核酶结构和GUX剪切位点原则 ,靶序列存在 32个这样的剪切位点 .通过计算机软件分析出核酶的最佳剪切位点 ,并对底物及核酶的二级结构进行预测及进行相应基因生物学功能和基因同源性分析 ,筛选出 2个锤头结构核酶 .针对这两位点设计的核酶分别命名为RZ2 777和RZ32 81.计算机分析显示 ,两核酶与底物切点两翼碱基形成锤头状结构 ,切点所在基因序列具有相对松弛的二级结构 ,位于该基因重要生物功能区内 ,是核酶的理想攻击区域 .通过基因库检索 ,在已知人类基因排除了与上述两核酶切点两翼碱基有基因同源性序列的可能性 .将两核酶用于体外剪切实验取得了良好的实验结果 ,认为借助计算机分析可帮助尽快从多个剪切位点选择出最适核酶     

丙型肝炎病毒RNA特异性核酶的切割活性研究

针对丙型肝炎病毒RNA(HCV-RNA)的5′非编码区和部分C区的二级结构,设计并合成了四个不同的锤头型核酶(ribozyme A, ribozyme B, ribozyme C₁, ribozyme C₂).首先应用体外切割实验筛选出作用于HCV-RNA起始密码子上游GTA↓位点的核酶RzA有较好的活性.为初步验证核酶RzA在细胞内的切割活性,经脂质体介导,将RzA-RNA与另一携带该核酶靶基因的质粒表达载体pCl-neo-luciferase(载体中荧光素酶基因受核酶靶基因的调控)共转染HepG₂细胞.通过测定荧光素酶基因的表达证实了核酶在细胞内有较好的切割活性.在此实验基础上,把RzA基因克隆至pCl-neo质粒表达载体中,再次经脂质体介导,将重组的表达载体pCl-neo-RzA与携带该核酶靶基因的质粒表达载体pCl-neo-luciferase共转染HepG₂细胞,获得了更好的切割效果.     

应用核酶体外切割马铃薯卷叶病毒外壳蛋白基因的研究

针对马铃薯卷叶病毒外壳蛋白基因第356～358位点“GUC”．设计、合成了一种“锤头状”核酶。将核酶基因克隆在体外转录载体PSPT19的SP6启动子下游;同时将PLRVCPcDNA亚克隆在体外转录载体pSPT18的SP6启动子下游。利用SP6RNA聚合酶分别体外转录,获得核酶分子和靶RNA序列。在41℃保温进行核酶切割反应,检测到预期大小且被切开的两个RNA短片段。     

特异切割12-脂加氧酶mRNA的核酶体外活性及动力学研究

根据锤头状核酶(Ribozyme)的作用模式,设计、合成并克隆了特异性切割12-脂加氧酶(12-LO)mRNA的核酶基因。以合成的25个核苷酸长的12-脂加氧酶RNA片段为底物与转录的核酶RNA一起保温检测其体外切割活性。实验结果表明,在37℃保温时,核酶在体外对12脂加氧酶具有较高的特异切割活性,其Km值为1300 nmol/L,其kcat值为0.083/min,在50℃保温时,核酶具有很高的切割活性,其kcat值为0.31/min。     

U6嵌合型抗caspase-3核酶的体外及体内活性鉴定

为探讨caspase-3基因在细胞凋亡中的作用,及不同表达核酶的载体在体内的表达效果,本研究对比了3种表达核酶的真核质粒,包括RNA聚合酶Ⅱ启动的p1.5RZ107(自我剪切)和pRZ107及RNA聚合酶Ⅲ启动的嵌合于U6中的pU6RZ107在体外和在肝细胞BRL-3A内的活性,以期获得细胞内切割活性较高的的核酶载体方面的信息.结果显示,具有自我剪切功能的质粒p1.5RZ107在体外切割靶RNA的效率最高,几达80%;而体内caspase-3在RNA,蛋白水平及蛋白功能活性上均显著下降,证明核酶在体内均可有效地表达并切割底物,以pU6RZ107切割效率最高,约达65%,pRZ107次之,p1.5RZ107最低.结果表明,U6嵌合型核酶pU6RZ107体内可有效地表达核酶及下调靶RNA水平,这不仅为探讨caspase-3在凋亡途径中的作用,也可为今后的基因治疗提供研究基础.     

