mekentosj.com | iRNAi - iRNAi, do you?

Overview: siRNA's, or short interference RNAs, are widely used in biological model systems to inactivate genes of interest. Recently, a plasmid based RNAi system has emerged based on a DNA vector called pSUPER. However, designing primers to make the pSUPER constructs can be an error prone and time-consuming task. Therefore, we made iRNAi, a tool to help scientists quickly design error free oligos. | Download >>

Key Features: Move mouse over buttons to learn more...; iRNAi, do you? - With the help of iRNAi, designing RNAi oligos is no longer a nightmare. Drop in your sequence, pick the proper target sequence, copy the oligo sequences and your ready to order.

New Features in iRNAi 2.0: With version 2.0, iRNAi has become even more powerful and easier to use. You can now view the thermodynamic parameters of the selected sequences to make you pick even better targets. Also the interface has been redesigned such that all possible targets, along with their details, are neatly organized in a tableview.

Importing your gene sequences has become even easier. You can still drag and drop, or copy and paste them into the sequence viewer, but what to think of direct search and retrieve from NCBI's nucleotide database? Type in the accession number or gene name, click the appropriate record, and fetch. There you have it. What's the Open Reading Frame? We'll find it for you!

Finally, iRNAi now supports file import of a wide range of sequence file format including FASTA and DNA Strider files, thanks to the opensource BioCocoa framework. What more is there to wish for!

The Science Behind...: What is RNAi? What are short hairpin oligos, and what's the difference between a knock-out and a knock-down? Learn the answer to these questions and what scientists use iRNAi for.; Learn more >>
How does it work?: iRNAi is just a tool that helps you to design primers for succesful knockdown constructs. To do so you need to follow a set of simple steps. We advise you to take a look at the manual page. Also, we have given a workshop on using iRNAi from which you can download the keynote slides as PDF.; iRNAi manual >>; iRNAi workshop PDF>>
Supermen: The pSUPER system has been designed by Reuven Agami and Thijn Brummelkamp, both working at the Netherlands Cancer Institute. Reuven's group is even working on our floor! Be sure to pay a visit to his homepage for more information on pSUPER and the work he performs with it.; Visit Agami group >>
Let us know: If you have any questions, suggestions, or know how to pick target sequences that are guaranteed to work 100%? Be sure to let us know!; Email your feedback...
System Requirements: iRNAi requires MacOSX 10.3 or later.