You can change the parameters for the oligo workbook on the Manual Sequence, Modification, and Add/Edit Building Blocks subpages of the Oligonucleotide Workbook Parameters page. See Oligonucleotide Calculator and Workbook commands and parameters for more information on these parameters.

Edit the Manual Sequence parameters

Procedure

  1. In the Oligonucleotide Calculator and Workbook Editor, select the Manual Sequence subtab (if necessary).
  2. On the right side of the Manual Sequence subpage, you can edit several parameters including the charge state, m/z, and mass ranges, as well as the number of isotopes for all or selected oligonucleotide sequences in the Results table.
  3. You can also choose to include adducts (Na+, K+) and base losses in the Results table by selecting the corresponding checkboxes.
  4. Edit the parameters as needed and select Apply.
  5. The Results table updates to include changes made to the Manual Sequence parameters.

Edit the Modification parameters

Procedure

  1. In the Oligonucleotide Calculator and Workbook Editor, select the Modification subtab.
  2. On the left side of the Modification subpage, you can make global changes the nucleotide bases, backbone linkers, 2' ribose groups, and 3'- and 5'-terminals for all or selected nucleotide sequences in the Results table.
  3. On the right side of the Modification subpage, you can make individual changes to the specific subunits. The Modification subpage functions similarly to the Oligonucleotide Sequence Editor. See Assign custom building blocks to an oligonucleotide sequence.
  4. The modifications that appear in the drop-down lists on the Modification subpage can be changed on the Add/Edit Building Blocks subpage.
  5. Add oligonucleotide modifications as needed and select Update.
  6. The Results table updates to include the modifications to the oligonucleotide sequences.

Edit the Add/Edit Building Blocks parameters

Procedure

  1. In the Oligonucleotide Calculator and Workbook Editor, select the Add/Edit Building Blocks subtab.
  2. On the Add/Edit Building Blocks subpage, you can edit or delete subunits in the table of building blocks. Changes made to oligo building blocks on the Add/Edit Building Blocks page are reflected on the Modification subtab.
  3. The Add/Edit Building Blocks subpage functions similarly to the Oligonucleotide Sequence Editor. See Edit custom modifications or oligo building blocks.
  4. In the table of building blocks, select the row for a subunit you want to modify and select Edit as needed.
  5. The "Oligo building block properties" section on the left side of the page populates with the properties of the selected subunit.
  6. Edit the oligo building block properties as needed and select Apply.
  7. The table of oligo building blocks updates to include the edited oligo building block, displayed in bolded purple font at the bottom of the table.
  8. On the table of building blocks, select the row for a subunit you want to modify and select Delete as needed.
  9. The subunit is removed from the table of building blocks.