切割HPV-6bE1和HPV-11E1通用核酶Rz 1282的体外活性鉴定

利用计算机分析 HPV- 6b E1和 HPV- 1 1 E1 m RNA的同源序列 ,设计出通用于两者的锤头状核酶—— Rz1 2 82 (HPV- 6b基因 1 2 82位 ) ,通过体外转录建立了体外大量制备 Rz1 2 82的方法 .体外的切割实验表明 ,Rz1 2 82可在体外准确和有效地切割 HPV- 6b/1 1 E1靶 RNA,形成 2 68nt/52nt和 2 31 nt/52 nt大小的切割产物 .对于 HPV- 6b,Km和 kcat值分别为 1 3.8nmol/L和 0 .0 7min-1;对于 HPV- 1 1 ,Km 和 kcat值分别为 2 3.0 nmol/L和 0 .2 4 min-1.结果表明 ,体外制备的 Rz1 2 82具有较好的特异催化切割活性 ,并通用于 HPV- 6b及 HPV- 1 1 .它有望发展成为在细胞内有效抑制HPV- 6b/1 1 DNA复制的核酸药物 .     

Design and specificity of hammerhead ribozymes against calretinin mRNA.

We obtained a partial sequence of mouse calretinin mRNA from cDNA clones, and designed hammerhead ribozymes to cleave positions within it. With a view to optimising hammerhead ribozymes for eliminating the mRNA in vivo, we varied the length and sequence of the three duplex 'arms' and measured the cleavage of long RNA substrates in vitro at 37 degrees C (as well as 50 degrees C). Precise cleavage occurred, but it could only go to completion with a large excess of ribozyme. The evidence suggests that the rate-limiting step with a large target is not the cleavage, but the formation of the active ribozyme: substrate complex. The efficiency varied unpredictably according to the target site, the length of the substrate RNA, and the length of the ribozyme; secondary structure in vitro may be responsible. We particularly investigated the degree of sequence-specificity. Some mismatches could be tolerated, but shortening of the total basepairing with the substrate to less than 14 bp drastically reduced activity, implying that interaction with weakly-matched RNAs is unlikely to be a serious problem in vivo. These results suggest that specific and complete cleavage of a mRNA in vivo should be possible, given high-level expression of a ribozyme against a favourable target site.     

细胞周期蛋白D1特异性核酶表达载体的构建及其活性

应用mfold程序对锤头状核酶(ribozyme,Rz)和大鼠细胞周期蛋白(cyclin)D1基因的二级结构进行分析,设计合成锤头状Rz基因,通过RT-PCR扩增获得大鼠细胞周期蛋白D1目的基因,将Rz基因和细胞周期蛋白D1基因分别克隆入载体pGEM-3Zf( )中,体外转录Rz基因和靶基因并进行切割实验;将Rz基因与逆转录病毒载体pLXSN重组得到Rz真核表达载体pLXSN-Rz,将其转染入HSC-T6细胞,G418筛选出阳性细胞克隆,用RT-PCR检测细胞周期蛋白D1基因的表达。结果显示:针对目的基因的832位点设计合成了Rz832,成功获得Rz832基因、细胞周期蛋白D1mRNA的体外转录载体pGEM3Zf-Rz832和pGEM3Zf-cD1,经体外转录出Rz832(105nt)及细胞周期蛋白D1mRNA(1079nt)。体外切割实验证实Rz832能够特异性切割细胞周期蛋白D1mRNA,产生1014nt和65nt的切割产物,切割效率为80%。所构建的pLXSN-Rz832经酶切电泳、PCR鉴定显示,插入的Rz832序列大小约为57bp,与预期结果相同,经测序证实Rz832序列正确。转染pLXSN-Rz832的肝星状细胞(hepaticstellatecells,HSCs)细胞周期蛋白D1mRNA的表达受到明显抑制,仅为对照组的42.22%(t=-193.443,P<0.01),结果表明:Rz832能够在体外特异性切割细胞周期蛋白D1mRNA、并在HSC-T6细胞内有效抑制细胞周期蛋白D1基因的表达。     

