RNA interference with 2′,4′-bridged nucleic acid analogues

In this study, a number of 2′,4′-BNA- and 2′,4′-BNA^NC-modified siRNAs were designed and synthesized. Their thermal stability, nuclease resistance and gene silencing properties against cultured mammalian cells were evaluated and compared with those of natural siRNAs. The 2′,4′-BNA- and 2′,4′-BNA^NC-modified siRNAs (named siBNA and siBNA^NC, respectively) showed very high T_m values, were remarkably stable in serum sample and showed promising RNAi properties equal to those exhibited by natural siRNAs. Thermally stable siBNAs composed of slightly modified sense and antisense strands were capable of suppressing gene expression equal to that of natural siRNA. A number of modifications on the sense strand by 2′,4′-BNA or 2′,4′-BNA^NC, either consecutively or separated by natural RNA nucleotides, is tolerable in RNAi machinery. Modifications at the Argonauate (Ago2) cleavage site of the sense strand (9–11th positions from the 5′-end of the sense strand) produced variable results depending on siRNA composition. Mostly, modification at the 10th position diminished siRNA activity. In moderately modified siRNAs, modification at the 11th position displayed usual RNAi activity, while modification at the 9th position showed variable results depending on siRNA composition.     

Gymnotic delivery and gene silencing activity of reduction-responsive siRNAs bearing lipophilic disulfide-containing modifications at 2′-position

Modified oligoribonucleotides used as siRNAs bearing biolabile disulfide-containing groups at some 2′-positions were synthesized following a post-synthesis transformation of solid-supported 2′-O-acetylthiomethyl RNA, previously described. Thus, the reduction-responsive and lipophilic benzyldithiomethyl (BnSSM) modification was introduced at different locations into siRNAs targeting the Ewing sarcoma EWS-Fli1 protein. Thermal stability, serum stability and response to glutathione treatment of modified siRNAs were thoroughly investigated. Among 17 modified siRNAs, significant gene silencing activities were demonstrated for the 8 most stable siRNAs in serum (half-life?>?1?h) when using a transfection reagent. Of special interest, two naked 2′-O-BnSSM siRNAs transfection exhibited a remarkable gene silencing activity after 24?h incubation. These inhibitions are consistent with an efficient gymnotic delivery demonstrated by the presence of the corresponding fluorescent siRNAs within cells.     

RNA interference in mammalian cells by siRNAs modified with morpholino nucleoside analogues

siRNAs modified with morpholino nucleoside analogues were synthesized and their biological properties were examined in details. The gene silence abilities of modified siRNAs were correlated to the positions of the modifications, some of which appeared to be more potent than the native siRNA. The 3′-end modification improved the stability of siRNAs in serum significantly. Furthermore, the dose–response and time-course experiments demonstrated that the siRNAs with 3′-end modification have potent gene silence activity at lower concentration and prolonged action time. These favorable properties make the morpholino modified siRNA a potentially useful tool in therapeutic applications.     

A large-scale chemical modification screen identifies design rules to generate siRNAs with high activity, high stability and low toxicity

The use of chemically synthesized short interfering RNAs (siRNAs) is currently the method of choice to manipulate gene expression in mammalian cell culture, yet improvements of siRNA design is expectably required for successful application in vivo. Several studies have aimed at improving siRNA performance through the introduction of chemical modifications but a direct comparison of these results is difficult. We have directly compared the effect of 21 types of chemical modifications on siRNA activity and toxicity in a total of 2160 siRNA duplexes. We demonstrate that siRNA activity is primarily enhanced by favouring the incorporation of the intended antisense strand during RNA-induced silencing complex (RISC) loading by modulation of siRNA thermodynamic asymmetry and engineering of siRNA 3′-overhangs. Collectively, our results provide unique insights into the tolerance for chemical modifications and provide a simple guide to successful chemical modification of siRNAs with improved activity, stability and low toxicity.     

Aberrant cryptic responsiveness of the pCAT 3- and pGL3-promoter reporter vectors

