Rational siRNA design for RNA interference

By A. Reynolds, D. Leake, Q. Boese, S. Scaringe, William S. Marshall, Anastasia Khvorova. Nature Biotechnology, 2004

2,151 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ebf27dc899926e0560ae7b11772b8b3fef0c05f6

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Design of a genome-wide siRNA library using an artificial neural network (2005, background): “Consequently, they need to be weighted, a process that is usually based upon arbitrarily selected factors 7 .”
Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis[W][OA] (2006, methodology): “In addition, the amiRNAs were designed with uridine at position 1 and, if possible, adenine at position 10, both of which are overrepresented among natural plant miRNAs and highly efficient siRNAs (Mallory et al., 2004; Reynolds et al., 2004).”
Gene silencing in plants using artificial microRNAs and other small RNAs. (2008, methodology): “For siRNAs, GC content of 30–50% has been suggested (Reynolds et al., 2004).”
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions (2016, background): “…interaction networks and their potential roles in disease mechanism and drug development [1, 4–7], including transcriptional and post-transcriptional regulatory networks [8–10], functional RNA networks [11–13], protein–protein interaction networks [14, 15], and metabolic networks [16, 17].”
Solid Lipid Nanoparticles for Drug Delivery: Pharmacological and Biopharmaceutical Aspects (2020, background): “This suppression mechanism, named RNA interference (RNAi), is a normal mechanism of gene expression control involving regulation of mRNA translation and degradation via the binding of short strands of homologous RNA generated by the Dicer enzyme (Reynolds et al., 2004).”
Perspective: machines for RNAi. (2005, background): “…before synthesizing siRNAs to reduce expression of a favorite gene (Khvorova et al. 2003; Amarzguioui and Prydz 2004; Hohjoh 2004; Naito et al. 2004; Reynolds et al. 2004; Ui-Tei et al. 2004; Yiu et al. 2005). siRNAs designed to load one strand into RISC to the near exclusion of the other are…”
Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy (2005, background): “A class of 'hyperfunctional' 21+2 siRNAs has been reported showing a similar extended duration of silencin”
On the art of identifying effective and specific siRNAs (2006, background): “In practice, however, different siRNAs often manifest a spectrum of potency, and only a fraction of them are highly effectiv”
Unlocking the potential of the human genome with RNA interference (2004, background): “Several groups took a ‘black box’ approach, which involved assaying large numbers of siRNAs, sorting them into classes depending on their potency, and then looking for characteristics that distinguished effective siRNAs from ineffective one”
Thermodynamics of RNA-RNA Binding (2006, background): “Several groups have proposed basically empirical rules for designing functional siRNAs, see e.g. Elbashir et al. (2002) and Reynolds et al. (2004), but the efficiency of siRNAs generated using these rules is highly variable.”
Human MicroRNA Targets (2004, background): “Lately, detailed characteristics associated with siRNA functionality were identified: low G/C content, a bias towards low internal stability at the39 terminus, lack of inverted repeats, and strand base preferences (positions 3, 10, 13, and 19) (Jackson et al. 2003; Reynolds et al. 2004).”