Oligo Overview

Benchling’s DNA and RNA oligo tools allow you to manage, analyze, design, and modify oligo constructs. Instead of relying on disparate software and files, you can centralize your oligo sequences in Benchling, improving organization as well as facilitates collaboration and ensuring data integrity. Every change to an oligo is tracked, allowing you to view and restore previous versions. This article provides guidance on creating, managing, and using oligos throughout your Benchling tenant.

Oligos vs. Sequences

In Benchling, you have the option to define a sequence-based entity as a DNA or RNA oligo or a DNA or RNA sequence. This section explains the differences between oligos and sequences.

• Strandedness
  • Oligos: single-stranded
  • Sequences: double-stranded
• Sequence length
  • Oligo limit: 2000bp
  • Sequence limit: 10M bp
• Molecular biology tools: Oligos and sequences are designed to work wit different molecular biology tools in Benchling. The table below compares the tools each entity type has access to:

Creating an oligo

To create an oligo, use one of the following methods.

Global create

1. Click Global Create Navigate to Oligo and select New DNA/RNA oligo from the menu
2. In the pop-up modal:
   1. Select the Nucleotide type
   2. Enter a Name
   3. Select a Project folder
   4. Select the Schema
   5. Select the Notation you want to use when creating your sequence
      1. Note: The ability to use different notations is only available for enterprise tenants. If you would like this feature and don’t have it available within your tenant, please reach out to Benchling support
   6. Enter the Bases
   7. Click Create

Note: Entities will not be automatically registered when using this method. For information on registering entities, see this article

Registry create

1. Click the Registry icon to open the registry application
2. Click the local create button in the upper right corner
3. Navigate to over DNA oligo or RNA oligo, depending on which you would like to register
4. Select the schema you would like to use for your oligo
5. In the pop-up modal:
   1. Select the Name and registry ID settings
   2. Enter an Entity name
   3. [Optional] Select a Project folder
   4. Fill out the schema-specific fields
   5. Select the Notation you want to use when registering your sequence
   6. Enter the Bases
   7. Click Register

To register an oligo using a registration table, see this article

Importing oligos in bulk

Global create

1. Click Global Create and hover over Oligo and click Import DNA/RNA oligos via spreadsheet
2. Within the pop-up modal:
   1. Select the Nucleotide type
3. Click Next
4. Check that the Import from field has Spreadsheet selected
5. Upload your spreadsheet and click Next
6. Map the spreadsheet column headers to the appropriate schema fields. Make sure to correctly identify your sequence field based on the notation used to avoid errors
7. Click Next
8. Review/resolve any errors that appear during the validation check to avoid having your import blocked
9. Click Import

Registry create

1. Click the Registry icon to open the registry application
2. Click the local create button in the upper right corner
3. Click Import entities from the dropdown menu
4. Within the pop-up modal:
   1. If your tenant has multiple registries, make sure the Registry field has the appropriate one selected
   2. Select a Schema
   3. Select a Project folder to associate these entities with
   4. Choose your Name and registry ID settings
   5. Click Next
   6. Check that the Import from field has Spreadsheet selected
   7. Upload your spreadsheet and click Next
   8. Map the spreadsheet column headers to the appropriate schema fields. Make sure to correctly identify your sequence field based on the notation used to avoid errors
   9. Click Next
   10. Review/resolve any errors that appear during the validation check to avoid having your import blocked
   11. Click Import

For updating an oligo using a registry table, see this article

View oligos and change display features

When viewing an oligo in Benchling, the toolbar at the top of the sequence map will display the following properties based on the full sequence:

• Length
  • Note: The total number of bases will appear on the right side of the bottom status bar
• GC%
• Melting Temperature
  • Note: Clicking on the Gear next to the Melting Temp will allow you to adjust your thermodynamic parameters

By highlighting a portion of the sequence, the bottom status bar will update the following properties based on the selected portion of the sequence:

• Length
• Start point
• End point
• GC%
• Melting Temperature (℃)
  • Note: Clicking on the Melting Temp will allow you to adjust your thermodynamic parameters

By highlighting a portion of the sequence, you can do the following:

• Change case:
  • Right click, hover over Change case and select Uppercase or Lowercase

By clicking the gear icon in the upper toolbar, you can toggle on/off the following display features on the sequence map:

• Annotations
• Axis
• Nucleotide structures
• Oligo properties

To search an oligo for specific bases, a string of bases, annotations, translations, or primers, click the magnifying glass from the upper toolbar. You could also access the search pop-up by using a keyboard shortcut:

• Mac: Command+F
• Windows: Control+F

If your oligo is linked to any DNA or RNA sequences as a primer, you can view a list of all linked sequences by clicking [#] linked sequences in the toolbar at the top of the sequence map

Edit Oligos

You can edit DNA and RNA oligos using many of the molecular biology tools. Here are the editing tools available from oligos:

• Insert bases:

1. Insert your cursor to the location you would like to add the bases within the sequence map
2. Begin typing your bases to see the pop-up summarizing all bases being added
3. Click enter/return on your keyboard to add the bases to your sequence

• Delete bases:

1. Highlight the bases you would like to delete
2. Right click then select Delete bases OR click the delete/backspace button on your keyboard then hit it again to confirm the deletion

• Annotations and Translations:
  • For more on this tool, see this help article
• Version History:
  • See a history of all edits made to the oligo and reset/clone from a previous version if desired
• Information:
  • Change the name, folder, or topology

Copy an oligo

To copy the bases of an oligo sequence, you can use any of the following methods:

• Use Copy button in the upper toolbar
• Keyboard shortcut:
  • Mac: Command+C
  • Windows: Control+C
• Right click then select Copy from the dropdown
• Right click, select Copy special, and choose which sequence type you would like to copy. You will be redirected to a preview pop-up and can select any of the following sequence types by clicking the preview box:
  • Original sequence (including modifications if applicable)
  • Sequence as RNA
  • RNA reverse complement
  • AA translation
  • AA reverse translation
  • Sequence as DNA
  • DNA reverse complement
  • HELM

Export an oligo

There are multiple ways to export a sequence depending on your desired file type. Find the section with the file type you desire below to see instructions for performing the export:

Export as PDF: 

1. Within the sequence map upper toolbar, click Create PDF
2. If everything looks correct within the PDF Preview pop-up modal, click Download in the bottom right corner of the modal

Export as Genank (.gb), FASTA (.fasta), SBOL RDF (.rdf), or Vector Linear Map (.svg):

1. Click the Information icon in the molecular biology toolbar
2. Within the pop-up, locate the Export data section
3. Using the Choose format… dropdown menu, select the file type you would like to export
4. Click Download