Pauls bootcamp notes

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1. AFM training. Are we going to bring them into the lab to play with our actual (ouch) instruments? Should we have Veeco come and demo an instrument? I would like them to demo a multimode with a nanoscope V so I could see how well that particular combination goes.... where would we actually set up the demo?
2. Lecture: Placement of DNA nanostructures on surfaces. Review of the state of the art from many groups.
3. Lecture: Combining DNA origami into larger structures. Review state of the art from many groups.
4. Lecture: Using caDNAno to design DNA structures.
5. Potential lecture: Adding biological sequences and protein interactions to DNA origami, custom DNA origami scaffolds.
6. Where is our lecture/lab space going to be?
7. How many days?
8. Potential lectures: (not paul) Practical side of DNA circuits in spectrofluorimeters, practical gels, etc.
9. Potential lecture: DNA/RNA thermodynamics theory, tools for computing
10. Potential lecture: DNA/RNA kinetics, tools for computing
11. Potential lecture: Compilation of circuits/complex systems, Part 1 on Hairpin pierce models, Part 2 on Winfree lab/Cardelli state of the art.
12. Guest lecturers? Luca Cardelli and William Shih?
13. If we are doing a week, each of the 5 MPP PIs can have one day for the lab activity. On the day of their lab activity, they give the lecture. Everyone does that activity that day. Then they get together in the evening and compare results. OK, this won't work. It won't scale because we don't have enough equipment for everyone to do any one activity on any given day. Let's consider AFM. We could reasonably expect 4-5 different people to mix up strands, anneal them, and do AFM in an 8-12 hour day.
14. Or maybe to allow everyone to do the activities, they can do them on different days. Maybe the first day is two parts: 5 lectures on the 5 activities that are going on during the week. Then people get scheduled on different days. In the afternoon of that day there are discussion sessions about whatever. Then for the next 5 days, there are morning lectures on whatever, the different aspects of molecular programming, but in the afternoons the different groups cycle through their different activities. Then on a final day after the 5 days are over, the groups get together, give presentations on what they learned at each of the different activities. If there are 5 groups and each group gives 12 minutes on each activity, then we are into 5 hours of presentations. During the week, at night, people analyze their data. Groups/students do not have to do all 5 projects that are available. They cannot do one all week because that would screw up the availability of instruments but depending on time they could go back. Perhaps there could be 4 different projects available, and on the 5th day students could go back to the project that they wanted to work on more/do data analysis. (This would also allow us to cut out 1 day if we only had 4 projects.)
15. Sample schedule:
16. Day 1: All 5 PIs give opening lecture on sample projects. Afternoon for students to think/digest their variations.
17. Day 2: Guest lecture in the morning / projects afternoon/evening.
18. Day 3: Guest lecture in the morning / projects afternoon evening.
19. Day 4: Guest lecture in the morning / projects afternoon evening.
20. Day 5: Guest lecture in the morning / projects afternoon evening.
21. Day 6: Guest lecture in the morning / projects afternoon evening.
22. Day 7: Morning students get ready for presentations. Afternoon presentations from groups doing the 5 different projects available, these are done in order or out, depending on how we feel, but at the end, PIs do wrap-ups talking about what the students "should have" taken

Rothemund lab project

Make origami with stacking bonds in some pattern. They get to pick the basic origami, rectangle, stacking V, or cross. Assemble in solution and on surface. See what the difference is. The experiment that they get to pick is what stacking bonds to put on the edges of the origami. Maybe also have some sticky end strands. Also choice of annealing schedule. Get back together in the evening to talk about what happened. Can use rectangular origami or triangular edge origami.

Concepts:

1. effect differences in annealing schedule---what is too fast? 0 min? 5 min? Can origami form at 37C? Etc.
2. effect of surface on origami assembly, dichotomy between bnods strong enough to form in solution and those strong enough to form on a surface.
3. Energetics of stacking bonds. What is an energy model for stacking bonds as a function of the number of helices?
4. What about the symmetry of stacking bonds? How does the major/minor groove break symmetry.
5. How does shape influence stacking bonds?