mRNA靶点筛选方法研究进展

mRNA靶点筛选问题是反义核酸领域的一个难题。近年来出现了多种筛选mRNA上可接近位点以确定靶位点的方法,包括mRNA实测分析法和计算机模拟分析两大类。其中mRNA实测分析法又包括多种针对自然折叠mRNA的实验分析技术;即基因walk技术,RNaseH作图技术、寡核苷酸微阵列技术,酶作图法确定二级结构技术,核酶导向型随机RNA库位点筛选技术和随机寡核苷酸库结合逆转录位点筛选技术。这些方法在鉴定RNA可接近位点及反义核酸的设计方面均有重要作用。     

大肠杆菌16S rRNA的核酶设计和初步应用

针对细菌rRNA研发抑制细菌增殖的新型抗菌素是抗生素研究领域的新课题。细菌rRNA与基因mRNA一样自然形成折叠卷曲高级结构,其结构上可以结合反义核酸的位点即靶点,靶点的阐明是设计有效反义核酸、核酶（Ribozyme）和脱氧核酶（DNAzyme）的关键。MAST方法固定16S rRNA,将其与寡核苷酸文库杂交筛选出靶点,获得了大肠杆菌16S rRNA的6个反义核酸结合靶点,并鉴定5个靶点有效,其中1个为高效。5个靶点的反义核酸能在通透性大肠杆菌菌株培养中不同程度地抑制其生长,针对高效靶点的核酶在转化大肠杆菌中表达而抑制其生长。     

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 .     

绿色荧光蛋白基因mRNA反义寡核苷酸的筛选和应用

基因mRNA的靶点筛选是设计反义寡核苷酸的关键.建立了PARASS(polyAanchoredRNAaccessiblesitesscreening)方法,即通过在mRNA末端引入polyA,与生物素标记的polyT退火结合,将其同链亲和素磁珠混合,使mRNA通过3’末端得到固定,保持mRNA的自然伸展和折叠,与寡核苷酸文库杂交筛选mRNA的结合靶点.PARASS筛选获得了绿色荧光蛋白(GFP)mRNA的3个反义寡核苷酸结合靶点,据其设计了多条反义寡核苷酸,与对照组相比,体外RNaseH分析显示3个靶点均为有效,在HeLa细胞内针对靶点的反义寡核苷酸能抑制GFP的表达,得到了Northern印迹结果支持.PARASS对反义寡核苷酸药物设计具有应用价值.     

Fas基因mRNA反义靶点筛选和体外验证

应用PARASS(poly-A anchored RNA accessible sites screening) 技术筛选Fas基因mRNA 获得3个潜在反义作用靶点,靶点1、2、3分别位于Fas基因297nt-317nt、619nt-639nt和662nt-682nt。设计了对应靶点的反义寡核苷酸A1、A2、A3,和10-23型DNAzyme D1、D2和D3。将反义寡核苷酸和Fas基因RNA结合再加入RNase H进行反应,10-23型DNAzyme则直接与Fas基因RNA作用,结果表明：3个靶点的反义寡核苷酸组及DNAzyme均能降解Fas基因RNA,为有效靶点,其靶点反应优势次序为靶点3>靶点1>靶点2;而非靶点对照组和有效靶点突变了2个碱基的对照组均没有反应。靶点2和靶点3与ISIS公司经过多次实验筛选到的Fas反义作用靶点位置基本相同,表明PARASS技术的有效性和可靠性。获得的有效反义寡核苷酸和DNAzyme为后续研究打下基础。     

10-23型DNA酶作为鉴定mRNA靶点有效性的新工具

10-23DNA酶是能主动切割mRNA的一类反义寡核苷酸.利用10-23DNA酶的直接切割作用验证mRNA结构靶点的有效性.对筛选的绿色荧光蛋白(GFP)基因mRNA的4个靶点平行设计了4条反义寡核苷酸和4条10-23DNA酶,对照组反义寡核苷酸将最佳靶点——靶点2的反义寡核苷酸突变2个碱基,对照组10-23DNA酶将靶点2的10-23DNA酶结合臂中央突变2个碱基.体外4条10-23DNA酶切割mRNA的结果和相应的4条反义寡核苷酸依赖的RNaseH降解结果完全相似,细胞内4条10-23DNA酶对绿色荧光蛋白的表达抑制作用与相应的4条反义寡核苷酸相似,表明10-23DNA酶显示的最佳作用靶点同样是最佳作用效果的反义寡核苷酸结合靶.10-23DNA酶可以作为评价mRNA结构靶点有效性的新工具.     

