Difference between revisions of "Ribozyme Switch"
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See also [[Riboswitches]] for additional information | See also [[Riboswitches]] for additional information | ||
== Experimental Design == | == 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 [http://en.wikipedia.org/wiki/Antisense_mRNA (Wikipedia)]. | + | 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 [http://en.wikipedia.org/wiki/Antisense_mRNA (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 they can stabilize due to Mg2+ concentrations |
http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700001.jpeg | http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700001.jpeg | ||
Revision as of 17:53, 6 December 2007
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
- This paper focuses on self-cleaving ribozymes with an aptamer sequence and a hammerhead ribozyme sequence
See also Riboswitches for additional information
Contents
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 they can stabilize due to Mg2+ concentrations http://www.pnas.org/content/vol104/issue36/images/large/zpq0340773700001.jpeg
Strand-Displacement
Helix-Slipping
Results
Modularity and Specificity of Strand-Displacement-based Ribozyme Switches
http://www.pnas.org/content/vol104/issue36/images/medium/zpq0340773700005.gif
Examples of Modularity of Various Ribozyme switches in Cellular Engineering Applications
http://www.pnas.org/content/vol104/issue36/images/medium/zpq0340773700006.gif
