In addition to the standard variable modifications included in the BioPharma Finder Oligonucleotide Sequence Editor, you can create custom 5'-terminal, 3'-terminal, base, backbone linker, and 2'-ribose modifications and assign them to a sequence.

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 Variable Modification area, enter the following parameters:
  3. In the Subunit dropdown list, select the type of custom modification you want to create.
  4. In the Name box, enter a unique name for the modification.
  5. In the Site dropdown list, select the checkboxes for the sites where you want to apply the modification.
  6. In the Monoisotopic Mass and the Average Mass boxes, enter the appropriate values for the modification.

  7. TIP

    If your modification involves a loss of mass, enter negative (−) mass values.

  8. (Optional) In the Formula box, enter the chemical formula for the modification.

  9. NOTE

    Specifying the formula for a custom modification is optional; however, if you enter a formula, it must match the entered mass values.

  10. NOTE

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

  11. TIP

    If a custom modification involves a loss of an element or chemical group, indicate the loss using a hyphen (−) before the eliminated element or group in the Formula box.

    For example, "F−OH" specifies the addition of a fluorine atom (F) and the loss of a hydroxyl group (OH).

  12. Select Apply.
  13. The modification is added to the appropriate Modifications lists in the Assign Variable Modifications pane and the Building Block and Variable Modification Editor table.

  14. TIP

    Custom modifications appear in bolded purple font in the Modifications lists and Building Block and Variable Modification Editor table.

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

  21. NOTE

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

  22. Use the Assign Variable Modifications pane to assign the custom modification to an oligonucleotide sequence as needed.