Getting started with oligo conjugates and oligo duplexes

Background

Bioconjugates are highly versatile but also inherently complex. In Benchling, bioconjugates combine multiple distinct entities — today, oligos and small molecules.

To model siRNA and ASO bioconjugates, Benchling supports oligo conjugate and oligo duplex schema types. These allow you to view the unique components of a bioconjugate, which may otherwise be represented as distinct schemas in Benchling. Oligo conjugates also allow users to create and view chemical connections and biophysical properties in one place. 

Oligo conjugates

Oligo conjugates are composed of an oligo-type schema (RNA or DNA) and a molecule-type schema. One example use-case is for ASOs.

Oligo duplexes

Oligo duplexes are composed of two oligo-type schemas (RNA or DNA) and a molecule-type schema. One example use-case is for siRNA. 

Configuring oligo conjugates/duplexes

Oligo conjugates and oligo duplexes are built to provide additional structural configuration fields that allow for visualization of the components of the complex entity.

Before configuration is possible, reach out to Customer Support or your CX representative to enable the oligo conjugate/duplex features in your desired environments. We recommend configuring and testing in a Test or Dev tenant before transitioning to Production.

Please note, modeling conjugate attachments requires the Chem Awareness features. Again, reach out to your CX representative to confirm you have the functionality required. 

Schema Creation

To configure an oligo conjugate or duplex Schema: 

1. Navigate to the Registry Settings and create a new entity schema
2. Select Custom Entity from the Entity type dropdown
3. Check the Configure as a complex polymer box 

4. Select the appropriate sub-type (oligo conjugate or oligo duplex)

5. Define the Structural configuration
   1. Select the allowed schemas for the backbone(s) and components 
      1. Note: The schemas you select here control the subset of entities that you can use in a complex polymer entity. Currently only molecule and oligo schemas can be selected for the components, and multiple can be selected on one complex polymer schema.
   2. For an oligo duplex, define two backbone schemas.  
6. Add any additional fields to your schema
7. Click Create
   1. Note: Upon creation of your complex polymer schema, the schemas selected for the backbone and conjugate(s) will automatically display as computed fields on your complex polymer schema.

❗️Note: The Entity type, sub-type, and Structural configurations can not be modified after creation at this time.

For more information on how to create oligo duplex and conjugate entities, see Creating oligo duplex and oligo conjugate entities.