Transfection analyses are an informative method to assess the activity of specific promoter or enhancer elements in mammalian cells. Commercially available reporter vectors can be extremely useful investigative tools for such studies. This study reports that the pCAT 3- and pGL3-promoter vectors display cryptic responsiveness to androgens when they contain a DNA insert, while the empty vector, a commonly used negative control, is nonresponsive. Our studies initially aimed to characterize novel androgen-responsive DNA sequences in human genomic DNA through transactivational analyses. An isolated DNA fragment, designated ARC-3, contained three putative androgen response element "half-sites" and was androgen-responsive when cloned into the pCAT3-promoter vector. While we originally believed this to be a novel enhancer element, subsequent analyses of this clone revealed that this vector displays cryptic activity in the presence of an androgen. This was confirmed by cloning several unrelated DNA fragments that did not contain any known classic response elements into the pCAT3-promoter vector, all of which were found to be responsive. The empty vector (negative control) was again nonresponsive. The ARC-3 DNA fragment was also weakly responsive to stimulation when cloned into the pGL3-promotor vector, which is identical to the pCAT3-promoter vector, with the exception of an intron located 5' of the chloramphenicol acetyltransferase gene, and the reporter genes. This work demonstrates that both the pCAT3- and pGL3-promoter vectors are inappropriate to assess androgen-responsive enhancers and emphasizes the importance of the careful selection of reporter vectors and controls when conducting transactivational analysis.     

Synthesis and characterization of small interfering RNAs with haloalkyl groups at their 3′-dangling ends

With the aim to create a small interfering RNA (siRNA) with enhanced activity and resistance to nuclease degradation, we synthesized and evaluated the properties of the following siRNAs containing haloalkyl β-d-ribofuranosides at their 3′-dangling ends: 2,2,2-trifluoroethyl β-d-ribofuranoside, 2,2,2-trichloroethyl β-d-ribofuranoside and 2,2,2-tribromoethyl β-d-ribofuranoside. The gene silencing activities of the modified siRNAs were investigated through a dual luciferase reporter assay using HeLa cells. The highest silencing activity was observed for the trichloroethyl analog modified siRNA, which was closely followed by the trifluoroethyl and tribromoethyl analogs. The modified siRNAs were found to show increased binding affinity towards the Piwi-Argonaute-Zwille (PAZ) domain protein based on computational analysis and an experimental study. Furthermore, the RNAs modified with the analogs at their 3′-ends exhibited improved resistance to hydrolysis by a 3′-exonuclease.     

Inhibition of MDR1 expression with altritol-modified siRNAs

Altritol-modified nucleic acids (ANAs) support RNA-like A-form structures when included in oligonucleotide duplexes. Thus altritol residues seem suitable as candidates for the chemical modification of siRNAs. Here we report that ANA-modified siRNAs targeting the MDR1 gene can exhibit improved efficacy as compared to unmodified controls. This was particularly true of ANA modifications at or near the 3′ end of the sense or antisense strands, while modification at the 5′ end of the antisense strand resulted in complete loss of activity. Multiple ANA modifications within the sense strand were also well tolerated. Duplexes with ANA modifications at appropriate positions in both strands were generally more effective than duplexes with one modified and one unmodified strand. Initial evidence suggests that the loss of activity associated with ANA modification of the 5′-antisense strand may be due to reduced phosphorylation at this site by cellular kinases. Treatment of drug resistant cells with MDR1-targeted siRNAs resulted in reduction of P-glycoprotein (Pgp) expression, parallel reduction in MDR1 message levels, increased accumulation of the Pgp substrate rhodamine 123, and reduced resistance to anti-tumor drugs. Interestingly, the duration of action of some of the ANA-modified siRNAs was substantially greater than that of unmodified controls. These observations suggest that altritol modifications may be helpful in developing siRNAs with enhanced pharmacological effectiveness.     

Expanding the chemical nature of siRNAs: Oxaliplatin as metalation reagent

Short interfering RNAs (siRNAs) can down-regulate protein production by site specific degradation of mRNA. We here report the in vitro efficiency of three siRNAs metalated with oxaliplatin. All siRNAs were selectively platinated in the sense strand, and designed to target the AU-rich 3′ UTR region of Wnt-5a mRNA cloned into a luciferase reporter plasmid. Two of the studied siRNAs reveal luciferase protein suppression levels well above 90% when used in nano-molar concentrations for both metalated and the corresponding native siRNA. The platinated siRNAs were also characterized with respect to thermal melting properties, and the number of platinum adducts on the different sense strands were determined by MALDI-ToF MS. In all cases, platination was accompanied by a decrease in melting temperature. Further, the dominating oxaliplatin metalation site was the r(GpG)-adduct. The study indicates that metalation can be used as a general strategy to further expand the chemical nature of siRNAs.     

