Genetic Scissors in a Beer Vat
How Undergraduates Are Editing Yeast DNA with CRISPR
In a groundbreaking shift from textbook diagrams to real-world lab benches, multi-week undergraduate courses are now employing baker's yeast as a simple, safe, and powerful model to teach the principles of CRISPR.
From Classroom to CRISPR Lab
Imagine having a word processor for DNA—a tool that lets you find a specific gene in a living organism and rewrite it with precision. This isn't science fiction; it's the reality of CRISPR/Cas9, a revolutionary technology that has transformed genetic engineering.
This exercise demystifies a complex technology, turning students from passive learners into active genetic editors. Let's dive into how a classroom of undergraduates can perform genetic surgery on a microscopic fungus.
Gene Editing
Precise modification of yeast DNA
Hands-On Learning
Multi-week laboratory experience
Undergraduate Focus
Designed for student researchers
What is CRISPR/Cas9? The Molecular Scalpel
At its heart, CRISPR/Cas9 is a bacterial defense system that scientists have co-opted into a programmable gene-editing tool. Think of it as a pair of "molecular scissors" that can be guided to a specific location in a vast genome.
This is a protein enzyme that acts as the cutting tool. It can snip both strands of the DNA double helix.
This is a small piece of RNA whose sequence is designed to be complementary to the specific gene you want to edit.
Once the DNA is cut, the cell's natural repair mechanisms kick in. Scientists can exploit these repair processes to disable a gene or even insert a new piece of DNA . This is the core concept that students master in the lab.
The Student Experiment: Knocking Out the CAN1 Gene
One of the most effective and visually striking experiments for students is to "knock out" a specific gene in yeast. A popular target is the CAN1 gene.
What is CAN1?
This gene produces a protein that allows yeast to import a toxic amino acid analog called canavanine from their environment.
The Goal
By using CRISPR/Cas9 to disrupt the CAN1 gene, students create mutant yeast cells that are resistant to canavanine. This resistance provides a clear, selectable marker for success .
Experimental Design Overview
A Step-by-Step Guide to Undergraduate Gene Editing
This multi-week lab is a journey in precision and patience. Here's how it unfolds:
Week 1: Design and Preparation
Students design a gRNA sequence that is unique to the CAN1 gene. Using bioinformatics tools, they ensure the sequence will guide Cas9 only to that location and nowhere else. They then assemble the CRISPR/Cas9 system inside a plasmid (a small, circular piece of DNA) that can be inserted into yeast cells.
Week 2: Transformation
This is the "gene surgery" day. Students take their baker's yeast and use a chemical process to make the cells' walls porous. They then introduce the CRISPR/Cas9 plasmid into the yeast cells. This process is called transformation.
Week 3: Selection and Observation
The transformed yeast are plated onto two different types of agar plates to grow:
- Control Plate (No Canavanine): All living yeast cells should grow here, confirming the transformation process didn't kill them.
- Experimental Plate (With Canavanine): Only yeast cells with a successfully edited (knocked-out) CAN1 gene will survive and form colonies.
Week 4: Analysis and Confirmation
Students count the colonies on each plate to calculate editing efficiency. They then perform a PCR (Polymerase Chain Reaction) to amplify the DNA around the CAN1 gene from a few surviving colonies and send it for sequencing—the gold-standard proof that their genetic scissors worked as intended .
Laboratory Tools and Materials
| Research Reagent / Material | Function in the Experiment |
|---|---|
| Guide RNA (gRNA) Plasmid | A circular DNA vector that carries the genetic code for the custom gRNA, the "GPS" that targets the CAN1 gene. |
| Cas9 Plasmid | A circular DNA vector that carries the code for the Cas9 protein, the "scissors" that cuts the DNA. |
| Baker's Yeast (S. cerevisiae) | The model organism; safe, easy to grow, and has a well-mapped genome, making it perfect for teaching. |
| Canavanine Agar Plates | The selection media. Only yeast with a successfully knocked-out CAN1 gene can grow on this toxic substance. |
| Lithium Acetate (LiAc) | A chemical used in the transformation process to make the yeast cell walls permeable, allowing the plasmids to enter. |
| PCR Reagents | The "DNA photocopier." Used to amplify the targeted region of the CAN1 gene from edited yeast colonies for sequencing. |
Results and Analysis: Reading the Genetic Receipt
The results are tangible and thrilling for students.
Colony Growth
The appearance of robust colonies on the canavanine plate is the first exciting sign of success. It visually demonstrates that they have altered the yeast's genetics.
Efficiency Calculation
By comparing the number of colonies on the canavanine plate to the control plate, students can calculate the transformation and editing efficiency.
Sequencing Proof
The DNA sequencing results provide the ultimate confirmation, showing a messy sequence or clear deletion at the exact spot where Cas9 cut.
Example Student Data for CAN1 Gene Knockout
| Plate Type | Number of Yeast Colonies | Interpretation |
|---|---|---|
| Control (No Canavanine) | ~500 colonies | Indicates a healthy number of yeast cells survived the transformation process. |
| Experimental (+ Canavanine) | ~50 colonies | These are the successful gene-edited mutants. They can grow because the CAN1 gene is broken. |
| Editing Efficiency | ~10% | (50 colonies / 500 colonies) * 100 = 10% of the transformed cells were successfully edited. |
PCR Confirmation of Edits
| Yeast Colony Sampled | PCR Product Size | Sequencing Result | Edit Confirmed? |
|---|---|---|---|
| Colony 1 (from Canavanine plate) | Larger than expected | Indels* found at target site | Yes |
| Colony 2 (from Canavanine plate) | As expected | No change in sequence | No |
| Colony 3 (from Canavanine plate) | Smaller than expected | Large deletion found at target site | Yes |
Editing Efficiency Visualization
More Than Just a Lab
This multi-week exercise is far more than a technical procedure. It's a powerful educational experience that bridges the gap between abstract theory and tangible application. Students don't just read about CRISPR; they do CRISPR. They experience the challenges of experimental design, the anticipation of waiting for results, and the thrill of seeing direct evidence of their genetic handiwork.
They learn not only how to use these powerful tools but also to understand their profound implications, ensuring they are prepared to shape the future of genetic engineering responsibly.
Innovative Education
Bringing cutting-edge technology to undergraduate classrooms
Hands-On Skills
Developing practical laboratory and analytical abilities
Future Impact
Preparing students for careers in biotechnology and research