Lesson Plan (Grades 9–12): CRISPR Gene-Editing Simulation – Modeling Precision Edits in Plant Genomes

Lesson Title: CRISPR Gene-Editing Simulation – Modeling Precision Edits in Plant Genomes

Grade Level: Grades 9–12

Subject Area: Biology (Molecular Genetics) / Bioinformatics / Biotechnology / Ethics

Overview CRISPR-Cas9 technology has revolutionized genetic engineering by allowing researchers to make precise, targeted changes in DNA. In agriculture, CRISPR holds promise for introducing traits like drought tolerance, pest resistance, and improved yield. However, it also raises concerns about off-target effects, ecological impacts, and ethical considerations. In this multi-part lesson, students will use a web-based bioinformatics platform to simulate CRISPR edits in a model plant genome (e.g., Arabidopsis thaliana). They will locate a drought-tolerance gene, design guide RNAs (gRNAs) to knock it out or insert beneficial alleles, predict off-target cleavage sites, and evaluate on-target efficiency. Finally, students will engage in a structured ethical debate on the responsible use of gene editing in crops. This inquiry-driven unit combines molecular biology concepts, computational skills, data analysis, and critical ethical reasoning.

Objectives and Standards

Learning Objectives

1. CRISPR Mechanism: Explain how the Cas9 nuclease and guide RNA form a ribonucleoprotein complex that recognizes a 20-nucleotide target sequence adjacent to a PAM (NGG) and induces a double-strand break.
2. gRNA Design: Use bioinformatics tools to identify target loci within the DREB1A drought-tolerance gene, design candidate gRNAs, and score them for on-target efficiency.
3. Off-Target Analysis: Simulate genome-wide alignment to predict potential off-target cleavage sites with up to two mismatches, and calculate specificity scores for chosen gRNAs.
4. Simulation of Edits: Model non-homologous end joining (NHEJ) knockouts and homology-directed repair (HDR) insertions, viewing before-and-after sequence chromatograms.
5. Ethical Evaluation: Critically assess the benefits, risks, and regulatory frameworks governing the use of CRISPR in crop improvement, articulating multiple stakeholder perspectives.

Standards Alignment

• Next Generation Science Standards (NGSS)
  • HS-LS1-1: Construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out essential functions of life.
  • HS-LS3-2: Make and defend claims based on evidence that inheritable genetic variations may result from new genetic combinations through meiosis and mutation, and from genome editing technologies.
• Common Core State Standards – Mathematics
  • HSS-ID.B.6: Represent data on two quantitative variables on a scatter plot and describe how the variables are related (e.g., gRNA efficiency vs. GC content).
• CSTA K–12 Computer Science Standards
  • 3A-DA-08: Use computational tools to analyze and interpret data sets, such as off-target site predictions.
• NGSS Crosscutting Concepts
  • Structure and Function: Relating gRNA sequence characteristics (GC content, seed region) to on-target binding and specificity.
  • Stability and Change: Balancing genome stability against desired edits for trait improvements.