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CUT! How Does CRISPR Work?

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Grade Range
Group Size
1-3 students
Active Time
3 hours 30 minutes
Total Time
3 hours 30 minutes
Area of Science
Genetics & Genomics
Genetic Engineering
Key Concepts
Gene editing, CRISPR
Svenja Lohner, PhD, Science Buddies
Schematic diagram of the CRISPR-Cas9 complex, showing the Cas9 protein, the guideRNA, and the cleaved target DNA.
Image credit: Marius Walter [CC BY-SA 4.0], Wikimedia Commons, 2017


In this lesson plan, students will take a closer look at the most recent developments in gene editing. Specifically, they will learn about the CRISPR technology using various interactive simulations and other resources. Based on their gained knowledge, students will create a model of the CRISPR-Cas9 components and create a stop-motion animation video of the molecular mechanism of CRISPR-Cas9.

Remote learning adaptation: This lesson plan can be conducted remotely. Students can work independently (individually or in virtual groups) to brainstorm, storyboard, and film using the Brainstorming Worksheet, the Storyboard Template, and the Grading Rubric for guidance. The videos can then be shared online on a class drive or classroom sharing apps like Flipgrid. The Engage and Reflect sections can either be dropped entirely, done individually remotely, or be conducted over a video chat.

Learning Objectives

NGSS Alignment

This lesson helps students prepare for these Next Generation Science Standards Performance Expectations:
This lesson focuses on these aspects of NGSS Three Dimensional Learning:

Science & Engineering Practices Disciplinary Core Ideas Crosscutting Concepts
Science & Engineering Practices MS
Developing and Using Models. Develop a model to describe unobservable mechanisms.

Developing and Using Models. Develop and use a model based on evidence to illustrate the relationships between systems or between components of a system.
Disciplinary Core Ideas MS
LS4.B: Natural Resources. In artificial selection, humans have the capacity to influence certain characteristics of organisms by selective breeding. One can choose desired parental traits determined by genes, which are then passed on to offspring.

LS1.A: Structure and Function. All cells contain genetic information in the form of DNA molecules. Genes are regions in the DNA that contain the instructions that code for the formation of proteins, which carry out most of the work of cells.
Crosscutting Concepts MS
Cause and Effect. Phenomena may have more than one cause, and some cause and effect relationships in systems can only be described using probability.

Science Addresses Questions About the Natural and Material World. Scientific knowledge can describe the consequences of actions but does not necessarily prescribe the decisions that society takes.

Structure and Function. Structures can be designed to serve particular functions by taking into account properties of different materials, and how materials can be shaped and used.

Structure and Function. Investigating or designing new systems or structures requires a detailed examination of the properties of different materials, the structures of different components, and connections of components to reveal their function and/or solve a problem.

Cause and Effect. Systems can be designed to cause a desired effect.


Materials needed for the 'CUT! How Does CRISPR Work?' lesson plan.

Background Information for Teachers

This section contains a quick review for teachers of the science and concepts covered in this lesson.

Reliable and inexpensive gene editing, used either to "fix" genetic defects in patients or to introduce genomic changes for further study in a research lab, is a much-desired technology. Since its development around 2012, CRISPR (short for clustered regularly interspaced short palindromic repeats) systems have gained recognition as powerful gene editing techniques. The resources and videos provided in the Additional Background section cover much of the information on how CRISPR works. CRISPR harnesses the natural immune system bacteria use to fight off viruses. The antiviral defense mechanism is based on the incorporation of DNA fragments from viruses into the bacterial DNA. This part of the DNA is called the CRISPR array. Within the CRISPR array, the acquired virus DNA fragments are separated by conserved short nucleotide sequence repeats (Figure 1). The bacteria can then use this acquired virus DNA to identify and defend themselves against new viral threats in the future.

 Schematic diagram of the CRISPR repeat-spacer array. Four orange boxes represent the repeats (conserved short nucleotide sequences) and the green lines between the orange boxes represent the spacers (virus DNA fragments) in  between the boxes.
Figure 1. Schematic view of a CRISPR repeat-spacer array.

