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    siRNA oligo or shRNA vector?

    The mature form of a siRNA  has following structure:

    5'   pNNNNNNNNNNNNNNNNNNNTT 3'
    3' TTNNNNNNNNNNNNNNNNNNNp   5'

  • The chemically synthesized siRNA has the structure as above. It contains
    19-21 bp and Its anti-sense strand is exactly complimatory to the mRNA that
    is going to be silenced.  The 3' extrusion increases its resistance to RNase.
  • in vivo vector expressed siRNA (from either a regular shRNA vector or a
    Lentiviral shRNA vector) is transcripted from genes that encode shRNA.
    shRNA is precursor of siRNA and is processed into mature siRNA in cells. Its
    3' extrusion is usually UU
  • The table below provides a general comparison between the two types of siRNAs
 
siRNA
shRNA
vshRNA
Customer receiving
Synthetic double strand
RNA oligos
Vector with shRNA
gene insertion
vshRNA vector or
Lentiviral particles
Interfering last
< 72 hrs
up to  10 days
> 30 days
Cell line requirement
High transfection
efficiency cells ( > 70%)
Low transfection
efficiency cells are ok .
Almost any cells
Transit interfering
experiment
Yes
Yes
Yes
Inducible interfering
No
Yes
Yes
Tissue specific interfering
No
Yes
Yes
One-time preparation cost
Lower
medium
Higher
Can be regenerated in
customer's own labs
No
Yes
No
Best for
Target site screening
Short term knockdown
shRNA control
>72 hours knockdown
Low transfection cells
Stable shRNA cell line
for long term gene
silence
...


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