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     

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。     

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.     

小鼠肝脏MicroRNA的提取与分离

本文对小鼠肝脏microRNA进行分离制备及相关性功能研究.采用poly(A)加尾方法,分离提取小鼠肝脏中的microRNA;利用T4 RNA连接酶,在microRNA两端加上连接引物,通过RT PCR制备microRNA的cDNA文库;经过对cDNA文库的质粒连接,克隆测序获得microRNA. 结果显示：获得4条有效序列,其中包括2条已知序列miR 122和2条未知小分子RNA序列.经查证, 2条microRNA片段在miRBase库中未有记录,在二级结构分析中可形成茎环结构,符合microRNA的特征. BLAST比对显示： 2个序列位于小鼠载脂蛋白B基因和小鼠28S核糖体RNA上,可能与基因调控有关,其功能有待进一步研究.     

ribozyme的用途

把ribozyme用在开发医药诊断药和化学试剂上的风险企业——Innovir公司已成立.通过该公司投资的风险资本美国Hambro国际风险投资公司在日本寻找合作者.作为当前的该公司开发目标,是艾滋病、乙型肝炎还有慢性白血病的治疗药.ribozyme是具有RNA切割活性的RNA分子.它是从类病毒和植物病毒、四膜虫属、大肠杆菌等多种生物中发现的.附着适应前后RNA序列的人工ribozyme特异地切断具有目的基因的     

基因药物研究现状和对策

生物技术药物以人类体细胞的基因组、转录本组和蛋白质组三个层次生物大分子为目标 ,基因药物的研究主要针对致病基因的DNA和基因转录本mRNA两类生物大分子 .mRNA从结构上考虑是研发核酸药物的最理想靶标和策略之一 .反义寡核苷酸、特异水解基因mRNA的核酸酶(ribozyme和DNAzyme)以及具有干扰作用的双链RNA(siRNA)是药物设计的策略之二 .mRNA结构靶点研究是研发反mRNA基因药物的基础 ,mRNA分子具有高度折叠的二级及三级结构 ,阐明其可及性位点 ,筛选其结构靶位点序列是关键 .近年研究报道的靶点筛选有约 7种mRNA的实测新技术 ,以及计算机辅助软件预测分析 .但发展分子生物学实验新技术以分析、确认靶点是药物研发策略之三 .     

基因突变的检测

1985年以前对基因中显著的缺失、插入、重排,可以用Southern杂交法来鉴定。一些小的变异,包括单碱基改变,只有当它们位于限制性内切酶的切点上时,方可被检出(如RFLP,限制性片段长度多态性)。如果这些小的变异不是位于限制性内切酶的切点上,那么只有对整个的基因进行顺序测定,当然,这是费时费力的。检测基因中的未知突变较为有效的方法于1985年     

大口鲶ob基因的克隆及其在毕赤酵母中的表达

1994年Zhang等人利用定位克隆技术首次成功地克隆出小鼠肥胖基因(obese gene,ob基因)及人类同源序列后[1],其他动物如鸡、鸭、猪等的肥胖基因结构和部分功能相继得到了报道,但关于鱼类ob基因的结构和功能研究报道较少.     

抗BmNPV即刻早期蛋白三联ribozyme在家蚕细胞中的表达

为了阻断家蚕核多角体病毒（BmNPV）的基因表达,以BmNPV的即刻早期蛋白基因(IE)为靶序列,设计了三联ribozyme．体外切割反应表明,该ribozyme能特异地切割靶序列的mRNA;细胞实验表明,细胞中表达的ribozyme也能够特异地切割靶序列,从而使受BmNPV感染的Bm-N细胞中的多角体减少约30％．     

三种丙型肝炎病毒转基因小鼠系的同时制备

为研究丙型肝炎病毒的致病致瘤机理及结构基因与非结构基因3区(NS3)的功能及其在HCV感染致病中的作用,建立一个HCV分子治疗的动物模型,构建了含金属硫蛋白启动子和HCV结构基因或NS3基因的质粒,将两者等量混合后用显微注射法接种于昆明白小鼠受精卵内制备转基因小鼠.通过PCR筛选获得三种整合HCV结构基因或/和NS3基因的首建鼠.结果表明:a.注射后卵存活率与仔鼠出生率分别为81%、30%;b.检测60只G0代小鼠,结构基因整合鼠6只(10%),NS3基因整合鼠4只(6.7%),双基因整合鼠9只(15%),总整合率为31.7%;c.RT-PCR法检测阳性鼠肝中有靶基因mRNA的转录;d.4只首建鼠与正常鼠回交获得38只G1小鼠,其中20只为整合鼠,整合率为52.6%;e.转基因鼠表型迄今无明显异常.表明一次显微注射同时获得了三种整合HCV结构基因或/和NS3基因的转基因小鼠.     

混合Ribozyme联合切割小鼠腺苷脱氨酶mRNA研究

采用计算机辅助设计得到针对小鼠腺苷脱氨酶ｍＲＮＡ的４种ｒｉｂｏｚｙｍｅ,它们均能在各自的切点切割ＲＮＡ分子,４种ｒｉｂｏｚｙｍｅ经组合后成混合ｒｉｂｏｚｙｍｅ,它们分别含有２种、３种和４种ｒｉｂｏｚｙｍｓ。通过对体外转录靶ＲＮＡ分子的联合切割研究表明,随着ｒｉｂｏｚｙｍｅ种数的增加,其中以（Ｒｚ２６２＋Ｒｚ４５５＋Ｒｚ５８３）组成最为理想,由此证明混合ｒｉｂｏｚｙｍｅ中,各种ｒｉｂｏｚｙｍｅ不仅保     

In vitro activity of minimised hammerhead ribozymes.

