Designing Hammerhead Ribozymes has never been so simple

Select what part of the RNA you will be targeting. No cut-sites (NUH) outside the selected areas will be considered.

Select what environment the ribozyme will be tested on. If in-vivo, you may specify an organism so that we may test that the ribozyme does not anneal to off-target locations. If the organism is not in the list, you may select other. You will then be prompted for a tax-id that can be found in the 'Blast' site. In the organism text box, you can find all organisms that NCBI has in their data base, then copy the tax-id unto this website.

Provide details of the environment in which the ribozyme will be used. This will allow for optimization over a wide range of annealing temperatures, and will help the algorithm predict better the secondary structure of the ribozyme.

Select one or multiple cut-sites for attachment on the target. Please note that a larger number of cut-sites means increased work-load and thus more waiting time. It is recommended that you use GUC and another alternate cut-site, but not more.

Choose the catalytic core that will be used to design the ribozyme.

These parameters relate to the length of the various helices on the ribozyme.

If the checkbox is checked, the T7 promoter will be added to the final DNA. If desired this should be used in vitro.

When verifying specificity, we can either find off-target locations where the ribozyme will cleave or it will hybridize strongly enough to silence the gene. If you select cleavage-only, non-cleaving sites will not be considered.