Henschel Andreas, Buchholz Frank, Habermann Bianca
Scionics Computer Innovation, GmbH, Pfotenhauerstrasse 110, 01307 Dresden, Germany.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W113-20. doi: 10.1093/nar/gkh408.
RNA interference (RNAi) is a powerful tool for inhibiting the expression of a gene by mediating the degradation of the corresponding mRNA. The basis of this gene-specific inhibition is small, double-stranded RNAs (dsRNAs), also referred to as small interfering RNAs (siRNAs), that correspond in sequence to a part of the exon sequence of a silenced gene. The selection of siRNAs for a target gene is a crucial step in siRNA-mediated gene silencing. According to present knowledge, siRNAs must fulfill certain properties including sequence length, GC-content and nucleotide composition. Furthermore, the cross-silencing capability of dsRNAs for other genes must be evaluated. When designing siRNAs for chemical synthesis, most of these criteria are achievable by simple sequence analysis of target mRNAs, and the specificity can be evaluated by a single BLAST search against the transcriptome of the studied organism. A different method for raising siRNAs has, however, emerged which uses enzymatic digestion to hydrolyze long pieces of dsRNA into shorter molecules. These endoribonuclease-prepared siRNAs (esiRNAs or 'diced' RNAs) are less variable in their silencing capabilities and circumvent the laborious process of sequence selection for RNAi due to a broader range of products. Though powerful, this method might be more susceptible to cross-silencing genes other than the target itself. We have developed a web-based tool that facilitates the design and quality control of siRNAs for RNAi. The program, DEQOR, uses a scoring system based on state-of-the-art parameters for siRNA design to evaluate the inhibitory potency of siRNAs. DEQOR, therefore, can help to predict (i) regions in a gene that show high silencing capacity based on the base pair composition and (ii) siRNAs with high silencing potential for chemical synthesis. In addition, each siRNA arising from the input query is evaluated for possible cross-silencing activities by performing BLAST searches against the transcriptome or genome of a selected organism. DEQOR can therefore predict the probability that an mRNA fragment will cross-react with other genes in the cell and helps researchers to design experiments to test the specificity of esiRNAs or chemically designed siRNAs. DEQOR is freely available at http://cluster-1.mpi-cbg.de/Deqor/deqor.html.
RNA干扰（RNAi）是一种通过介导相应mRNA的降解来抑制基因表达的强大工具。这种基因特异性抑制的基础是小的双链RNA（dsRNA），也称为小干扰RNA（siRNA），其序列与沉默基因的外显子序列的一部分相对应。为靶基因选择siRNA是siRNA介导的基因沉默中的关键步骤。根据目前的知识，siRNA必须具备某些特性，包括序列长度、GC含量和核苷酸组成。此外，还必须评估dsRNA对其他基因的交叉沉默能力。在设计用于化学合成的siRNA时，通过对靶mRNA进行简单的序列分析，大多数这些标准都是可以实现的，并且可以通过针对所研究生物体的转录组进行单次BLAST搜索来评估特异性。然而，出现了另一种产生siRNA的方法，即使用酶消化将长片段的dsRNA水解成较短的分子。这些内切核糖核酸酶制备的siRNA（esiRNA或“切割”RNA）在沉默能力方面变化较小，并且由于产物范围更广，避免了RNAi序列选择的繁琐过程。尽管这种方法很强大，但它可能更容易对靶标本身以外的其他基因进行交叉沉默。我们开发了一种基于网络的工具，可促进用于RNAi的siRNA的设计和质量控制。该程序DEQOR使用基于最先进的siRNA设计参数的评分系统来评估siRNA的抑制效力。因此，DEQOR可以帮助预测：（i）基于碱基对组成在基因中显示高沉默能力的区域，以及（ii）具有高沉默潜力用于化学合成的siRNA。此外，通过针对所选生物体的转录组或基因组进行BLAST搜索，对输入查询产生的每个siRNA进行可能的交叉沉默活性评估。因此，DEQOR可以预测mRNA片段与细胞中其他基因发生交叉反应的概率，并帮助研究人员设计实验来测试esiRNA或化学设计的siRNA的特异性。可在http://cluster-1.mpi-cbg.de/Deqor/deqor.html免费获取DEQOR。
