BLOCK-iT™ RNAi Designer

The easiest way to design effective RNAi molecules for great results

See also001:

Synthetics for in vivo RNAi

Target Design Options:

Stealth RNAi™ siRNA

miR RNAi

shRNA

siRNA to Stealth RNAi™ siRNA

siRNA to shRNA

Step 1: Enter an accession number or provide a nucleotide sequence

Accession number:

Nucleotide sequence: Enter only A, C, G, T, and U. See the online Help for additional information

Step 2: If you entered an accession number in Step 1, select regions for target design

Open reading frame (ORF)

5' UTR

3' UTR

Step 3: Choose database for Blast

NOTE: BLAST is used to compare input sequence with sequences in the database to find unique regions against which to design RNAi targets. The databases contain representative gene sequences for that species. Blast databases were updated on March 23, 2013 and the design output reflects the most up-to-date designs.

Step 4: Choose minimum and maximum G/C percentage

Minimum G/C percentage:

Maximum G/C percentage:

Step 5: Select vector and strand orientation and click "RNAi Design" to design shRNA.

Vector:			NOTE:Choose pENTR™/H1/TO for inducible shRNA expression and pENTR™/U6 for constitutive expression. If you want to design shRNA oligo compatible with both vectors, select pENTR™/U6 vector.

Strand orientation:

Guarantee: The BLOCK-iT™ Designer uses a proprietary algorithm to design shRNA with the latest resesarch data to optimize for promoter requirements and stem-loop structure. The recommended shRNA sequences designed using the BLOCK-iT™ RNAi Designer have an improved probability over random picking of inducing target gene silencing. However, more than one shRNA may need to be tested for a given gene.