Create your dream dynamic DNA nanostructure
Description:
The goal is to have the theoretical and practical basis to develop DNA nanostructures that can move in the nanoscale with high precision.
We will replace some of the literature reading by implementing tutorial videos on software use and related small activities/projects, to get hands on with the software. (e.g. use of CADNANO for designing a DNA nanostructure with an smiley face or NUPACK for designing molecular computers).
Intended Learning Outcomes:
- Understand the principles of DNA nanotechnology self-assembly and dynamic behavior
- Get hands-on experience with design software
- Create a DNA (dynamic) nanostructure
| Resources | Tasks | Supports | |||
|---|---|---|---|---|---|
| ← |
Software (CADNANO) video tutorial |
← |
Download the software and install the proper scripts. Watch video tutorial |
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Forum for peer/teacher feedback |
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Lecture (45 min) + quiz and discussion |
Understand the theoretical basis of DNA origami design ↓ |
← |
feedback and flip classroom exercise/quiz based on literature |
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|
step-by-step protocol/guide for the DNA nanostructure |
Design a DNA origami with a smiley face using CADNANO (30-45 min) ↓ |
← |
Forum for peer/teacher feedback |
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|
Lecture (45 min) + guided quiz |
Solve problems of strand displacement reactions and toehold design (quiz) ↓ |
← |
In-class group activity with peer feedback and teacher support |
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Software (NUPACK) video tutorial (30 min) |
Watch video and design two DNA strand displacement reactions (15-30 min) ↓ |
← |
Forum Q&A with peer and teacher feedback |
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Own -out-of-class work which will be evaluated in-class with a general discussion involving peers and teacher with 15% of the grade |
Create a dynamic DNA nanostructure blending CADNANO AND NUPACK software tools. |
← |
Forum Q&A with peer and teacher feedback to support out-of-class work |
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Additional information
The idea is that:
1)students play around and get hands on experience with the software,
2) engage in an interactive task
3) apply the theory and concepts from the course to create a DNA nanostructure with dynamic function.
Feedback with peers and teacher will be constant through forums and in-class activities. Flipping classroom activities where students present their designs will be also implemented.
My role will be to moderate discussions and re-introduce (summarize) concepts that has been learned in lectures or out-of-class activities. Moreover, I will evaluate the different projects and selected ideas will be put together for future master research projects if students are interested in developing them