计算机辅助设计联合斑点杂交筛选铜绿假单胞菌PAO1 motA基因反义寡核苷酸序列

为了筛选出能与铜绿假单胞菌PAO1 motA基因的mRNA结合紧密的反义寡核苷酸序列,采用全基因寻靶技术（full length gene targeting,FLGT）,运用计算机软件（Mfold和RNA Structure4.6）模拟铜绿假单胞菌PAO1 motA基因mRNA的二级结构,根据最小自由能原理设计出8条寡核苷酸探针序列;PCR扩增出全长motA基因,克隆motA基因并进行体外转录,同时用地高辛标记mRNA,以斑点杂交方法筛选出与motA基因mRNA结合紧密、杂交信号较强的寡核苷酸序列。斑点杂交结果显示8条寡核苷酸中的4条有较强的杂交信号,从而成功筛选到了能与motA mRNA牢固结合的反义序列,为进一步研究以motA基因为靶的反义技术抑制生物膜形成打下基础。     

逆转录法筛选mRNA靶点设计核酶对GPA的表达干预实验研究

采用自行设计5’固定3’随机的文库对基因mRNA进行杂交用于逆转录反应以筛选mRNA的寡核苷酸结合靶点。对人I型跨膜糖蛋白-血型糖蛋白A （glycophorin A,GPA）的mRNA筛选了4个反义寡核苷酸可结合靶点,分别设计反义核酸（Antisense）,分别加入mRNA中用RNase H验证各靶点的核酸结合和切割效率,最终确定2个高效结合和切割靶点。再设计Ribozyme,构建表达核酶（Ribozyme）质粒,利用慢病毒（Lentivirus）包装技术,感染人源红系白血病细胞株K562细胞,在细胞水平验证其下调GPA基因表达的效果,对转染细胞mRNA进行反转录和Real Time PCR分析mRNA表达水平,并在蛋白水平进行了Western Blot分析。结果表明文库结合逆转录方法筛选靶点设计的Ribozyme具有高效率下调膜受体表达的作用,GPA为I型跨膜糖蛋白,该实验为筛选mRNA靶点提供参考方法,并对膜受体表达干预有参考价值。     

Survivin反义核酸结合位点的体外筛选及鉴定

合成 2 0mer随机寡核苷酸文库 ,与体外转录出的全长survivincRNA杂交 ,RNaseH酶切割后 ,经引物延伸、放射自显影 ,共筛选出 13个针对survivin基因的反义结合位点 (antisenseaccessiblesites ,AAS) .运用RNADraw软件分析、选定具有显著茎环结构的 4个位点 ,合成互补性反义寡核苷酸AS ODN1、AS ODN2 、AS ODN3 、AS ODN4并转染高表达survivin基因的胃癌细胞株MKN 4 5 .逆转录聚合酶链反应和Western印迹检测发现MKN 4 5细胞的survivinmRNA和蛋白水平均有显著的下降 ;MTT比色法证实 6 0 0nmol LAS ODN1～AS ODN4转染 2 4h后细胞生长受到明显抑制 ,透射电镜、annexinⅤ FITC和PI双染色流式细胞术均检测到细胞凋亡 .说明运用随机寡核苷酸文库 RNaseH酶切割与计算机分析相结合的方法 ,在体外有效筛选出survivin的反义核酸结合位点 ,其相应的反义寡核苷酸能阻断survivin基因的生物学功能 .     

