User-guide for the siRNA design tool
Please click here to go straight to the siRNA design tool.
Instructions
General information
Microsynth's online siRNA tool is an in-house-development to allow our customers to design siRNAs in an easy, comfortable manner. The algorithm is based on the published Reynolds-criteria with some proprietary extensions. The use of this tool is free and not linked to any order requirement.
Step 1: Provide your sequence information
You can either enter (copy/paste) your sequence directly into the box, alternatively enter the accession number ("NM_xxxxxx"), or the GI number of your sequence. For your convenience, a sequence upload tool lets you upload your sequence information from your local harddisk drive.
Step 2: Specify options
For a standard search, leave all parameters set to the default. The more experienced user may:
- Exclude stretches of identical bases (e.g. difficult to synthesize G-stretches, 3-4 recommended) (1)
- Avoid selecting the mRNA targets to start with AA (e.g. you would like to extend the hits) (2)
- Select the G/C content of his/her siRNA (3)
- Exclude/include a specific sequence motif in his/her search (e.g. NARN(17)YNN). (4)
After entering all parameters, press the submit button ("start design")
Step 3: Analyze the output
The siRNA candidates (mRNA targets, respectively) are sorted by rank. Top-scorers have the highest chance of being highly effective. The center part indicates 19 bases of the mRNA target. These 19 bases are also the sense strand of the siRNA core. The 5' region may form base-pairs with the antisense-strand-3'-overhang (e.g. if it is AA then the overhang is ideally dTdT for historical reasons).
On the right hand side you have the possibility to perform a blast search of the candidates to detect possible off-target-effects.
To order a siRNA, you may simply copy/paste the core sequence (19mers in the center part) into Microsynth's siRNA orderform.
Please note that you use this tool at your own responsability and that Microsynth can not be held liable for non-effective siRNA candidates.
Feedback
We appreciate your comments. Please feel free to tell us how the tool worked for you and what functions should be included in the future.
