In the Oligonucleotide Sequence Editor, you can change the 5'-terminal, 3'-terminal, base, backbone linker, and 2'-ribose groups for an entire oligonucleotide sequence or within a specific chain using the Edit Sequence pane.

TIP

You can create custom oligo building blocks and assign them to a sequence using the Edit Sequence pane.

Prerequisites

  1. You are viewing the Oligonucleotide Sequence Editor.

Procedure

  1. In the Oligonucleotide Sequence Editor, expand the Edit Sequence pane on the right side of the page.
  2. In the Select Chain dropdown list, do either of the following:
  3. To apply global changes to all oligo building blocks, select All Chains.
  4. To apply changes to a specific chain only, select the appropriate chain number.
  5. Edit Sequence pane showing Select Chain options
    Figure Edit Sequence pane showing Select Chain options
  6. If you selected All Chains, do the following:
  7. Select a subunit from the Subunit dropdown list.
  8. In the From dropdown list, select the building block you want to change.
  9. In the To dropdown list, select the new building block you want to use for the selected subunit.
  10. Select Apply.
  11. The Oligo Sequence Map updates and displays the entire oligonucleotide sequence comprised of the specified building blocks.
  12. The Sequence Information pane updates and displays the recalculated Target Oligonucleotide and Chain parameters.
  13. If you selected a specific chain, do the following:
  14. Above the table, in the 5'-Terminal dropdown list, select the 5'-terminal for the specified chain.
  15. In the table, use the dropdown lists to specify the backbone linker, base, and 2'-ribose building blocks for each triplet in the specified chain.
  16. Below the table, in the 3'-Terminal dropdown list, select the 3'-terminal for the specified chain.
  17. Select Apply.
  18. The Oligo Sequence Map updates and displays the chain comprised of the specified building blocks.
  19. The Sequence Information pane updates and displays the recalculated Target Oligonucleotide and Chain parameters.
  20. Save the oligonucleotide sequence.