In addition to the standard oligo building blocks included in the BioPharma Finder Oligonucleotide Sequence Editor, you can create custom 5'-terminal, 3'-terminal, base, backbone linker, and 2'-ribose groups and assign them to an entire oligonucleotide sequence or within a specific chain.

Prerequisites

  1. You are viewing the Oligonucleotide Sequence Editor.

Procedure

  1. In the Oligonucleotide Sequence Editor, expand the Building Block and Variable Modification Editor pane on the right side of the page.
  2. In the Oligo Building Block area, enter the following parameters:
  3. In the Subunit dropdown list, select the type of custom building block you want to create.
  4. In the Name box, enter a unique name for the building block.
  5. In the Symbol dropdown list, select a one-letter symbol for the building block.

  6. IMPORTANT

    For a custom base, the application does not accept the letter symbols A, G, U, T, C, I, or H. These letter symbols are reserved for the default bases.

  7. In the Formula box, enter the chemical formula for the building block.
  8. The read-only Monoisotopic Mass and the Average Mass fields automatically populate with the values for the input formula.

  9. NOTE

    For base, backbone linker, and 2'-ribose subunits, only elements C, H, O, N, S, P, and F are supported.

  10. Custom backbone linker (thiol) created in the Oligonucleotide Sequence Editor
    Figure Custom backbone linker (thiol) created in the Oligonucleotide Sequence Editor
  11. Custom 5'-terminal (hydroxide) created in the Oligonucleotide Sequence Editor
    Figure Custom 5'-terminal (hydroxide) created in the Oligonucleotide Sequence Editor
  12. Select Apply.
  13. The building block is added to the Building Block and Variable Modification Editor table.

  14. TIP

    Custom oligo building blocks appear in bolded purple font in the Building Block and Variable Modification Editor table.

  15. To delete a custom building block, select the building block in the Building Block and Variable Modification Editor table and select the Delete button.
  16. The modification is removed from the Building Block and Variable Modification Editor table.
  17. To edit a building block, select the building block in the Building Block and Variable Modification Editor table and select the Edit button.
  18. The Oligo Building Block area displays the parameters associated with the selected building block.
  19. In the Oligo Building Block area, modify the parameters as needed and then select Apply.
  20. The application overwrites the existing building block with the new input information.

  21. NOTE

    You cannot delete or edit/overwrite a custom oligo building block if the building block is used in any sequences loaded to the Sequence Manager.

  22. Use the Sequence Editor pane to assign the custom building block to an entire oligonucleotide sequence or within a specific chain.