Adapting Lab Courses for Virtual Learning on Benchling

A practical guide for instructors

Problem-Based Learning Module: The Basics of Primer Design for PCR

Primer design and PCR are two essential skills taught in every molecular biology lab course. Benchling helps students learn how to design primers and model PCR in a way that emulates what they would do experimentally. In this example, we’ll describe how your students can employ the primer design tools in Benchling to isolate a gene of interest from a model organism given a sample of DNA. Lessons like this produce specific, accessible deliverables from students that allow you to identify gaps in their understanding.

Student Learning Outcomes

  1. Design primers effectively and in real-time

  2. Utilize secondary structure analysis of primers as a design principle

  3. Standardize primer design using robust software calculations

  4. Simulate PCR and analyze PCR products

  5. Capture and record every step of this scientific workflow

Getting This Module Started on Benchling

  1. Create a research prompt where teams of 2-4 students investigate how to isolate a particular gene from an organism. Ensure that the organism’s genome can be imported or is already uploaded to Benchling’s database.

  2. Assign each team a different gene and challenge them to obtain the DNA sequence into Benchling from a method of their choosing.

  3. Populate Notebook templates for students and have them follow a set of tasks. For instance, ask students to gather information on their gene of interest such as (1) accession number, (2) gene context / biological pathway, and (3) sequence length.

  4. Ask students to manually design primer pairs that would isolate their specific gene from genomic DNA if they were using PCR.

  5. Ask them to tabulate primer properties and secondary structure prediction values from Benchling in a Notebook entry.

  6. Finally, have them simulate PCR, describe how to analyze PCR products on a gel, and deposit the final PCR products along with their primer pairs as sequences for you to review or grade.

Tools and Analysis within Benchling

  • Secondary structure prediction for nucleotides (homo- and mono-dimers)

  • Automatic primer design based on the Primer3 wizard

  • Drag-and-click / manual primer design

  • Thermodynamic parameters and nucleotide properties (GC content, length, melting temperature)

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