反义核酸技术应用难点及研究进展

反义核酸技术已被广泛用于治疗药物、药物靶点确认、探知病理基因的表达。目前对其作用原理的研究集中于其被吸收入细胞的机制、在细胞内的分布、反义核酸序列的最佳长度和性质,并针对体内可能抑制反义核酸活性的影响因素,采取了各种相应的反义核酸优化技术,如对反义核酸的化学修饰、联结高效的转运载体、确定最佳的反义结合位点等,通过这些技术来提高其体内稳定性、跨细胞转运的效率,识别靶序列的特异性,以获得更多更好的反义药物投入实用。     

mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides

A solution-based method, mRNA accessible site tagging (MAST), has been developed to map the accessible sites of any given mRNA in high throughput fashion. mRNA molecules were immobilized and hybridized to randomized oligonucleotide libraries. Oligonucleotides specifically hybridized to the mRNA were sequenced and found to be able to precisely define the accessible sites of the mRNA. A number of ways were used to validate the accessible sites defined by the MAST process. Mapping of rabbit β-globin mRNA demonstrates the efficacy and advantage of MAST over other technologies in identifying accessible sites. Antisense oligonucleotides designed according to the accessible site map of human RhoA and Renilla luciferase mRNA result in knockdown effects that are in good correlation with the degrees of accessibility. The MAST methodology can be applied to mRNA of any length using a universal protocol.     

Determination of optimal sites of antisense oligonucleotide cleavage within TNFalpha mRNA

Antisense oligonucleotides provide a powerful tool in order to determine the consequences of the reduced expression of a selected target gene and may include target validation and therapeutic applications. Methods of predicting optimum antisense sites are not always effective. We have compared the efficacy of antisense oligonucleotides, which were selected in vitro using random combinatorial oligonucleotide libraries of differing length and complexity, upon putative target sites within TNFα mRNA. The relationship of specific target site accessibility and oligonucleotide efficacy with respect to these parameters proved to be complex. Modification of the length of the recognition sequence of the oligonucleotide library illustrated that independent target sites demonstrated a preference for antisense oligonucleotides of a defined and independent optimal length. The efficacy of antisense oligonucleotide sequences selected in vitro paralleled that observed in phorbol 12-myristate 13-acetate (PMA)-activated U937 cells. The application of methylphosphonate:phosphodiester chimaeric oligonucleotides to U937 cells reduced mRNA levels to up to 19.8% that of the untreated cell population. This approach provides a predictive means to profile any mRNA of known sequence with respect to the identification and optimisation of sites accessible to antisense oligonucleotide activity.     

Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis

RNA interference can be considered as an antisense mechanism of action that utilizes a double-stranded RNase to promote hydrolysis of the target RNA. We have performed a comparative study of optimized antisense oligonucleotides designed to work by an RNA interference mechanism to oligonucleotides designed to work by an RNase H-dependent mechanism in human cells. The potency, maximal effectiveness, duration of action, and sequence specificity of optimized RNase H-dependent oligonucleotides and small interfering RNA (siRNA) oligonucleotide duplexes were evaluated and found to be comparable. Effects of base mismatches on activity were determined to be position-dependent for both siRNA oligonucleotides and RNase H-dependent oligonucleotides. In addition, we determined that the activity of both siRNA oligonucleotides and RNase H-dependent oligonucleotides is affected by the secondary structure of the target mRNA. To determine whether positions on target RNA identified as being susceptible for RNase H-mediated degradation would be coincident with siRNA target sites, we evaluated the effectiveness of siRNAs designed to bind the same position on the target mRNA as RNase H-dependent oligonucleotides. Examination of 80 siRNA oligonucleotide duplexes designed to bind to RNA from four distinct human genes revealed that, in general, activity correlated with the activity to RNase H-dependent oligonucleotides designed to the same site, although some exceptions were noted. The one major difference between the two strategies is that RNase H-dependent oligonucleotides were determined to be active when directed against targets in the pre-mRNA, whereas siRNAs were not. These results demonstrate that siRNA oligonucleotide- and RNase H-dependent antisense strategies are both valid strategies for evaluating function of genes in cell-based assays.     

TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA

SUMMARY: TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotide (AO) selection based on mRNA accessible site tagging (MAST) and secondary structures of target mRNA. To make MAST result intuitive, both the alignment result and tag frequency profile is illustrated. As theoretical reference, secondary structure and single strand probability profile of target mRNA is also represented. All of these sequences and profiles are displayed in aligned mode, which facilitates identification of the accessible sites in target mRNA. Graphical, user-friendly interface makes TargetFinder a useful tool in AO target site selection. AVAILABILITY: The software is freely available at http://www.bioit.org.cn/ao/targetfinder.htm CONTACT: sqwang@nic.bmi.ac.cn.