Strand Analysis, a free online program for the computational identification of the best RNA interference (RNAi) targets based on Gibbs free energy

Abstract

The RNA interference (RNAi) technique is a recent technology that uses double-stranded RNA molecules to promote potent and specific gene silencing. The application of this technique to molecular biology has increased considerably, from gene function identification to disease treatment. However, not all small interfering RNAs (siRNAs) are equally efficient, making target selection an essential procedure. Here we present Strand Analysis (SA), a free online software tool able to identify and classify the best RNAi targets based on Gibbs free energy (ΔG). Furthermore, particular features of the software, such as the free energy landscape and ΔG gradient, may be used to shed light on RNA-induced silencing complex (RISC) activity and RNAi mechanisms, which makes the SA software a distinct and innovative tool.

Multiple genes contribute to anhydrobiosis (tolerance to extreme desiccation) in the nematode Panagrolaimus superbus

“…Dicer substrates were designed for 50 targets (genes whose target codes start with “si”, on ), using the freeware Strand Analysis ( Pereira et al , 2007 ) and extended three nucleotides at each end. These molecules are 27 RNA duplexes, with two nucleotide 3′ overhangs and phosphate groups at the 5′ ends.…”

Microsatellite variability reveals beekeeping influences on Iberian honeybee populations

“…The area including the points shows the minimum distance of genetic isolation and refers to a panmictic population structure (Kraus 2005 Solignac et al (2003). Allele sizes were determined in an ABI PRISM 3700 DNA Sequencer (Applied Biosystems) and scored using STRand v2.3.106 (Pereira et al 2007). …”

Isolation and characterization of microsatellite loci for the cavehopper Palmorchestia hypogaea (Amphipoda: Talitridae)

“…Genotypes of 30 P. hypogaea individuals, collected from the two caves mentioned above were screened using STRand version 2.3.106 (Pereira et al 2007). Heterozygosities and genotypic linkage disequilibrium were calculated using GENEPOP version 3.4 (Raymond and Rousset 1995b).…”