雄激素应答元件假冒DNA对PSA基因启动子的抑制作用

研究雄激素应答元件假冒DNA(AREdecoy)对前列腺特异抗原 (PSA)基因启动子的抑制作用 .联合运用报告基因和假冒DNA策略 ,构建了含PSA基因 5′侧启动子区 6 40bpDNA的萤光素酶表达载体pGL3 PSA ,与人工合成的双链硫代ARE假冒DNA共转染前列腺癌细胞株PC3 M并作用不同的时间 (2 4h、4 8h、72h) .应用双萤光素酶测定系统 ,检测萤光素酶的表达活性 .结果显示 :AREdecoyDNA显著抑制报告基因萤光素酶的表达 ,抑制率可达 95 % ,而对照decoyDNA无此作用 .作用不同的时间对萤光素酶活性的抑制无显著性差异     

TGF-β1通过RUNX2调控人肝星状细胞系LX－2中骨桥蛋白表达

目的：探讨人肝星状细胞系LX-2中促纤维化因子TGF-β1对骨桥蛋白（Osteopontin,OPN）的转录调控作用,研究其潜在关系及作用通路。方法：经重组因子TGF-β1刺激后,westernblot检测人肝星状细胞系LX-2中OPN和RUNX2的表达水平。通过生物信息学分析软件预测RUNX2在OPN启动子序列上的结合位点。构建基于pGL3-Basic的人OPN启动子载体和相应截短体,与RUNX2共转染HEK293细胞,结合双荧光素酶报告基因实验分析RUNX2对OPN启动子的转录调控作用。结果：经TGF－61刺激后,LX-2细胞系中OPN与RUNX2的蛋白表达水平均升高,提示二者均为TGF-81下游效应分子。TESS生物信息学分析显示OPN启动子序列-78-73存在RUNX2的结合位点ACCACA。通过双荧光素酶报告基因实验结果显示：RUNX2对OPN启动予具有正向调控作用,且通过截短删除之前预测的结合位点后,该调控作用消失。结论：TGF-β1可促进人肝星状细胞系中OPN的表达,该作用部分通过其下游转录因子RUNX2作用于OPN启动子区域的ACCACA序列而实现。     

RNA interference tolerates 2'-fluoro modifications at the Argonaute2 cleavage site

Short interfering RNA (siRNA) molecules with good gene-silencing properties are needed for drug development based on RNA interference (RNAi). An initial step in RNAi is the activation of the RNA-induced silencing complex RISC, which requires degradation of the sense strand of the siRNA duplex. Although various chemical modifications have been introduced to the antisense strand, modifications to the Argonaute2 (Ago2) cleavage site in the sense strand have, so far, not been described in detail. In this work, novel 2'-F-purine modifications were introduced to siRNAs, and their biological efficacies were tested in cells stably expressing human tartrate-resistant acid phosphatase (TRACP). A validated siRNA that contains both purine and pyrimidine nucleotides at the putative Ago2 cleavage site was chemically modified to contain all possible combinations of 2'-fluorinated 2'-deoxypurines and/or 2'-deoxypyrimidines in the antisense and/or sense strands. The capacity of 2'-F-modified siRNAs to knock down their target mRNA and protein was studied, together with monitoring siRNA toxicity. All 2'-F-modified siRNAs resulted in target knockdown at nanomolar concentrations, despite their high thermal stability. These experiments provide the first evidence that RISC activation not only allows 2'-F modifications at the sense-strand cleavage site, but also increase the biological efficacy of modified siRNAs in vitro.     

人SATB1基因5′上游序列的转录激活功能分析

在对人SATB1基因进行生物信息学分析的基础上 ,采用PCR技术 ,扩增人基因组DNA中SATB1基因 5′上游序列的 - 2 95 5～ - 9片段 ,构建了 3个分别由SATB1基因 5′上游 - 2 95 5～ - 9,- 172 7～ - 9和 - 76 0～ - 9序列片段驱动的报告载体 -pGL3 SP2 94 6 luc ,pGL3 SP1718 luc和pGL3 SP75 1 luc ,分别瞬时转染JurkatT ,K5 6 2 ,U937和HeLa细胞 ,通过测定荧光素酶的表达活性 ,观察SATB1基因 5′上游序列片段 3个删除突变体在不同细胞内活性的差异 .结果显示 ,SATB1上游序列- 2 95 5 - 9在 4种细胞中的转录激活能力为U937>JurkatT >K5 6 2 ,在HeLa细胞中基本无激活 ,提示SATB1的转录激活可能具有一定的细胞类型特异性 .3种 5′删除突变体转录激活性由大至小顺序为 - 76 0 - 9>- 2 95 5 - 9>- 172 7 - 9,提示SATB1的核心启动子可能存在于其 5′上游序列的- 76 0至 - 9bp区域中 .     