A number of minimised hammerhead ribozymes (minizymes) which lack stem II have been kinetically characterised. These minizymes display optimal cleavage activity at temperatures around 37 degrees C. The cleavage reactions of the minizymes are first order in hydroxide ion concentration up to around pH 9.3 above which the cleavage rate constants decline rapidly. The reactions show a biphasic dependence on magnesium-ion concentration; one of the interactions has an apparent dissociation constant of around 20 mM while the other appears to be very weak, showing no sign of saturation at 200 mM MgCl2. The minizymes are significantly less active than comparable, full-size ribozymes when cleaving short substrates. However, at a particular site in a transcribed TAT gene from HIV-1, minizymes are more effective than ribozymes.     

The effect of structure in a long target RNA on ribozyme cleavage efficiency.

Inhibition of gene expression by catalytic RNA (ribozymes) requires that ribozymes efficiently cleave specific sites within large target RNAs. However, the cleavage of long target RNAs by ribozymes is much less efficient than cleavage of short oligonucleotide substrates because of higher order structure in the long target RNA. To further study the effects of long target RNA structure on ribozyme cleavage efficiency, we determined the accessibility of seven hammerhead ribozyme cleavage sites in a target RNA that contained human immunodeficiency virus type 1 (HIV-1) vif - vpr . The base pairing-availability of individual nucleotides at each cleavage site was then assessed by chemical modification mapping. The ability of hammerhead ribozymes to cleave the long target RNA was most strongly correlated with the availability of nucleotides near the cleavage site for base pairing with the ribozyme. Moreover, the accessibility of the seven hammerhead ribozyme cleavage sites in the long target RNA varied by up to 400-fold but was directly determined by the availability of cleavage sites for base pairing with the ribozyme. It is therefore unlikely that steric interference affected hammerhead ribozyme cleavage. Chemical modification mapping of cleavage site structure may therefore provide a means to identify efficient hammerhead ribozyme cleavage sites in long target RNAs.     

Modified binary hammerhead ribozymes with high catalytic activity

A series of binary hammerhead ribozymes was designed and assessed in terms of cleavage activity and nuclease resistance. Enhanced nuclease resistance of binary ribozymes was achieved by incorporation of Z-modified nucleotides at the selective positions along with addition of 3'-3-linked thymidine cap. These modified binary ribozymes efficiently cleave 190-nucleotides long MDR1 mRNA fragment and display catalytic activity much higher then respective full-length analogs.     

MODIFIED BINARY HAMMERHEAD RIBOZYMES WITH HIGH CATALYTIC ACTIVITY

A series of binary hammerhead ribozymes was designed and assessed in terms of cleavage activity and nuclease resistance. Enhanced nuclease resistance of binary ribozymes was achieved by incorporation of 2′-modified nucleotides at the selective positions along with addition of 3′-3′-linked thymidine cap. These modified binary ribozymes efficiently cleave 190-nucleotides long MDR1 mRNA fragment and display catalytic activity much higher then respective full-length analogs.     

Studies of the recognition sequence of phi X174 gene A protein. Cleavage site of phi X gene A protein in St-1 RFI DNA.

It is already known that phi X gene A protein converts besides phi X RFI DNA also the RFI DNAs of the single-stranded bacteriophages G4, St-1, alpha 3 and phi K into RFII DNA. We have extended this observations for bacteriophages G14 and U3. Restriction enzyme analysis placed the phi X gene A protein cleavage site in St-1 RF DNA in the HinfI restriction DNA fragment F10 and in the overlapping HaeIII restriction DNA fragment Z7. The exact position and the nucleotide sequence at the 3'-OH end of the nick were determined by DNA sequence analysis of the single-stranded DNA subfragment of the nicked DNA fragment F10 obtained by gelelectrophoresis in denaturing conditions. A stretch of 85 nucleotides of St-1 DNA around the position of the phi X gene A protein cleavage site was established by DNA sequence analysis of the restriction DNA fragment Z7F1. Comparison of this nucleotide sequence with the previously determined nucleotide sequence around the cleavage site of phi X gene A protein in phi X174 RF DNA and G4 RF DNA revealed an identical sequence of only 10 nucleotides. The results suggest that the recognition sequence of the phi X174 gene A protein lies within these 10 nucleotides.     

BCR3/ABL2核酶的设计、构建及对K562细胞增殖与集落形成的抑制作用和凋亡诱导作用

利用计算机模拟设计合成了针对 K5 62细胞致癌融合 bcr3/abl2 m RNA的锤头状核酶 .该核酶以融合点附近 UUC为识别切割三联体 ,在核酶的 3′端增加一段 T7噬菌体终止子序列 .用基因克隆结合体外转录的方法 ,肯定了核酶的体外切割活性 .进而将核酶基因克隆到 p CEP4真核细胞高效表达载体上 ,利用脂质体 Lipofectin AMINE介导的转染技术将核酶与核酶基因导入靶细胞 ,从抑制靶细胞 K5 62的增殖与集落形成及引起靶细胞凋亡等方面验证了核酶在细胞水平上对融合基因 bcr3/abl2 m RNA的特异切割作用 ,并观察到了 T7噬菌体终止子序列对核酶切割效率的增强影响 .