What is SiRNA? Questions

SiRNA, also known as small interfering RNA, is a molecule that reduces gene expression by blocking the translation of mRNA into proteins. The development of siRNA technology in the early 2000s by three scientists who won a Nobel Prize opened up the possibility of silencing genes that cause disease and paved the way for new therapeutics to treat disease.

What is SiRNA?

siRNA is a small RNA molecule that is used to regulate gene expression by degrading mRNAs. It is a type of RNA interference (RNAi), which is an endogenous process that protects cells from viruses and other pathogens by degrading their RNA. siRNA can also be used to silence genes in higher organisms, including humans.

What are small interference RNAs (siRNAs)?

Small interfering RNAs (siRNAs) are short double-stranded RNA molecules that are derived from long dsRNA. They are produced by RNA-dependent RNA polymerases, and they silence gene expression in transgenic organisms by base pairing with complementary messenger RNAs (mRNAs).

Therefore, siRNAs can be used to modulate gene expression.

What are the differences between siRNAs and shRNAs?

Small interfering RNA (siRNA) is a double stranded RNA molecule that is 20-25 nucleotides long. It functions in gene silencing by transcript cleavage and/or translational inhibition of target mRNAs.

ShRNA is a single stranded RNA molecule that is 39 nucleotides long. shRNA can be transcribed from DNA or synthesized chemically, although the latter method has not been used with human cells to date.

How does an siRNA find its target mRNA?

When an siRNA finds its target mRNA, the siRNA binds to it through a process called complementary base pairing. The entire sequence of the siRNA is complementary to a segment of the target mRNA, so when they meet and bind, they form a complex that cannot be cleaved by RNase enzymes.

The two main types of base pairing are Watson-Crick and Hoogsteen. In Hoogsteen base pairing, the two strands are stacked on top of each other so that their bases line up in an overhang structure; in Watson-Crick base pairing, one strand has more protruding bases than the other does and therefore forms loops when it does not fully cover another strand’s exposed bases (see image below).

How does an siRNA cause mRNA degradation?

To understand how an siRNA causes mRNA degradation, you have to know that RNAi is a double-stranded RNA that binds with the target mRNA. The binding of an siRNA can lead to mRNA degradation by two different means:

  • The RNAi machinery degrades the target mRNA directly
  • A ribonuclease 3′->5′ exonuclease (RNase III) degrades the target transcript from 5’ end towards 3’ end

siRNA can minimize the expression of genes by degrading mRNAs.

siRNAs are small, single-stranded RNAs that can be designed to match a desired target. These double-stranded siRNAs then interact with an enzyme known as Dicer to produce a single strand of RNA. Single strands of RNA can also be produced by other enzymes in the cell without going through Dicer, but they aren’t considered true siRNAs because they aren’t encoded by genes.

Dicing is an important step because it’s how you get your siRNA from the longer dsRNA—the dicing takes out one strand and leaves you with a short piece of dsRNA that will act as your guide for cleaving mRNA molecules with matching sequences.


As we’ve seen, using siRNA is a powerful way to gain insight into genes and develop gene therapies. Hopefully, we’ve answered some questions you may have had about siRNAs. If this has left you with more questions about how siRNAs work or how they can benefit your research, drop us a line! We would love to help you find the best solution for your needs.