How Benchling helps scientists track and organize RNAi design during therapeutics R&D

Kyrstin Lou Ward

With a growing number of companies developing RNA-based therapeutics, teams need tools that can speed their workflows and increase efficiency to get to market faster than the competition. Benchling gives scientists that edge with fit-for-purpose capabilities that streamline RNAi design and simplify the process of iterating through design-assessment cycles.

Get everyone speaking writing in the same language

One task that can take a surprising amount of time is the simple act of accurately and concisely communicating the structure of each RNA molecule. It’s not uncommon for organizations to lack a  clear standard for indicating the type and exact location of chemical modifications in each RNAi design. In these cases, many scientists, labs, and vendors end up developing their own notation systems. Translating all of these  unique notations into a commonly understood language to share insights and order oligos can take valuable time out of a scientist’s day. In addition, every manual translation event is an opportunity to inadvertently introduce errors, leading to production of the wrong molecule.

Fit-for-purpose tools streamline RNAi design and modification

With Benchling’s Molecular Biology application, scientists can easily design and modify oligos with complex chemical modifications through an intuitive user interface.

RNA entities are represented using the increasingly popular HELM notation system, which standardizes sequence design and ensures sequence and naming uniqueness during registration. What’s critical to understand about this system is that each ribonucleotide is described by three entities that are called “monomers” in HELM—the base, the sugar, and the phosphate group (Figure 1).


Figure 1. In HELM notation, a ribonucleotide is described by three monomers, the phosphate group, the sugar group, and the base.

In Benchling Molecular Biology, you can build a sequence of standard ribonucleotides as well as ribonucleotides with modifications on any of the three monomers using simple dropdown menus (Figure 2).

Dropdown menus are populated from a centralized prebuilt monomer library that is accessible to all relevant users designing sequences, and it can be further customized to meet organizational needs. This not only secures institutional knowledge but also ensures information is disseminated and used across the organization in a consistent manner.


Figure 2. Each ribonucleotide can be modified using entities loaded from a custom or pre-existing monomer library.

In Figure 2 you can see the rich user interface which separates information about the monomer, sequence, and entity into different nested windows, also called “modals”. This visual organization makes it easy to quickly find relevant information by keeping conceptually similar items in the same window.

Automation enhances efficiency

Benchling also enables high-throughput, automated RNAi design and modification with REST APIs. With Benchling Molecular Biology, you can design or modify oligo sequences with HELM syntax in a high-throughput manner. Leverage API endpoints to list out specific modified oligos, create modified oligos, or update modified oligos via HELM.

Effortless translation facilitates oligo ordering and internal/external collaboration

Another advantage of using Benchling for RNAi design and modification is the ability to quickly convert HELM notation into IDT notation and vice versa for easy oligo ordering. The Benchling team can work with your team to support additional custom notation formats.

Find oligo information and experimental data quickly and easily

By bringing RNAi design into Benchling, you get all the advantages of our industry-leading unified informatics solution for RNA therapeutics R&D.

Search that’s sensitive to chemical modifications

One of the strengths of standardizing on HELM notation is that it enables users to search for specific oligos that differ by chemical modification. Benchling’s advanced search functionality, including sorting and filtering options, lets you quickly find oligo sequences, improving overall transparency and accessibility across teams with just a few clicks.

Registration that’s sensitive to chemical modifications

In addition to a better search experience, you can reduce duplicative efforts at the registration step. As you may expect, registering identical oligos will return a “duplicate entry” message, but to be identical, the oligo must have the same sequence and chemical modifications. In Benchling, oligos with the same sequence but different chemical modifications will not return a duplicate entry message.

Centralized and interlinked data with oligos and robust visualization tools ensure insight generation from any viewpoint

Benchling improves data traceability and makes it easier to track the experimental history of an oligo sample. Automatically link key data related to an oligo entity such as inventory location, pertinent experiments, sequence history, and associated analytical results.

You can also leverage Benchling’s in-platform visualization tools to extract insight whether you start with oligo structures, assay type, or any other viewpoint. Benchling makes it easy to aggregate data so you can save time and avoid tedious, error-prone cut-and-paste tasks.

Accelerate RNA therapeutics innovation with Benchling


Benchling gives RNA therapeutics R&D teams intuitive, fit-for-purpose informatics tools that can drive efficiency, standardization, productivity, and collaboration. Check out the webinar "Design, analyze, and develop RNA therapeutics on Benchling" to see some of our RNA-specific capabilities in action, and be sure to contact us if you have any questions about how Benchling can drive your RNA therapeutics R&D.

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