Procedure

  1. In the Oligonucleotide Sequence Editor, select the title bar for the Building Block and Variable Modification Editor.
  2. The Building Block and Modification Editor pane opens, displaying the Oligo Building Block and Oligo Variable Modification areas.
  3. For more information on creating custom variable modifications, see Add custom modifications.
  4. In the Oligo Building Block area, select the subunit for the type of custom building block you want to create from the Subunit list.
  5. The subunit types you can customize include base, backbone linker, 2'-ribose, and 3'- and 5'-terminal.
  6. In the Name box, enter a unique name for the custom building block.
  7. In the Symbol box, select a symbol to denote the custom building block.

  8. NOTE

    For a custom base, the application does not accept the following symbols: A, G, U, T, C, I, or H. These symbols appear in the list, but are reserved for the default bases.

  9. In the formula box, enter the chemical formula of the custom building block.
  10. The application only recognizes the symbols for the elements in the periodic table and integers for the number of atoms.
  11. For the base, backbone linker, and 2' ribose subunits, the application supports only these elements: C, H, O, N, S, P, and F.
  12. To define the loss of a 2'-ribose group as custom building block, type a hyphen (-) at the beginning of the formula.
  13. The application does not accept the loss of bases, backbone linkers, the 5'-terminal, or the 3'-terminal as a custom building block.
  14. Enter the monoisotopic mass and the average mass for the modification in the respective fields.
  15. If your modification involves a loss of mass, enter negative monoisotopic and average mass values.
  16. Select Apply.
  17. The application saves the custom building block and the modification appears in purple in the modification list at the bottom of the pane.
  18. Repeat steps 2 through 7 to create additional custom building blocks as necessary.
  19. Examples of custom oligo building blocks are shown in the figures below.
  20. Custom 3'-terminal (N-acetylgalactosamine) created in the Oligonucleotide Sequence Editor
    Custom 3'-terminal (N-acetylgalactosamine) created in the Oligonucleotide Sequence Editor
  21. Custom 5'-terminal (hydroxide) created in the Oligonucleotide Sequence Editor
    Custom 5'-terminal (hydroxide) created in the Oligonucleotide Sequence Editor
  22. Custom backbone linker (thiol) created in the Oligonucleotide Sequence Editor
    Custom backbone linker (thiol) created in the Oligonucleotide Sequence Editor