Creating, importing, and exporting modified oligonucleotides

You can create and import DNA and RNA oligos containing chemical modifications to view and edit, then export them for use elsewhere. This article will explain how to create, import, and export modified oligonucleotides.

Create a modified oligo

To create a modified oligo:

1. Click + in the left-side menu. Under Oligo, select New DNA / RNA Oligo.

2. Enter the name and select a folder to store the sequence in.

3. Under Nucleotide Type, select DNA or RNA, then under Notation, select Natural Bases or HELM to create the sequence with.

4. Under Bases, enter the bases in the notation format you selected.

5. Select a color to assign to the oligo. This can make visual categorization and organization easier.

6. Click Create.

Import a modified oligo

You can import modified oligos using Registration tables in notebook entries or via bulk import.

Registration table

To import a new modified oligo in a notebook entry:

1. From the Insert menu in the toolbar, select Registration table.
2. Select Create new entities or Register existing entities depending on if you want to import new entities or register existing, unregistered entities.
3. Select the Registry schema for the entity. A table preview will display for you to review before inserting into the entry. Use this to confirm your selection.
   
   • If you select an Oligo schema, a Bases column and a Notation type drop-down menu display. The notation type selected here determines which type the Registration table is configured to accept.
4. Enter information about the entity into a row of the Registration table. Each row corresponds to one entity.
5. Click Submit to register the entities.

Note: The columns of the table are defined in the Registry configuration.

Bulk import

To import modified oligos in bulk:

1. Click + in the left-side menu. Under Oligo, select Import DNA / RNA Oligos from spreadsheet.

2. Under Import location, select a project or folder to store the oligo.

3. Under Nucleotide type, select either DNA or RNA depending on the oligo you’re importing.

4. Under Import from, choose your import method. Select:

   • Spreadsheet, then click Choose a file. Select the file, then click Open.

   • Raw text, then paste or manually enter the text.

5. Click Next.

6. Validate the data, then click Import.

Formatting your data

Imported data must be formatted in a way Benchling recognizes. If you’re importing via:

• Spreadsheet, the first row must contain unique column headers. Each subsequent row must specify individual oligos.

• Raw text, separate oligo names and bases using commas or tabs. Alternatively, you can paste directly from Excel.

Export a modified oligo

To export a modified oligo:

1. Open the folder containing the modified oligo, then click the > icon to expand the project view.

2. Select the oligo(s) you need to export.

3. Click the Export icon in the top-right corner and select your export method:

   • CSV exports natural and modified oligos in HELM and IDT notation.

   • GenBank or FASTA file formats only represent the natural oligo.