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shrna-designer-v1

Design shRNA Oligonucleotides
This design tool selects from a preliminary list of 19-mer candidates with high dG differences between positions 1-2 and 18-19 and an overall dG within an ideal range2. If there are not enough candidates for you to choose at least 5 from, the program will extend this range up to 3 times in an attempt to recover more shRNA targets. Preference is given to candidates located within the CDS region (if known) of each gene, as well as candidates whose GC% falls within a desired range. Further discrimination is based on the Ui-Tei scoring algorithm, modified to reduce false-positive selection rate1.
For more information about our rules for efficient shRNA construction, please visit our protocol page.
Step 1. Enter Accession Number or Sequence and Desired GC% Composition:

Enter (Human, Mouse, or Rat) Accession Number:
Enter sequence:

Minimum GC% Maximum GC%

Additional Notes:
*Biosettia grades each designed oligo based on the probability that it will knock down your target RNA by at least 70%.
Grades are based on a combination of a modified Ui-Tei scoring method as well as free energy values of both terminal and overall regions of each oligo.
shRNA Converter

Convert Your Own siRNA into shRNA

Paste your 19-21nt sequence here to construct a compatible oligo for use with Biosettia's vectors:

References:

1. Taxman, Debra J., et al., Criteria for effective design, construction, and gene knockdown by shRNA vectors. BMC Biotechnology, 2006. 6:7.
2. Matveeva, O.V., et al., Optimization of duplex stability and terminal asymmetry for shRNA design. PLoS One, 2010, Apr 20;5(4):e10180.