Managing monomers in the Monomer Library

  • Updated

Benchling’s Monomer Library houses all the modifications that can be applied to an oligonucleotide sequence. In the Monomer Library, tenant admins can create, edit, and archive monomers, view and search for available monomer modifications, filter by monomer type, and edit monomer colors.

Note: To enable this feature, contact Benchling Support.

Access the Monomer Library

To access the library:

  1. Click your avatar in the bottom-left corner.
  2. Under Feature Settings, select Monomer Library.

Only tenant admins can take action in the Monomer Library. All other users have read-only access to the library.

Create a monomer

To create a monomer in the Monomer Library, click Add new monomer. You will be presented with a few different ways to create new monomers.

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Search HELM Library

You can add predefined monomers directly from the HELM core library by searching the HELM core library for monomer symbols and/or monomer names. You can edit any monomers from the HELM core library after they’re added to your library.

Monomers added from the HELM core library have all necessary monomer metadata already filled out.

If a monomer is unavailable in the HELM core library, that monomer is already added to the monomer library or the monomer is not available in the predefined library. Tenant admins can then follow the process for creating new monomers.

Non-admins can access the HELM library to view which monomers have already been imported and copy the symbols of monomers to send to their tenant admin to add.

Note: The HELM core library is populated from the Pistoia Alliance repository and is not managed by Benchling.

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Create new monomer

You can use the wizard to guide you through defining custom monomers, but you’ll need to define the following information:

  • Monomer name
  • Monomer symbol - the symbol used in HELM to refer to this monomer
  • Natural analog - does this monomer describe a Ribose-sugar derivative, Phosphate-linker derivative, or derivative of ACTGU?
  • Chemical structure via SMILES with designated attachment points

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Benchling definitions

Benchling will try to help with defining cap groups and monomer/polymer type.

Monomer type is derived from the natural analog set:

  • Ribose-sugar derivatives and Phosphate-linker derivatives are defined as Backbone monomers
  • Derivatives of ACTGU are defined as Branch monomers

We now offer 2 different ways to specify cap groups:

  • SMILES - provide SMILES strings that have both the attachment point and cap group specified inside. For example, F[C@H]1[C@H]([OH:3])O[C@H](CO[H:1])[C@H]1O[H:2]
  • Drop-down selection - provide a SMILES string that only has attachment points defined. Benchling will then prompt you to fill in cap group information. This enables you to draw a monomer in a chemical sketching tool using R-groups to specify the attachment points, and bring in that SMILES.

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Upload .csv of multiple monomers

You can upload a .csv of monomers to bulk create monomers. Before importing, ensure your .csv is formatted correctly.

Column name Captured information
name Monomer name
symbol Monomer symbol
smiles A SMILES string representation of the monomer’s chemical structure with attachment points and capping groups specified
naturalAnalog The natural analog
customMolecularWeight (Optional) Custom molecular weight


Troubleshooting the .csv import

If your import fails, confirm your .csv has none of the following issues:

  • Duplicate symbols - symbols can’t match existing monomers or symbols in other rows in the .csv
  • Incorrect columns - ensure columns are spelled exactly as above and that there are no extra columns
  • Invalid natural analog values - natural analog values must be one of the IUPAC base symbols
  • Invalid SMILES strings - SMILES strings must be parsable and have valid capping groups with defined attachment points

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Edit a monomer

You can edit these attributes of any existing monomer:

  • Attachment points and capping groups
  • Custom molecular weight
  • Monomer name
  • Monomer symbol

Note: Natural analog can’t be changed, as this might alter the natural bases of existing sequences/oligos.

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Archive a monomer

To archive a monomer, click Archive to the right of the monomer you’re archiving.

When a monomer is archived:

  • Existing oligos/sequences that refer to that monomer stay unchanged. Any existing computed field that generates HELM/Custom syntax will continue to generate syntax according to that monomer symbol.
  • No new references to that monomer can be made. It can no longer be selected from monomer drop-down menus or be included in HELM/Custom syntax strings during import.

Archived monomer symbols

Archived monomer symbols can’t be reused in new monomers since archived monomers may still be referenced in existing oligos/sequences.

To recycle a monomer symbol, you must change that monomer’s symbol before archiving.

Export your monomer library

You can export your monomer library in two .csv formats, depending on your intended use:

  • Export for reimport with Benchling - this format exports a .csv that only contains the columns needed to import into Benchling.
  • Export with all fields - this format exports a .csv with all stored metadata for each monomer. This format can’t be imported back into Benchling since it contains more information than importing currently allows. Extra columns include:
    • originalSMILES - the chemical structure SMILES string we received as input when creating the monomer
    • attachmentPoints - list of capping groups for each of the monomer’s attachment points
    • calculatedMolecularWeight - weight calculated based on the canonical SMILES structure saved on the monomer
  • Export custom syntax notations - this format exports a .csv that contains the custom token mappings which correspond to the HELM monomers set across the tenant 



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