Benchling Educator Resources are an ever-growing collection of practical, tried and tested resources created on Benchling and shared by educators. You’ll find varied and exciting approaches to incorporating Benchling into worksheets, lab classes, online and in-person teaching.

New to Benchling?

If you or your students are new to Benchling, we suggest you start here, to get familiar with the look and feel of Benchling and find out more about the range of tools available.

You can learn more about how to set up and organize your course on Benchling by checking out our Training Kit for Educators.

Self-serve molecular biology lessons

We don’t want you spending your time helping students get up to speed with Benchling. Instead, we have put together a collection of self-guided molecular biology lessons for your students to work through at their own pace.

By moving through these simple worksheets, students can be prepared for labs before they arrive, and actively enhance their learning and understanding of practical molecular biology.

Use these worksheets to:

  • Run effective pre-labs for your students before class

  • Help run more of your course asynchronously or online

  • Encourage more analysis and evaluation of lab protocols and data

  • Reflect on their predictions and results in Notebook

  • Create new experiments

  • Prepare your students to use genuine tools from the research community

Here are some simple ideas for adapting and extending the concepts from each of our worksheets - but you should take and adapt these resources in any way you want.

1. PCR and Primer Design

Pre-lab exercises

  • Ask your students to evaluate a range of primers ahead of the class, write protocols and make predictions on the PCR product size that will be produced

  • Compare predictions to recorded gel bands

  • Introduce students to primer design tools using Benchling’s inbuilt Primer Wizard

Post-lab exercises

  • Incorporate their predictions and results in Notebook

  • Encourage reflection: assess the quality and analysis of their data, the implementation of their protocols, self-assess the structure of their notes.

2. Gel Electrophoresis and Restriction Enzymes

Pre-lab exercises

  • Choose the ‘right’ restriction enzyme for a practical or computational exercise

Post-lab exercises

  • Reflect on any key differences between virtual and real gel electrophoresis e.g. band intensities and DNA size

  • Provide a structured notebook for students to copy including key questions, reflection points or learning outcomes you want them to focus on.

  • Notebooks can be exported as pdfs if you want students to hand in results

3. Molecular Cloning Methods

Design an insertion from a PCR product

  • Use the primer design functions on Benchling (see here) to make primers which include restriction sites for unidirectional cloning.

  • Note: Remember to encourage students to base primer conditions on the template binding portion of the primer and to add 6 bases upstream of the restriction site to optimised digestion with most enzymes.

Design a strategy that uses Type IIS scarless restriction enzymes

  • Examples include BsmBI and BsaI

  • Encourage students to check that these restriction sites have been removed from final assembly constructs.

Correct a mistake in a planned cloning strategy

  • Provide the sequences for a cloning strategy but include a deliberate mistake in the cloning protocol in the accompanying Notebook. Ask students to fix this plan so the cloning will work

Examples could include

  • Incorrect orientation of an insert

  • Primers that do not capture the correct gene region

  • Non-complementary sticky ends

  • Restriction enzymes that produce unintended extra cleavage points.

Multiple insert cloning

  • Many experiments might require a more complex setup than only inserting one sequence into a vector.

  • Use the Benchling assembly wizard to put two (or more) inserts into the correct orientation and assemble with the Backbone.

4. CRISPR Knockouts

CRISPR experiments in the lab can be cheap and highly effective laboratories for understanding fundamental concepts of genome editing and molecular biology

In-lab exercises

  • Students can design gRNAs or validate existing gRNAs against simple DNA sequences (plasmids or amplicons). Afterwards, they can incubate Cas9, template DNA and gRNAa and run gel electrophoresis to check for cutting.

  • Take this further by designing CRISPR-Cas9 mediated editing of E.coli like here

In silico analysis and design

Interested in other ways to transform your class with Benchling? Check out our Virtual Laboratory Course Guide.

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