siRNA and How It Is Used

siRNA, which stands for small interfering Ribonucleic Acid, is a class of double-stranded RNA molecules. It is sometimes known as short interfering RNA or silencing RNA.

Small interfering RNA (siRNA) are small pieces of double-stranded (ds) RNA, usually about 21 nucleotides long, with 3' (pronounced three-prime) overhangs (two nucleotides) at each end that can be used to "interfere" with the translation of proteins by binding to and promoting the degradation of messenger RNA (mRNA) at specific sequences.

siRNA Function

Before diving into what exactly siRNA is (not to be confused with miRNA), it's important to know the function of RNAs. Ribonucleic Acid (RNA) is a nucleic acid present in all living cells and acts as a messenger carrying instructions from DNA for controlling the synthesis of proteins.

In doing so, siRNAs prevent the production of specific proteins based on the nucleotide sequences of their corresponding mRNA. The process is called RNA interference (RNAi), and may also be referred to as siRNA silencing or siRNA knockdown.

Where They Come From

siRNA are generally considered to have come from longer strands of exogenous growing or originating from outside an organism (RNA which is taken up by the cell and undergoes further processing).

The RNA often comes from vectors, such as viruses or transposons (a gene that can change positions within a genome). These have been found to play a role in antiviral defense, degradation of over-produced mRNA or mRNA for which translation has been aborted, or preventing disruption of genomic DNA by transposons.

Each siRNA strand has a 5' (five-prime) phosphate group and a 3' hydroxyl (OH) group. They are produced from dsRNA or hairpin looped RNA which, after entering a cell, is split by an RNase III–like enzyme, called Dicer, using RNase or restriction enzymes.

The siRNA is then incorporated into a multi-subunit protein complex called RNAi-induced silencing complex (RISC). RISC "seeks out" an appropriate target mRNA, where the siRNA then unwinds and, it is believed, the antisense strand directs degradation of the complementary strand of mRNA, using a combination of endo- and exonuclease enzymes.

Uses of siRNA

When a mammal cell is faced with a double-stranded RNA such as a siRNA, it may mistake it as a viral by-product and initiate an immune response. In addition, the introduction of a siRNA may cause unintended off-targeting where other non-threatening proteins may also be attacked and knocked out. 

Introducing too much siRNA to the body can result in nonspecific events due to innate immune response activation, but given the ability to beat any gene of interest, siRNAs have the potential for many therapeutic uses.

Many diseases can potentially be treated by inhibiting gene expression, by chemically modifying siRNAs to enhance their therapeutic properties. Some properties that could be enhanced are: 

• Enhanced activity
• Increased serum stability and fewer off-targets
• Decreased immunological activation

Therefore, the design of synthetic siRNA for therapeutic uses has become a popular objective of many biopharmaceutical companies.

A detailed database of all such chemical modification is manually curated at siRNAmod, a manually curated database of experimentally validated chemically modified siRNAs.