Creating a new Modified Oligo Sequence
DNA or RNA sequences containing chemical modifications can be created individually using the Global Create button on the Navigation Bar. To create a new Modified Oligo Sequence:
Click the Global Create button, navigate to Oligos, and select New Oligo
Define the Name and choose the folder where the sequence will be created
Choose DNA or RNA as Nucleotide Type, and select Natural Bases or HELM as the notation you will use to create the sequence.
Input the Bases (Natural Bases or HELM notation, depending on what is selected in step #3)
Select a color to assign to the sequence (for easy categorization/organization), and click “Create”.
Importing a Modified Oligo Sequence
DNA or RNA sequences containing chemical modifications can be imported into Benchling for viewing and editing. To import a new modified oligo sequence:
Navigate to the “+” create icon in the Navigation Bar and hover over the “Oligo” dropdown menu. Select “Import DNA Oligo” or “Import RNA Oligo” depending on the desired sequence to be imported.
Select a Project location which will house the newly imported sequence(s).
Importing can be performed either from a spreadsheet or as raw text. If importing from a spreadsheet, the first row of the spreadsheet should specify column headers, which must be unique. Every subsequent row should specify an individual sequence to be imported.
For importing from raw text, the Name of the sequence and its Bases can be listed in comma- or tab-separated text, or pasted directly from Excel.
Exporting a Modified Oligo Sequence
Modified oligonucleotides can be exported from Benchling. To export a modified oligonucleotide sequence:
Navigate to the Project which contains the modified oligo sequences to be exported. Expand the arrow icon to expand the project view.
Select one or multiple modified oligos to be exported. Navigate to the Export dropdown menu, and select CSV to export natural and modified sequences in HELM and IDT notation. Note that GenBank and FASTA file formats will represent the natural sequence only.