Teaching CRISPR-Cas9 Genome Editing Through Novel Research in a Multi-week Lab Module - 5-6 Week Lab Module

Oct 15, 2026

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CRISPR-Cas9 is presented as a transformative genome-editing approach for research, disease treatment, and crop development, making it essential for undergraduates to learn its principles and ethical use. The module describes a multi-week, independent-research–based laboratory experience where students design CRISPR-Cas9 constructs and perform genotype screening for novel knockout mutants. Students screen Zea mays seedlings for mutations in the MAD2 gene, supporting studies of meiotic chromosome segregation.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages7

Reading Time18 min

AccessFree to download

Introduction

CRISPR-Cas9 precision and targeting

Repair pathways and specificity

Lab module structure

Unit timeline and weekly activities

Teaching CRISPR-Cas9 Genome Editing Through Novel Research in a Multi-week Lab Module Natalie J. Nannas, PhD Department of Biology, Hamilton College, Clinton, NY 13323 | Abstract: CRISPR-Cas9 is revolutionizing how we conduct scientific research, treat disease, and develop new crops. The widespread impact of this genome-editing technology makes it critical for undergraduate students to understand and engage with this new tool. In this article, we describe a multi-week lab module that teaches undergraduates how to design CRISPR-Cas9 constructs and screen for CRISPR-modified genotypes. The module is conducted through the lens of independent research; students conduct a genotype screen for novel knockout mutations. In our module, students screen Zea mays (maize) seedlings for mutations in the MAD2 gene, which assists our ongoing investigation of meiotic chromosome segregation. This module can be adapted to knockout any gene in any organism, and thus align with an instructor’s research program. Engaging in original research helps undergraduate students develop independence and initiative in the lab as well as the molecular techniques of CRISPR-Cas9 .
Keywords: CRISPR-Cas9, sgRNA, vector, genotype screen | | | --- | --- | | Introduction
The revolutionary genome editing technology CRISPR-Cas9 is changing our world by providing new tools for scientific research, medicine and agriculture. The pioneers of CRISPRCas9 were recently awarded the Nobel Prize in recognition of its impact (Ioannidis et al., 2020) . The power of CRISPR comes from its precision; unlike previous techniques, CRISPR enables direct editing of the genetic code at one specific location in the genome. With this precision, scientists can delete, insert or modify any gene in any organism. This powerful tool is now a standard tool in the molecular toolkit for scientific experimentation (Adli, 2018) . The ability to use CRISPR is critical for students considering a career in the biological sciences. However, understanding the technology allows all students, regardless of career path, to participate in informed discussions of its ethical usage. This article describes a 5-6 week lab module that teaches undergraduate students how to use CRISPR by engaging them in a novel research project. The module is broken into five units, and each unit can be performed in a single 2-3 hour lab section (Table 1) .
The module will span five weeks if a unit is performed each week. We typically execute this module over six weeks, building in a buffer week after Unit 3 to allow students to troubleshoot and repeat failed protocols. This module was designed for our intermediate-level genetics course, Biology 248: Genes and Genomes, a course taken primarily by sophomores and juniors who have completed a pre-requisite introductory biology course. We have implemented and | iterated this module over three years with 40-60 students per year (lab sections of 20 students) .
The precision of CRISPR-Cas9 is based on complementary base pairing. Scientists can target a specific genomic location for modification by introducing a single stranded RNA molecule, called a single guide RNA (sgRNA) . The sgRNA is designed to complement the target DNA sequence; it scans the genome and anneals to the sequence like primers in a PCR reaction (Fig. 1A) . The sgRNA consists of two components, the crRNA (CRISPR RNA) and the tracrRNA (trans-activating CRISPR RNA) . The crRNA is approximately 20bp long and complementary to the target sequence (Fig. 1B) . The tracrRNA is 75bp long and contains a hairpin loop that binds Cas9 nuclease and recruits it to the target sequence (Fig. 1A) . While there are now multiple types of Cas9, the original nuclease creates a double-stranded DNA break. Cleavage occurs a few bases away from a specific sequence called PAM (proto-spacer adjacent sequence), a three base pair sequence, 5’-NGG-3’where N is any base (Fig. 1A) . Because NGG is only three bases long, there is a hi

FAQs

What learning outcomes does the multi-week CRISPR-Cas9 lab module target for undergraduates?

Students design CRISPR-Cas9 constructs and conduct a genotype screen for CRISPR-modified genotypes. The module is structured as independent research to build lab initiative and molecular technique skills.

How does the module explain CRISPR targeting using sgRNA and PAM?

It describes sgRNA base-pairing to a target DNA sequence and Cas9 cleavage near a PAM site, using 5’-NGG-3’ as the PAM example. Specificity is attributed to bringing Cas9 to one PAM sequence within the genome.

What organisms and gene are used as the example research project?

Students screen Zea mays (maize) seedlings for mutations in the MAD2 gene. The choice supports an ongoing investigation of meiotic chromosome segregation.

Oct 15, 2026

Upload by Bulrr