Several different types of CRISPR systems have been identified, but the one most studied is the CRISPR-Cas9 system. In this system, the genes next to the CRISPR repeat-spacer array encode a unique defense mechanism consisting of a single-guide RNA and an endonuclease (Cas9), a protein that is able to cut double-stranded DNA. The single-guide RNA (sgRNA or gRNA) helps target the dangerous virus DNA, and the Cas9 endonuclease degrades foreign nucleic acids by inducing a double-strand break. The sgRNA contains one or more acquired CRISPR sequences from the CRISPR repeat-spacer array. In the event of a virus infection, the sgRNA combines with the Cas9 nuclease to build a sgRNA-Cas9 complex and guides it to the appropriate target in the virus DNA (Figure 2).

Because the CRISPR mechanism can cut anywhere in the DNA, the bacteria must protect its own DNA from being damaged. The PAM (protospacer adjacent motif) region is a short DNA sequence that is an essential targeting component that allows the bacteria to distinguish its own DNA from foreign DNA. The sgRNA will only adhere to and disable a DNA sequence that contains a PAM sequence nearby. The sgRNA locks onto the PAM sequence and starts unzipping the DNA double-strand to test if the sgRNA matches the target DNA. Once a matching sequence is found, the sgRNA binds to the target genomic site through complementary base pairing, and the Cas9 nuclease cuts the double-stranded virus DNA, inactivating the virus.

 Schematic diagram of the CRISPR-Cas9 complex, showing the Cas9 protein, the guideRNA, and the cleaved target DNA.
Figure 2. The single-guide RNA combines with Cas9 and guides the nuclease to the target within a double-stranded genomic DNA. The sgRNA locks onto the DNA target directly next to the required PAM sequence. If the sgRNA matches with the target DNA, the Cas9 nuclease cuts the DNA double-strand 3 base pairs upstream of the PAM motif. (Image credit: Marius Walter [CC BY-SA 4.0], Wikimedia Commons, 2017)

Researchers have now found a way to manipulate the nucleotide sequence of the sgRNA so the Cas9 system can target any DNA sequence for cleavage. Once the Cas9 nuclease cuts the target DNA, the cell's natural DNA repair mechanisms kick in. There are two main pathways within a cell that result in the repair of DNA double-strand breaks. The first pathway is the non-homologous end joining (NHEJ) pathway, which is error-prone and can lead to insertion or deletion mutations within the DNA. The second pathway is the homologous direct repair (HDR) mechanism, which allows for insertion of a specific DNA template (single or double-stranded) at the target site. Currently, the two most common applications of the CRISPR technology are the targeted mutation of specific genes resulting in functional gene knockouts, and the replacement of a gene variant with another. Both strategies harness the natural CRISPR mechanism. Knockouts and gene replacement have made it much easier to probe gene functions and establish causal linkages between genetic variations and biological phenotypes.

The CRISPR-Cas9 technology has been successfully used in bacterial and mammalian cells, allowing for the creation of transgenic animals with targeted mutations. Most CRISPR research has focused on treating diseases by introducing genetic changes into blood, lung, or brain cells. Researchers have high hopes that this technology will one day enable scientists to repair disease-causing gene variants in patients with certain genetic diseases. This approach is especially promising in diseases such as sickle cell anemia, cystic fibrosis, or Huntington's disease, each of which is linked to a single gene variant. In 2019, the first gene-editing clinical trials began, targeting patients with sickle cell anemia. In the future, CRISPR might also significantly impact agriculture and the environment, including their impact on human health. For instance, we may one day be able to modify crops to make them more drought- or pest-resistant, or eradicate disease-spreading insects such as mosquitoes.

Although genome editing brings significant potential benefits, it also raises profound ethical questions. What CRISPR safety standards are appropriate? Where are the limits of this technology? Does gene editing bring us closer to "designer babies"? What about potential genetic discrimination? How can we grant equitable access to gene editing technologies? In 2018, Chinese researcher He Jiankui claimed to have edited the genomes of two human embryos, which then developed into two human babies, highlighting the need for ongoing public discourse to address these fundamental ethical issues related to CRISPR.

Prep Work (15 minutes)

Engage (15 minutes)

Explore (165 minutes)

Reflect (30 minutes)


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