Benchling has a built-in monomer library that can be used to modify DNA and RNA oligos and sequences. This monomer library is built off the Pistoia HELM Core Library. Modified oligos often contain more than one modification, leading to a complex chemical structure that is difficult to visualize using chemical notation or the sequence alone. HELM is a scientific language developed to solve this issue by standardizing the representation, registration, and visualization of these complex chemical structures. 

If you are interested in Benchling’s modified oligo/sequence tools and don’t see a monomer library in your Benchling tenant, please reach out to Benchling support at support@benchling.com.

Access the monomer library

While the monomers in the monomer library can be used by any end user with permissions to edit sequences, configuration and maintenance of the monomer library must be done by a tenant admin. To access the monomer library:

1. Click your avatar in the lower corner of your Navigation Bar
2. In the dropdown menu that appears, hover over Feature settings and select Monomer library

Note: Users without tenant admin privileges can still access the monomer library, but will have read only permissions and are only able to view monomers already added to the library

Navigate the monomer library

Once in the monomer library, tenant admins can take a few actions, such as creating, editing, and archiving monomers.

Create new monomers

To create a new monomer for use in modifying a sequence, click the Add new monomer button in the upper right corner. If desired, you can add more than one monomer at once. If the monomer symbol is greyed out within the HELM core library that means it already exists within your monomer library. New monomers can be added by one of the following methods:

Search HELM library

This method allows you to search via the symbol or name of the monomer within the HELM core library to add pre-defined monomers. 

• All monomers added from this method will have the following pre-populated monomer metadata:
  • Name
  • Symbol
  • Chemical structure
  • Visual
  • Natural analogue
  • Polymer type
  • Monomer type
  • Canonical SMILES
  • Original SMILES
  • Calculated exact molecular weight

Note: Subsequent edits, such as changes to capping groups or adding a custom molecular weight, can still be made to the monomer after addition to the library

Create new monomer

This method allows tenant admins to use a wizard to design custom monomers. You will need to define the following

• Monomer name
• Monomer symbol: the symbol used in HELM to define this monomer
• Natural analog: does this monomer describe a ribose-sugar derivative, phosphate-linker derivative, or nucleotide derivative (A, G, T, C, U)
  • Monomer type will be automatically set based on the natural analog set:
    • Ribose-sugar and phosphate-linker derivatives will be defined as backbone monomers
    • Nucleotide derivatives are defined as base monomers
• Chemical structure via SMILES
• Polymer type: as of now, Benchling only supports the polymer type RNA, so this will automatically be selected
• Cap groups: Benchling offers two different ways to describe cap groups
  • Via SMILES: a SMILES string can be added that defines the leaving groups and cap groups within it (ex: F[C@H]1[C@H]([OH:3])O[C@H](CO[H:1])[C@H]1O[H:2])
  • Via dropdown selection: if a SMILES string is added that only has attachment points defined, the following information can be defined via a dropdown
    • Sketch the monomer with the chemical sketching tool using R groups to define the attachment points. This will automatically update the SMILES string.

Upload CSV

Tenant admins can add monomers to your library in bulk by uploading a CSV with the following column headers. Click the “Upload CSV” option within the monomer library to download a template CSV to assist with this import

• name: monomer name
• symbol: symbol the monomer will be referred to within HELM sequences
• smiles: chemical structure defined by the SMILES string
• naturalAnalog: defines the natural analog of the monomer (ribose-sugar derivative, phosphate-linker derivative, or nucleotide derivative)
• customMolecularWeight: Optionally, define a custom molecular weight for the monomer

Potential errors within CSV import:

• Incorrect columns: the CSV headers must match the headers above exactly, including case. No extra columns other than “customMolecularWeight” should be present
• Invalid natural analog values: natural analogs must use one of the IUPAC base symbols
  • Additional symbols: “d” for deoxyribose, “r” for ribose, “p” for phosphate
• Invalid SMILES string: SMILES strings must be parsable and have valid capping groups with defined attachment points
• Duplicate symbols: symbols of new monomers can’t match an existing monomer’s symbol or another monomer being added via the same spreadsheet

Edit monomers 

Tenant admins can edit the following attributes of existing monomers to better fit their use case or give more exact computed fields

• Monomer name
• Monomer symbol
• SMILES
• Attachment points and capping groups
• Custom molecular weight
  • If you add a custom molecular weight, this will override the existing molecular weight in all computed field calculations
• Visual symbol (in the monomer listings page)

The natural analog can’t be changed as that may alter the natural bases of existing oligos/ sequences. To edit a monomer, you will need to locate it within the monomer library and click the edit button at the far right end of the monomer’s row.

