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109
Sfold web server for statistical folding and rational design of nucleic acids
- Nucleic Acids Res
, 2004
"... nucleic acids ..."
A computational study of offtarget effects of RNA interference
- Nucleic Acids Res
, 2005
"... RNA interference (RNAi) is an intracellular mechanism for post-transcriptional gene silencing that is frequently used to study gene function. RNAi is initiated by short interfering RNA (siRNA) of 21 nt in length, either generated from the double-stranded RNA(dsRNA)byusingtheenzymeDicerorintroduced e ..."
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Cited by 40 (0 self)
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RNA interference (RNAi) is an intracellular mechanism for post-transcriptional gene silencing that is frequently used to study gene function. RNAi is initiated by short interfering RNA (siRNA) of 21 nt in length, either generated from the double-stranded RNA(dsRNA)byusingtheenzymeDicerorintroduced experimentally. Following association with an RNAi silencing complex, siRNA targets mRNA transcripts that have sequence identity for destruction. A phenotype resulting from this knockdown of expression may inform about the function of the targeted gene. However, ‘off-target effects ’ compromise the specificity of RNAi if sequence identity between siRNA and random mRNA transcripts causes RNAi to
Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res
, 2005
"... Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not all 27mer duplexes show increased potency. Evaluation of the products of in vitro dicing reactions usin ..."
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Cited by 33 (10 self)
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Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not all 27mer duplexes show increased potency. Evaluation of the products of in vitro dicing reactions using elec-trospray ionization mass spectrometry reveals that a variety of products can be produced by Dicer cleav-age. Use of asymmetric duplexes having a single 2-base 30-overhang restricts the heterogeneity that results from dicing. Inclusion of DNA residues at the ends of blunt duplexes also limits heterogeneity. Combination of asymmetric 2-base 30-overhang with 30-DNA residues on the blunt end result in a duplex form which directs dicing to predictably yield a single primary cleavage product. It is therefore possible to design a 27mer duplex which is processed by Dicer to yield a specific, desired 21mer species. Using this strategy, two different 27mers can be designed that result in the same 21mer after dicing, one where the 30-overhang resides on the antisense (AS) strand and dicing proceeds to the ‘right ’ (‘R’) and one where the 30-overhangresides onthesense (S)strandanddicing proceeds to the ‘left ’ (‘L’). Interestingly, the ‘R ’ version of the asymmetric 27mer is generally more potent in reducing target gene levels than the ‘L ’ version 27mer. Strand targeting experiments show asymmetric strand utilization between the two different 27mer forms, with the ‘R ’ form favoring S strand and the ‘L ’ form favoring AS strand silencing. Thus, Dicer processing confers functional polarity within the RNAi pathway.
Lipidic carriers of siRNA: differences in the formulation, cellular uptake, and delivery with plasmid DNA, Biochemistry 43
, 2004
"... ABSTRACT: RNA interference (RNAi) has become a popular tool for downregulating specific gene expression in many species, including mammalian cells [Novina, C. D., and Sharp, P. A. (2004) The RNAi revolution, Nature 430, 161-164]. Synthetic double-stranded RNA sequences (siRNA) of 21-23 nucleotides h ..."
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Cited by 28 (1 self)
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ABSTRACT: RNA interference (RNAi) has become a popular tool for downregulating specific gene expression in many species, including mammalian cells [Novina, C. D., and Sharp, P. A. (2004) The RNAi revolution, Nature 430, 161-164]. Synthetic double-stranded RNA sequences (siRNA) of 21-23 nucleotides have been shown in particular to have the potential to silence specifically gene function in cultured mammalian cells. As a result, there has been a significant surge of interest in the application of siRNA in functional genomics programs as a means of deciphering specific gene function. However, for siRNA functional genomics studies to be valuable and effective, specific silencing of any given target gene is essential, devoid of nonspecific knockdown and toxic side effects. For this reason, we became interested in investigating cationic liposome/lipid-mediated siRNA delivery (siFection) as a meaningful and potentially potent way to facilitate effective functional genomics studies. Accordingly, a number of cationic liposome/lipid-based systems were selected, and their formulation with siRNA was studied, with particular emphasis on formulation parameters most beneficial for siRNA use in functional genomics studies. Cationic liposome/lipid-based systems were selected from a number of commercially available products, including lipofectAMINE2000 and a range of CDAN/DOPE systems formulated from different molar ratios of the cationic cholesterol-based polyamine lipid N1-cholesteryloxycarbonyl-3,7-diazanonane-
E-RNAi: a web application to design optimized RNAi constructs
, 2005
"... RNA interference (RNAi) has become a powerful genetic approach to systematically dissect gene function on a genome-wide scale. Owing to the penetrance and efficiency of RNAi in invertebrates, model organisms such as Drosophila melanogaster and Caenorhabditis elegans have contributed significantly to ..."
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Cited by 24 (6 self)
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RNA interference (RNAi) has become a powerful genetic approach to systematically dissect gene function on a genome-wide scale. Owing to the penetrance and efficiency of RNAi in invertebrates, model organisms such as Drosophila melanogaster and Caenorhabditis elegans have contributed significantly to the identification of novel components of diverse biological pathways, ranging from early development to fat storage and aging. For the correct assessment of phenotypes, a key issue remains the stringent quality control of long double-stranded RNAs (dsRNA) to calculate potential off-target effects that may obscure the phenotypic data. We here describe a web-based tool to evaluate and design optimized dsRNA constructs. Moreover, the application also gives access to published predesigned dsRNAs. The E-RNAi web application is available at
A systematic analysis of the effect of target RNA structure on RNA interference
- Nucleic Acids Res
, 2007
"... RNA interference ..."
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T: Specific residues at every third position of siRNA shape its efficient RNAi activity
- Nucleic Acids Res
"... RNAi activity ..."
Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
- Nucleic Acids Res
, 2007
"... and transparent method ..."
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More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature
, 2006
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Prediction of siRNA functionality using generalized string kernel and support vector machine
- FEBS Lett
, 2005
"... Abstract Small interfering RNAs (siRNAs) are becoming widely used for sequence-specific gene silencing in mammalian cells, but designing an effective siRNA is still a challenging task. In this study, we developed an algorithm for predicting siRNA functionality by using generalized string kernel (GSK ..."
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Cited by 12 (0 self)
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Abstract Small interfering RNAs (siRNAs) are becoming widely used for sequence-specific gene silencing in mammalian cells, but designing an effective siRNA is still a challenging task. In this study, we developed an algorithm for predicting siRNA functionality by using generalized string kernel (GSK) combined with support vector machine (SVM). With GSK, siRNA sequences were represented as vectors in a multi-dimensional feature space according to the numbers of subsequences in each siRNA, and subsequently classified with SVM into effective or ineffective siRNAs. We applied this algorithm to published si-RNAs, and could classify effective and ineffective siRNAs with
