CRISPR as an Experimental Tool
Experimental Design domain · Lesson 10 of 20 · Biomedical Innovations (BI)
Today's goal: Students will explain how CRISPR-Cas9 edits a chosen DNA site using a guide RNA, and identify the two checks (sequence-verify the edit, search for off-target cuts) that make a CRISPR experiment trustworthy.
This is a model of the work you should turn in. Use it to check your own: match the structure and the level of detail, do not copy it. Your wording should be your own.
CRISPR experiment plan (proposed, instructor-designed, not a published result):
- Guide RNA target: the IRF6 regulatory site (the noncoding region that controls IRF6 expression).
- Intended edit: install the IRF6 regulatory risk variant at that site, steering the cell's repair to make the single intended change.
- Off-target check: search the genome for near-match sites the guide could also cut, and sequence those candidate sites to confirm they were not edited.
- Mosaicism check: sequence-verify the edited site in the animals and report the editing efficiency (the percent of alleles actually carrying the intended change).
- Rescue step: in a separate group, re-add the correct (non-risk) IRF6 regulatory sequence and check whether the cleft phenotype disappears, which is the strongest causal proof.
Why the mice clefted so the variant causes clefts is not yet safe: an off-target cut elsewhere could have caused the cleft, and mosaicism means the intended edit may not even be present in the right cells, so the conclusion holds only after both checks pass and the rescue closes the loop.
This model shows the level of evidence and organization needed to complete: A one-paragraph CRISPR plan with both trust checks and a rescue step.
- Identify the purpose, hazards, and required controls.
- Write the procedure in a usable order.
- Confirm materials, measurements, and waste handling before starting.
Keep the structure. Replace the question, facts, measurements, and evidence. Then recheck units, vocabulary, and whether the conclusion goes beyond the evidence.
Also due today: Label this plan as a proposed experiment, with IRF6 framed as the exemplar cleft gene under study, not Mateo's confirmed cause.
The finished product above did not appear all at once. Here is the path from the question to the turned-in work, so you can follow the same steps.
- 1Start from today's question: How do scientists make one planned change without trusting a cut in the wrong place?
- 2Work the Model and the Explore questions to reason it out before writing anything.
- 3Pull the specific evidence the product needs from the reading and any database you used.
- 4Write it up in the required format: Write a one-paragraph experiment plan to test whether the IRF6 regulatory risk variant can contribute to clefting in a mouse, naming the guide RNA target, the intended edit, one check, one mosaicism (sequence-verification) check, and the rescue step, then explain why the mice clefted so the variant causes clefts is not yet a safe conclusion.
- 5Check it against the rubric, then submit.
| Criterion | Proficient | Developing | Beginning |
|---|---|---|---|
| Complete | Every required part of the artifact is present and filled in. | Most parts are present, but one is missing or left blank. | Several parts are missing. |
| Accurate | The science and data are correct and match the evidence. | Mostly correct, with a small factual slip. | Key science or data is wrong. |
| Scientific reasoning (CER) | States a claim, backs it with specific evidence, and explains the reasoning. | Has a claim and evidence, but the reasoning is thin or missing. | Gives an answer with no evidence or reasoning. |
| Professional communication | Clear, organized, and labeled the way a clinician or scientist would write it. | Readable but disorganized or missing labels. | Hard to follow. |
| Submitted | Turned in through the route named under Submit here and confirmed. | Turned in, but in the wrong place or unconfirmed. | Not turned in. |
- CompleteProficient: Nothing is left blank: the model fills every part of "Write a one-paragraph CRISPR experiment plan to test whether the IRF6 regulatory risk variant can contribute to clefting in a mouse, naming the guide RNA target, the intended edit, one off-target check, one mosaicism (sequence-verification) check, and the rescue step, then explain why the mice clefted so the variant causes clefts is not yet a safe conclusion.".
- AccurateProficient: Every number and claim matches the case evidence.
- Scientific reasoning (CER)Proficient: It names a claim, cites the specific evidence, and explains the reasoning, not just the answer.
- Professional communicationProficient: It is organized and labeled like a real chart note.
- SubmittedProficient: It would be attached to your class form or handed in, and confirmed.
One exam-style question that uses exactly what you practiced today. Try it before you reveal the answer, then read why each choice is right or wrong.
Tap an answer to see the full explanation. Nothing is recorded or graded.
It builds this reusable test skill: Identifying the checks that make a CRISPR result trustworthy.
- Name the concept or data pattern being tested.
- Cross out choices that violate that rule or the evidence.
- Justify the best remaining choice before checking the answer.