What are toehold switches?

Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses.

How does a toehold switch work?

The toehold switch is turned on when a stimulating “input” RNA binds to the toehold and induces the hairpin structure to open up, giving the ribosome access to its recognition sequence to start the synthesis of the encoded protein downstream.

What is Riboswitch and how is it work?

The riboswitch is a ribozyme that cleaves itself in the presence of sufficient concentrations of its metabolite. Riboswitch alternate structures affect the splicing of the pre-mRNA. A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript.

Why is 3 UTR important?

3′ untranslated regions (3′ UTRs) of messenger RNAs (mRNAs) are best known to regulate mRNA-based processes, such as mRNA localization, mRNA stability, and translation. Therefore, 3′ UTR-mediated information transfer can regulate protein features that are not encoded in the amino acid sequence.

What is the purpose of 5 UTR?

The 5′ untranslated region (UTR) contains secondary and tertiary structures and other sequence elements. RNA structures such as pseudoknots, hairpins and RNA G-quadruplexes (RG4s), as well as upstream open reading frames (uORFs) and upstream start codons (uAUGs), mainly inhibit translation.

How is 3 UTR calculated?

A common approach is to obtain cDNA sequence and use a sequence translation software program (e.g. ExPASy) to find the longest ORF. In most cases, the sequence between the 5’end and the start codon of the longest ORF will be the 5’UTR. The sequence between the stop codon and the poly(A) will be the 3’UTR.

Why is the 5 UTR important?

This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5′ UTR or a portion of it is sometimes translated into a protein product.

What is the coding sequence of a toehold switch?

Toehold switch systems are composed of two RNA strands referred to as the switch and trigger (Figure 1B). The switch RNA contains the coding sequence of the gene being regulated.

How is the toehold switch kept in its off state?

In the absence of the “input” RNA, the toehold switch is kept in its OFF state by forming a hairpin structure that uses part of the “input” recognition sequence and the ribosome recognition sequence, which is kept inaccessible.

Where are the toehold switches located in a gene?

Toehold switches are located upstream of the site at which translation begins. The switch has an exposed single-stranded region called the toehold sequence that is designed to be complementary to the trigger RNA.

How are toehold switches used in synthetic biology?

Wyss Institute researchers have engineered a new type of regulator, a “toehold switch”, which enables precise control over the expression of a gene of interest in response to a defined environmental stimulus in diverse synthetic biology applications. This opens in a new window.