小鼠Lrp5基因5′端调控区域的功能

为研究小鼠低密度脂蛋白(LDL)受体相关蛋白5(LRP5)基因5′端调控序列的功能,PCR扩增小鼠Lrp5基因翻译起始位点上游3041bp(-2909bp~+132bp)DNA序列.PCR产物定向克隆到pGL3-basic载体上,重组质粒命名为pGL3-2909.以pGL3-2909质粒为模板,以不同的引物扩增出不同长短的DNA片段,分别定向克隆到含小鼠Lrp5基因基本启动子并含有荧光素酶报道基因的pGL3-103载体上,构建了12种荧光素酶报告基因表达体系:pGL3-267,pGL3-513,pGL3-535,pGL3-560,pGL3-575,pGL3-623,pGL3-645,pGL3-719,pGL3-770,pGL3-1032,pGL3-1330,pGL3-1619.以pRL-TK为内参照质粒,瞬时转染COS-7细胞,48h后收集细胞测定荧光素酶相对表达活性,pGL3-575(-2909bp~-2334bp)活性是pGL3-513(-2909bp~-2396bp)的20%,pGL3-535(-2909bp~-2374bp)的活性是pGL3-513的44%,pGL3-575的活性是pGL3-560(-2909bp~-2349bp)的48%,均有显著性差异.结果表明,在-2396bp与-2374bp之间的22bp区域内以及-2349bp与-2334bp之间的15bp区域内存在负调控元件.软件分析表明,此区域含有IK2,LYF1及MZF1调控元件.     

Improved silencing properties using small internally segmented interfering RNAs

RNA interference is mediated by small interfering RNAs (siRNAs) that upon incorporation into the RNA-induced silencing complex (RISC) can target complementary mRNA for degradation. Standard siRNA design usually feature a 19–27 base pair contiguous double-stranded region that is believed to be important for RISC incorporation. Here, we describe a novel siRNA design composed of an intact antisense strand complemented with two shorter 10–12 nt sense strands. This three-stranded construct, termed small internally segmented interfering RNA (sisiRNA), is highly functional demonstrating that an intact sense strand is not a prerequisite for RNA interference. Moreover, when using the sisiRNA design only the antisense strand is functional in activated RISC thereby completely eliminating unintended mRNA targeting by the sense strand. Interestingly, the sisiRNA design supports the function of chemically modified antisense strands, which are non-functional within the context of standard siRNA designs. This suggests that the sisiRNA design has a clear potential of improving the pharmacokinetic properties of siRNA in vivo.     

DNA end-binding specificity of human Rad50/Mre11 is influenced by ATP

The Rad50, Mre11 and Nbs1 complex is involved in many essential chromosomal organization processes dealing with DNA ends, including two major pathways of DNA double-strand break repair, homologous recombination and non-homologous end joining. Previous data on the structure of the human Rad50 and Mre11 (R/M) complex suggest that a common role for the protein complex in these processes is to provide a physical link between DNA ends such that they can be processed in an organized and coordinated manner. Here we describe the DNA binding properties of the R/M complex. The complex bound to both single-stranded and double-stranded DNA. Scanning force microscopy analysis of DNA binding by R/M showed the requirement for an end to form oligomeric R/M complexes, which could then migrate or transfer away from the end. The R/M complex had a lower preference for DNA substrates with 3′-overhangs compared with blunt ends or 5′-overhangs. Interestingly, ATP binding, but not hydrolysis, increased the preference of R/M binding to DNA substrates with 3′-overhangs relative to substrates with blunt ends and 5′-overhangs.     

The number of ribosomes on simian virus 40 late 16S mRNA is determined in part by the nucleotide sequence of its leader.

The size distributions of polyribosomes containing each of three simian virus 40 late 16S mRNA species that differ in nucleotide sequence only within their leaders were determined. The two 16S RNA species with shorter leaders were incorporated into polysomes that were both larger (on average) and narrower in size distribution than was the predominant wild-type 16S RNA. Therefore, the nucleotide sequence of the leader can influence the number of ribosomes present on the body of an mRNA molecule. We propose a model in which the excision from leaders of sizeable translatable regions permits more frequent utilization of internally located translation initiation signals, thereby enabling genes encoded within the bodies of polygenic mRNAs to be translated at higher rates. In addition, the data provide the first direct evidence that VP1 can, indeed, be synthesized in vivo from the species of 16S mRNA that also encodes the 61-amino acid leader protein.     

Introduction of 2-O-benzyl abasic nucleosides to the 3′-overhang regions of siRNAs greatly improves nuclease resistance

Chemically modified siRNAs containing 2-O-benzyl-1-deoxy-d-ribofuranose (R^H_OBn) in their 3′-overhang region were significantly more resistant towards serum nucleases than siRNAs possessing the natural nucleoside in this region. The knockdown efficacies and binding affinities of these modified siRNAs to the recombinant human Argonaute protein 2 (hAgo2) PAZ domain were comparable with that of siRNA with a thymidine dimer at the 3′-end.