Ribozyme Switch

A ribozyme switch is a part of an mRNA that can directly bind to a small target molecule and whose binding affects the gene's ability. There are two aspects of a riboswitch, the aptamer and the expression platform. The aptamer portion binds to a target molecules and changes shape, affecting the expression platform, which is how gene expression is regulated. Some types of riboswitch mechanisms include:

Formation of transcription termination hairpins
Blockage of translation by folding to isolate ribosome-binding sites
Effect of folding on splicing of mRNA
Self-cleavage ribozymes that cleave themselves in the presence of a target molecule
- This paper focuses on self-cleaving ribozymes with an aptamer sequence and a hammerhead ribozyme sequence
  - Strand-Displacement based switch
  - Helix-Slipping based switch

See also Riboswitches for additional information

The lab of Maung Nyan Win and Christina D. Smolke uses ribozymes to control Post-transcriptional gene regulation regulation within a cell.

Experimental Design

The setup of the ribozyme utilizes portability, utility and composability, all importants factors in the goal for this paper. The first component of this design is the placement of the ribozyme within the 3' UTR of a gene, in this case connected to GFP. The purpose of this design is to insure that any gene regulation occurs from cleavage of the ribozyme rather than from inhibition of translation iniation, which can occur with antisense RNA (Wikipedia). The second component ensures that there are no interactions between the ribozyme and the rest of the transcript by placing spacer sequences around the 3' and 5' end of the ribozyme. Lastly, the third component involves keeping loops I and II intact so that their tertiary interactions will be stable against Mg2+ concentrations (Figure 1A). For this reason, this paper uses a specific method to couple the ribozyme with an aptamer so that neither loop is destroyed (Figure 1B). http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700001.jpeg

Figure 1. "General design strategy for engineering ribozyme switches. The color scheme is as follows: catalytic core, purple; aptamer sequences, brown; loop sequences, blue; spacer sequences, yellow; brown arrow, cleavage site. (A) General compositional framework and design strategy for engineering cis-acting hammerhead ribozyme-based regulatory systems. Restriction enzyme sites are underlined. (B) Modular coupling strategies of the sensor and regulatory domains to maintain in vivo activity of the individual domains" (Win and Smolke 2007). Image Permission Pending.