You can create and import DNA and RNA oligos containing chemical modifications to view and edit, then export them for use elsewhere. This article covers:

Create a modified oligo

To create a modified oligo:

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

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Import a modified oligo

To import a new modified oligo:

  1. Click + in the left-side menu. Under Oligo, select Import DNA Oligo or Import RNA Oligo, depending on the oligo you’re importing.

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

  3. Under Import from, select:

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

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

  4. Click Next.

  5. 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.

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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.

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