You can replace the bases, backbone linkers, and 2' ribose subunits of an oligonucleotide sequence with custom building blocks or add custom chemical groups to the 5' and 3' terminals of the sequence chains using the Oligonucleotide Sequence Editor. For information on how to create and manage custom building blocks, see Manage custom modifications and building blocks for oligonucleotides.

Procedure

  1. In the Oligonucleotide Sequence Editor, select the title bar for Assign Variable Modifications.
  2. Oligo Sequence Map area displays all the oligo building blocks comprising the sequence in read-only mode.
  3. On the right side of the Oligonucleotide Sequence Editor, select the Edit Sequence title bar to open the Edit Sequence pane.
  4. Edit Sequence pane showing Select Chain options
    Edit Sequence pane showing Select Chain options
  5. To edit a specific chain, select the chain number that you want modify in the Select Chain drop-down list.
  6. image/svg+xml Custom 5' terminal Custom base for triplet 2 Custom sugarfor triplet 3 Custom 3' terminal
    Custom building block options for each triplet in a chain
  7. Select a 5'-terminal for the chain from the drop-down list above the table.
  8. In the table, use the drop-down lists to specify the three building blocks (backbone linker, base, and 2'-ribose) for each triplet in the sequence.
  9. Select a 3'-terminal for the chain from the drop-down list below the table.
  10. Select Apply.
  11. The updated oligo building blocks appear in the chain in the Oligo Sequence Map pane.
  12. The application displays the recalculated masses and the revised formula in the Sequence Information.
  13. To edit all of the chains in the sequence, select the All Chains option in the Select Chain drop-down list and then do the following:
  14. image/svg+xml From dropdown list To dropdown list
    Subunit, To, and From selections in the Edit Sequence pane
  15. Select a subunit from the Subunit drop-down list.
  16. Select the building block or modification you want to change from the From drop-down list.
  17. Select the building block or modification you want to add from the To drop-down list.
  18. Select Apply.
  19. All subunits of the specified type with be globally replaced with the custom building block.
  20. The updated oligo building blocks appear in the chain in the Oligo Sequence Map pane.
  21. The application displays the recalculated masses and the revised formula in the Sequence Information.
  22. image/svg+xml Custom 3' terminal Custom 5' terminal Custom base for triplet 2 Custom sugar for triplet 3
    Oligo Sequence Map showing oligonucleotide sequence modified with custom building blocks
  23. Select Save or Save as New in the command bar to save the modifications. Or, if you do not want to save the modifications to the sequence, select Cancel.
  24. See Save an oligonucleotide sequence.