Effects of variations in length of hammerhead ribozyme antisense arms upon the cleavage of longer RNA substrates.

The efficacy of intracellular binding of hammerhead ribozyme to its cleavage site in target RNA is a major requirement for its use as a therapeutic agent. Such efficacy can be influenced by several factors, such as the length of the ribozyme antisense arms and mRNA secondary structures. Analysis of various IL-2 hammerhead ribozymes having different antisense arms but directed to the same site predicts that the hammerhead ribozyme target site is present within a double-stranded region that is flanked by single-stranded loops. Extension of the low cleaving hammerhead ribozyme antisense arms by nucleotides that base pair with the single-stranded regions facilitated the hammerhead ribozyme binding to longer RNA substrates (e.g. mRNA). In addition, a correlation between the in vitro and intracellular results was also found. Thus, the present study would facilitate the design of hammerhead ribozymes directed against higher order structured sites. Further, it emphasises the importance of detailed structural investigations of hammerhead ribozyme full-length target RNAs.     

Hammerhead ribozyme cleavage of hamster prion pre-mRNA in complex cell-free model systems.

The cleavage properties of a trans-acting hammerhead ribozyme targeted 51 bases upstream of the putative splicing branch point in the hamster prion pre-mRNA intron were investigated in cell-free model systems in vitro. The specificity of cleavage was demonstrated by the inability of this ribozyme to cleave a non-homologous synthetic message encoding part of the beta amyloid peptide precursor, beta APP, and by the inability of the prion pre-mRNA to be cleaved by a ribozyme targeted to beta amyloid peptide precursor mRNA. Also, the addition of total RNA isolated from rat brain had only a minimal effect on the cleavage of the prion substrate pre-mRNA by the ribozyme. Finally neither the presence of 100 ng of nuclear or cytoplasmic proteins were found to affect the rate of cleavage in vitro.     

Oligonucleotide facilitators may inhibit or activate a hammerhead ribozyme.

Facilitators are oligonucleotides capable of affecting hammerhead ribozyme activity by interacting with the substrate at the termini of the ribozyme. Facilitator effects were determined in vitro using a system consisting of a ribozyme with 7 nucleotides in every stem sequence and two substrates with inverted facilitator binding sequences. The effects of 9mer and 12mer RNA as well as DNA facilitators which bind either adjacent to the 3'- or 5'-end of the ribozyme were investigated. A kinetic model was developed which allows determination of the apparent dissociation constant of the ribozyme-substrate complex from single turnover reactions. We observed a decreased dissociation constant of the ribozyme-substrate complex due to facilitator addition corresponding to an additional stabilization energy of delta delta G=-1.7 kcal/mol with 3'-end facilitators. The cleavage rate constant was increased by 3'-end facilitators and decreased by 5'-end facilitators. Values for Km were slightly lowered by all facilitators and kcat was increased by 3'-end facilitators and decreased by 5'-end facilitators in our system. Generally the facilitator effects increased with the length of the facilitators and RNA provided greater effects than DNA of the same sequence. Results suggest facilitator influences on several steps of the hammerhead reaction, substrate association, cleavage and dissociation of products. Moreover, these effects are dependent in different manners on ribozyme and substrate concentration. This leads to the conclusion that there is a concentration dependence whether activation or inhibition is caused by facilitators. Conclusions are drawn with regard to the design of hammerhead ribozyme facilitator systems.