Yes, you can generally use a scramble control plasmid with a different promoter than the one driving your target shRNA expression, as long as the scramble sequence itself is designed to not target any known genes and is expressed at a similar level to your target shRNA; the key factor is that the scramble sequence is the important control element, not the promoter driving its expression.

Some cell lines are known to silence the CMV promoter so I would use the same promoter as your targeting plasmid. however, since this would be a negative control it might not matter. A reviewer might ask when you submit the paper so if it is easy to do now at the beginning of the project then I would do it so that question is not raised.

Exact-shRNA is an shRNA service for the special needs outside our pre-designed shRNA products. Examples are:

shRNA targeting species other than Human, Mouse or Rat

Integrate an effective siRNA oligo sequence into an shRNA vector

Isoform-specific knock down

Have shRNA constructs that target multiple species

Reproduce a published result where shRNA sequence is available/disclosed

A scrambled negative control is included. Other control vectors can be ordered.

Lentiviral and AAV vectors available!

Custom shRNA

Figure 1. tGFP-expression in HEK293T cells (48 hours post-transduction). tGFP expression in HEK293T cells was knocked down by lenti-shRNA particles (right, co-transduction of lentiviral particles expressing tGFP and lenti-shRNA targeting tGFP) compared to control (left, transduction of lentiviral particles expressing tGFP).

There are two modes of service with Exact-shRNA:

Self-design: Customers specify the short hairpin sequences (stem and loop), choose a vector and OriGene constructs the plasmid. This is targeted to researchers who have gained knowledge of the effective target sequence, either from previous research or from published work. Up to 4 constructs are allowed for each project. Additional constructs can be submitted as a new project.

OriGene-design: Customers define the transcript sequence(s) and OriGene designs the shRNA (stem and loop) using our proprietary algorithm. Four constructs will be designed when possible.

When placing an order, refer to the catalog number on the request form. If you would like some assistance in the design of your shRNA constructs, we have experienced molecular biologists on our technical support team ready to help. Contact the Exact-shRNA team at 301.340.3188 option 2.