You can add variable modifications to the 5'-terminal, 3'-terminal, bases, backbone linkers, and 2'-ribose groups in an oligonucleotide sequence.

In addition to the standard modifications included in the BioPharma Finder Oligonucleotide Sequence Editor, you can create custom modifications and building blocks and assign them to a sequence.

TIP

Upon installation, the BioPharma Finder application includes a default list of variable modifications. You can use the Define Modification List feature to customize the list visible in the Oligonucleotide Sequence Editor and define a custom sublist for quick loading.

Prerequisites

  1. You are editing an oligonucleotide sequence in the Oligonucleotide Sequence Editor.

Procedure

  1. In the Oligonucleotide Sequence Editor, expand the Assign Variable Modifications pane on the right side of the page.
  2. At the top of the pane, in the Max # Modifications area, type the maximum number of modifications the application can apply to the sequence.
  3. The maximum number of modifications is 8.

  4. IMPORTANT

    Setting the "Max # of Modifications" parameter to a high value greatly increases the possible combinations of modifications in the sequence which might prolong job processing time.

  5. (For single-chain oligonucleotide sequences with the "Intact Deconvolution" category) In the Terminal Truncation Search area, enter the appropriate parameters.

  6. TIP

    Enable the Terminal Truncation Search feature to search for truncated oligo products in your Intact Mass Analysis experiment.

  7. NOTE

    The Terminal Truncation Search feature is supported for Intact Mass Analysis of single-chain oligonucleotide sequences.

    If you select Enable for a multi-chain oligonucleotide, an error message appears when you save the sequence.

  8. NOTE

    The Terminal Truncation Search area is not visible for oligonucleotide sequences with the "Sequencing" category.

  9. Next, add variable 5'-terminal, 3'-terminal, and base/building block modifications from the Modifications lists (left) to the Modifications Selected for Search lists (right):
  10. To assign a modification, select it from the Modifications list, and then select the Add button.
  11. To remove a modification, select it from the Modifications Selected for Search list, and then select the Remove button.
  12. To quickly assign all modifications in the default sublist, select the Load Default Mods button.
  13. Assign Variable Modifications pane with Terminal Truncation Search (Intact Deconvolution) with default 5'-terminal and 3'-terminal modifications loaded
    Figure Assign Variable Modifications pane with Terminal Truncation Search (Intact Deconvolution) with default 5'-terminal and 3'-terminal modifications loaded
  14. Continue adding modifications from the Modifications list (left) to the Modifications Selected for Search lists (right) as necessary.
  15. Save the oligonucleotide sequence.