What Is siRNA and How Is It Used?

A Look at Small Interfering RNA and Uses in Molecular Genetics Research

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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.

What is siRNA?

Before diving into what exactly siRNA is, 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 (note: in some viruses RNA rather than DNA carries the genetic information as well).

Small interfering RNA (siRNA) are small pieces of double-stranded (ds) RNA, usually about 21 nucleotides long, with 3' overhangs (2 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.

In doing so, siRNA 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 Do 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, like viruses or transposons, and have been found to play a role in antiviral defense, degradation of over-produced mRNA or mRNA for which translation has been aborted, and preventing disruption of genomic DNA by transposons.

Each siRNA strand has a 5' 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 are 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.

Medical and Therapeutic Uses

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 an siRNA may cause unintended off-targeting where other nonthreatening protein may also be attacked and knocked out. 

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

By chemically modifying siRNAs to enhance their therapeutic properties such as:  

  • enhanced activity
  • increased serum stability and less off-targets
  • decreased immunological activation

Many diseases can potentially be treated by inhibiting gene expression.

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.


Tsai, C.S. Biomacromolecules: Introduction to structure, function and informatics. Wiley-Liss, 2007.

Whitehead, K. A.; Dahlman, J. E.; Langer, R. S.; Anderson, D. G. (2011). "Silencing or Stimulation? SiRNA Delivery and the Immune System". Annual Review of Chemical and Biomolecular Engineering 2: 77–96.

Alekseev OM, Richardson RT, Alekseev O, O'Rand MG (2009)."Analysis of gene expression profiles in HeLa cells in response to overexpression or siRNA-mediated depletion of NASP". Reproductive Biology and Endocrinology: 45.

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