Adapting Lab Courses for Virtual Learning on Benchling

A practical guide for instructors.

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Inquiry-Based Learning Module: Investigating Molecular Cloning Methods

Molecular cloning is a critical foundation for modern biology education, but the various methods are often taught through rote memorization rather than practice. In this module, we’ll discuss a virtual lesson that motivates students to learn by doing.

Student Learning Outcomes

1 / Understand design principles and considerations for molecular cloning

2 / Learn how to obtain and import sequences from external databases

3 / Extract protocols from reagent manufacturers

4 / Identify trade-offs between each method of cloning of this scientific workflow

Getting This Module Started on Benchling

  1. Create a list of molecular cloning techniques that you will have students choose from. For this example, we’ll use the three strategies of restriction, Gibson, and Golden Gate cloning, all of which are natively supported on Benchling.

  2. Arrange students into groups of six, and then into pairs. Each pair should be assigned a different cloning technique to investigate.

  3. Provide a model insert for each group to use, but have them determine a suitable backbone vector to use. Have each pair find a suitable vector on a database like Addgene and have them import it into Benchling.

  4. Task each pair to use their respective cloning strategy to design the desired construct (manually and/or by using Benchling’s Assembly Wizard). Have them find and attach experimental protocols from established reagent.

  5. Ask every pair to show other members of their group how they designed and generated their construct on Benchling.

  6. The entire group should evaluate one another’s methods, discuss the pros and cons of each method, and recommend situations where each method would be appropriate.

  7. Evaluate your entire class by giving them a new, standard set of inserts and vectors where they’ll utilize each cloning method to generate constructs for assessment.

Tools and Analysis within Benchling

  • Sequence visualization and annotation for manual cloning

  • Restriction cloning assembly wizard with primer design to incorporate restriction sites

  • Gibson cloning assembly wizard with primer design to add sequence complementarity

  • Golden Gate cloning assembly wizard with primer design for including BsaI sites


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