Add custom modifications - BioPharma Finder Software - Add custom modifications - BioPharma Finder Software - BioPharma Finder Software

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 oligo building blocks, see Add custom building blocks.
2. In the Oligo Variable Modification area, select the subunit for the type of custom modification you want to create from the Subunit list.
3. The subunit types you can customize include base, backbone linker, 2'-ribose, and 3'- and 5'-terminal.
3. In the Site box, select the checkboxes for the sites where you want to apply the custom modification.
1. Base: A, G, U, T, C, I, H, and any custom bases previously created
2. Backbone linker: p, s, t, and any custom bases previously created
3. 2'-ribose: d, r, m, f, e, and any custom sugar groups previously created
4. 5'-terminal
5. 3'-terminal

6. TIP

   In the modification list at the bottom of the Building Block and Variable Modification Editor pane, the letter codes corresponding to the modification sites are defined in the table.

4. In the Name box, enter a unique name for the custom modification.
5. Enter the monoisotopic mass and the average mass for the modification in the respective fields.
6. If your modification involves a loss of mass, enter negative (-) monoisotopic and average mass values.
6. (Optional) In the formula box, enter the chemical formula of the modification.
7. Adding a chemical formula is optional; however, if you enter a formula, it must match the specified mass.
8. The application only recognizes the symbols for the elements in the periodic table and integers for the number of atoms.
9. For the base, backbone linker, and 2' ribose subunits, the application supports only these elements: C, H, O, N, S, P, and F.
10. Hyphens specify the loss of an element or chemical group.
11. For example, F−OH specifies the addition of a fluorine atom (F) and the loss of a hydroxyl group (OH).
7. Select Apply.
8. The application saves the custom modification and the modification appears in purple in the modification list at the bottom of the pane.
9. You can add your custom modification to the default list of modifications for quick loading.
10. See Change the default modifications for oligonucleotide sequences.
8. Repeat steps 2 through 7 to create additional custom modifications as necessary.