Part:BBa_K4506001:Design
Silence CAT gene
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 153
Illegal XhoI site found at 159 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
Our software takes into consideration different parameters which we identified to be relevant for the functioning of sRNAs in order to make our gene silencing system more effective. Their design includes the presence of an HFQ binding domain in the sRNA sequence, capable of recruiting a chaperone protein able to increase the sRNA-mRNA binding efficiency and a full-complementarity between these two molecules (excepting the HFQ binding domain). The software is based on two mathematical models to generate the scoring method: in the first model, the energy landscape, suboptimal and local minima sRNA structures, together with the degree of uracil load on the sRNA sequence and the dinucleotide combination among all the tested sequence are considered. In the second one the binding energies between the sRNA and the mRNA, and the mRNA target region itself are considered, with an mRNA accessibility factor. The developed software analyzes an entire gene sequence in a 24-nt sliding window, creating the corresponding mRNA and its corresponding sRNA fragment, adds the HFQ binding domain to the sRNA and scores the mRNA-sRNA pairs. The sRNAs designed with these programs will be tested against those designed with conventional methods to evaluate the extent of their improved functioning.
Source
Synthetic