Archive monomers 

If you would like to prevent users from using a monomer to modify a nucleotide, you are able to archive the monomer.  When a monomer is archived, all existing sequences/ oligos that refer to that monomer will stay unchanged and any existing computed field that generates HELM or custom syntax will continue to be able to generate syntax according to that monomer symbol. No new references to the monomer can be made.

Export the monomer library

If you would like to store your monomer library within an internal database or use it to update another Benchling tenants monomer library, you are able to export it to a CSV. There are three options to export your monomer library. To select an export method, click the Export button in the upper right corner to access the dropdown menu.

Export monomers as CSV with all fields

This method will export all monomer metadata into a CSV. Metadata included in this export:

• Name
• Symbol
• Natural analog
• Original SMILES
• Canonical SMILES
• Attachment points
• Calculated molecular weight
• Custom molecular weight

This CSV cannot be re-imported back into Benchling since it contains extra fields.

Export monomers to CSV for reimport into Benchling

This method will export monomers with the required metadata for re-importing the spreadsheet into Benchling. Metadata including in this export:

• Name
• Symbol
• Natural analog
• SMILES
• Custom molecular weight

HELM, IDT, and custom notation for modified oligos/sequences

HELM notation is the foundation for tracking modified oligos/sequences. However modified oligos can also be represented using other syntaxes, such as IDT. These are represented in Benchling by a library of custom notation tokens mapped to HELM tokens. Custom syntaxes are enabled and maintained via the monomer library.

Enable custom notation

To enable Benchling’s custom notation feature, please reach out to Benchling support at support@benchling.com or in app support messaging. With enablement of custom notation, you can optionally have support configure a small library of IDT notations. 

Configure your monomer library

Once enabled, you can configure a custom syntax library following these steps:

1. Access your monomer library by clicking your avatar in the lower right corner, then hover over Feature settings and click Monomer library
2. Click Custom notations in the upper right corner
3. Click Create
4. Within the configuration modal:
   • Enter a name
   • Case sensitivity: If toggled on, custom syntax tokens must be an exact case match to the token in the custom notation library
   • Used shared delimiter: A shared delimiter is a single character that separates adjacent tokens. If toggled on, you can define this shared deliminator/separater. It is not necessary to include the delimiter when defining individual aliases.
   • Extract terminals to schema fields: If toggled on, your custom notation library will support extracting a 5’ or 3’ terminal modification(s) from an entity’s schema field to the custom syntax computed field. Once toggled on, you will need to define a single set of acceptable delimiters that will be used to separate the terminal modification tokens from the rest of the custom syntax string.
     • Note: If you would like to be able to add up to 2 terminal modification tokens at the 3’ and/or 5’ end of your custom notation string, toggle on Allow up to 2 terminals at each end?
   • Always set the last phosphate to none: If toggled on, the last nucleotides phosphate monomer will always be set to none regardless of how the custom syntax notation is configured
5. Click Save and your custom notation library will be added to the dropdown in the upper left corner

Once you have configured your custom notation library, you will want to add tokens to your library. Since HELM is the basis for modified oligos/sequences within Benchling, custom notation tokens will be mapped to their corresponding HELM token/triple. Tokens are added using the text box in the middle of the screen. Optionally, 3’ and/or 5’ variants can be configured. 

• Formatting of HELM token/triple:
  • HELM token/triple format: sugar(base)phosphate
    • Note: Prior to configuring a HELM token make sure the corresponding monomer is within your monomer library
    • Note: There may be some variation in the delimiters used within your HELM token/triple
• Format to add custom notation token to library: custom notation token,HELM token,custom notation 5’ variant token,custom notation 3’ variant token

Use custom notations

Once you have configured your custom notation tokens, you are able to start registering modified oligos and sequences using these notations. To have the custom notation string appear within an entity’s metadata, a computed field will need to be added to your entity schema. Please reach out to Benchling support to have this configured.

Export custom notation

You can export your custom notations for reimport into another Benchling tenant's monomer library or to update an internal custom notation library. To perform the export:

1. Open the monomer library
2. Click the export button in the upper right corner
3. Select Export custom notations as CSV

Frequently asked questions

Q: My custom notation computed field is showing a computing failed error. How can I resolve this?

A: Hover over the red circle with a question mark in it to view an explanation of the error. If you are still unsure of how to resolve the error, reach out to Benchling support