Biochemical and Biophysical Research Communications
An algorithm for selection of functional siRNA sequences☆
Section snippets
Materials and methods
siRNA preparation and nomenclature. 21-Nucleotide RNAs were synthesized, quantified, and annealed as described [14]. SiRNA were targeted to four different genes: human tissue factor (hTF) (Accession No. M16553), murine tissue factor (mTF) (Accession No. M26071), human protein serine kinase H1 (PSK) (Accession No. AJ272212), and human c-src tyrosine kinase (CSK) (Accession No. NM_004383). Each siRNA duplex was identified according to the position of the first nucleotide of the sense strand
siRNA design
The siRNA included in this analysis were designed over a 2-year period using different criteria. All hTF siRNA and five PSK siRNA (PSK132, PSK314, PSK546, PSK566, and PSK739) contained TT overhangs and have been described previously [14]. Most of the hTF target sites were derivative in nature, i.e., they were derived either from sites previously targeted by hammerhead ribozymes (hTF167, hTF478, hTF372, and hTF562) or from an efficiently targeted site (i.e., hTF siRNA targeting the region
Discussion
We have performed a statistical analysis of 80 siRNA duplexes from two independent sets of siRNA for the purpose of identifying sequence features that are correlated with functionality. Since the overhangs in siRNA appear to have little or no effect on activity [7], [14], [21], [22], [23], [24], only the 19 bp duplex region was considered. The parameters that were evaluated for correlation with functionality at the 70% knockdown level included: (1) the GC content, (2) the potential for
Acknowledgements
This work was supported by grants from the Norwegian Cancer Society, Health and Rehabilitation, and the Research Council of Norway (RCN) to H.P. M.A. is a post-doctoral research fellow of RCN.
References (33)
- et al.
ATP requirements and small interfering RNA structure in the RNA interference pathway
Cell
(2001) - et al.
Single-stranded antisense siRNAs guide target RNA cleavage in RNAi
Cell
(2002) - et al.
Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis
J. Biol. Chem.
(2003) - et al.
Effective small interfering RNAs and phosphorothioate antisense DNAs have different preferences for target sites in the luciferase mRNAs
Biochem. Biophys. Res. Commun.
(2003) - et al.
The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript
J. Biol. Chem.
(2003) - et al.
Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways
Mol. Cell
(2002) - et al.
RNAi in human cells: basic structural and functional features of small interfering RNA
Mol. Cell
(2002) - et al.
Functional siRNAs and miRNAs exhibit strand bias
Cell
(2003) - et al.
Asymmetry in the assembly of the RNAi enzyme complex
Cell
(2003) microRNAs: tiny regulators with great potential
Cell
(2001)
Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans
Nature
RNA interference
Nature
Gene silencing in mammals by small interfering RNAs
Nat. Rev. Genet.
Role for a bidentate ribonuclease in the initiation step of RNA interference
Nature
An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells
Nature
A Drosophila fragile × protein interacts with components of RNAi and ribosomal proteins
Genes Dev.
Cited by (312)
Asymmetric trichotomous partitioning overcomes dataset limitations in building machine learning models for predicting siRNA efficacy
2023, Molecular Therapy Nucleic AcidsTerminal bridging of siRNA duplex at the ribose 2′ position controls strand bias and target sequence preference
2023, Molecular Therapy Nucleic AcidsDesigning potential siRNA molecules for silencing the gene of the nucleocapsid protein of Nipah virus: A computational investigation
2022, Infection, Genetics and EvolutionComputational study and design of effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains
2022, Computational Biology and Chemistry
- ☆
Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.bbrc.2004.02.157.
- 1
Present address: Department of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.