George Mason University     |      Departments of MMB & Mathematics

Search for all possible siRNA seats within well-known human oncogene "KRAS"

Strategy:

It is important to remember that the best minimization of the off-target hybridization is achieved with the smallest possible siRNA seat. However, human genes differ by their ability to hybridize off-target. For example, genes that belong to large families tend to cross-hybridize within the family; this phenomenon contributes to off-target effects.

To develop siRNA specific to well-known human oncogene KRAS, one should start with the siRNA seats with minimal length of nucleotide available in the database (n=12). If these seats are not found in given gene, one should move up to a higher number of nucleotides (n=13) or (n=14).

Step-wise of siRNA search for "KRAS"

  1. Go to the "Search" page
  2. If you want to search with the gene name (example "KRAS"), in first window choose HUGO gene symbol (default) as identifier.
  3. Type HUGO gene symbol into second window.
  4. In third window, choose unique sequence length, in this case: 12 (default = 15).
  5. Press "Search" button.
  6. You will be redirected to the report page, where you will receive the information of the gene analyzed alon with the siRNA seats.
  7. If the search for unique sequence length equal to 12 is not successful, the following note will be displayed:

    There are no siRNA seats associated with this Gene under this criteria.Please select a larger UNIQUE sequence length.

  8. In case if you receive this note, proceed your search with higher unique sequence length. In case of KRAS gene, there are a number of possible siRNA seats with N (unique sequence length) = 13.
  9. As you can see from the example depicted above, there are a number of possible siRNA seats corresponding to KRAS gene. Minimal length of the seat is 19 nt (smallest siRNA), however, there are larger siRNA seats available (e.g., with length n = 28). Any siRNA selected within larger seat will be characterized by minimized off-target hybridization.

  10. As you can see from the example depicted above, each predicted siRNA seat is linked to the respective location on the NCBI gene map (pointed at the Figure below by green arrow). This feature will help you to quickly identify exonic location of given siRNA seat.
  11. Please note that that the siRNA seats resulted from your search shall be subjected to further siRNA selection using conventional siRNA design programs