Design of active small interfering RNAs

Integrated DNA Technologies Inc, 1710 Commercial Park, Coralville, IA 52241, USA.
Current opinion in molecular therapeutics (Impact Factor: 3.42). 05/2007; 9(2):110-8.
Source: PubMed

ABSTRACT Small interfering RNAs (siRNAs) have become the experimental tool of choice to suppress gene expression in a wide variety of organisms. Site selection and optimization does not appear to be as difficult for siRNAs as would be expected from historical experience with antisense oligonucleotides. Nevertheless, not all sites within a target gene perform equally. Significant progress has been made in defining sequence features that contribute to siRNA potency, and a variety of computational tools are available from academic and commercial sources to assist with siRNA design. Potential siRNA sequences should be screened for homology to other genes within the target organism's transcriptome to minimize cross-hybridization and inadvertent knockdown of unrelated genes via off-target effects. In addition to rational design criteria, chemical modification of the RNA can improve function by improving stability, reducing the potential for off-target effects and avoiding stimulation of the innate immune system.

  • Source
    • "RNAi function and is therefore counterproductive, a pattern of alternating 2'-O-methyl bases is comparable with the activity of unmodified RNA, and is quite stable in serum (Choung et al., 2006; Czauderna et al., 2003; Peek and Behlke, 2007) . Conjugation of peptides to the dsRNA is also developed, to increase cell membrane permeability (Ifediba et al., 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Molecular genetics insight into the pathogenesis of several neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease and amyotrophic lateral sclerosis, encourage direct interference with the activity of neurotoxic genes or the molecular activation of neuroprotective pathways. Oligonucleotide-based therapies are recently emerging as an efficient strategy for drug development and these can be employed as new treatments of neurodegenerative states. Here we review advances in this field in recent years which suggest an encouraging assessment that oligonucleotide technologies for targeting of RNAs will enable the development of new therapies and will contribute to preservation of brain integrity.
    Brain research 04/2014; 1584. DOI:10.1016/j.brainres.2014.04.005 · 2.83 Impact Factor
  • Source
    • "Many of these issues can be addressed through various chemical modification approaches. A variety of strategies for siRNA modification have been pursued including alterations in the backbone chemistry, 2′-sugar modifications, nucleobase modifications and others, as recently reviewed (Corey, 2007; De Paula et al., 2007; Kurreck, 2003; Manoharan, 2004; Peek and Behlke, 2007). One approach that we have extensively employed is to replace the pentose ring of RNA with six carbon moieties forming altritol, cyclohexenyl, or hexitol nucleic acids (Allart et al., 1999; Froeyen et al., 2000). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Increasing the effectiveness of siRNAs through chemical modification is an important task. Here we describe altritol and hexitol modified oligonucleotides targeting the B-Raf oncogene that is critical for the growth and survival of melanoma cells. Using assays for apoptosis, DNA synthesis, colony formation and B-Raf protein and message levels, we demonstrate that certain hexitol modifications can improve the effectiveness of B-Raf siRNAs and also increase duration of action. Altritol modified siRNAs were similar to or slightly less effective than unmodified B-Raf siRNA. Modifications at the 3' or 5' end of the sense strand, at the 3' end of the antisense strand, or within either strand were well tolerated. The basis for the increased effectiveness of the hexitol-modified siRNAs is not fully understood but may be partly due to increased stability to nucleases.
    European journal of pharmacology 02/2009; 606(1-3):38-44. DOI:10.1016/j.ejphar.2009.01.030 · 2.68 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Predicting the bed composition in estuaries and tidal lagoons is of great practical importance. At present however, horizontal and vertical bed composition variations are often neglected in sediment transport and morphological models. In this paper a process-based sand-mud model is proposed, the model behaviour is analysed and model results are compared to field measurements. In general, it can be concluded that with such a process- based model, governing time scales and dimensionless parameters can be derived which can significantly increase the physical understanding. Furthermore, an expression is derived for the equilibrium mud content at the bed surface when both deposition and erosion occur during the tidal period. In this expression, the settling velocity for mud, the mud concentration and the erosion rate form an important dimensionless parameter. For low parameter values (
Show more


Available from