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| =Meeting #1 (4/25/12)=
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| == Readings ==
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| <br> Challenges and opportunities for structural DNA nanotechnology [http://www.nature.com/nnano/journal/v6/n12/abs/nnano.2011.187.html]
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| <br> Dynamic DNA nanotechnology using strand-displacement reactions [http://www.nature.com/nchem/journal/v3/n2/full/nchem.957.html]
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| <br> Harnessing biological motors to engineer systems for nanoscale transport and assembly [http://www.nature.com/nnano/journal/v3/n8/abs/nnano.2008.190.html]
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| == Brainstorm (bolded ideas spurred positive discussion about feasiblity): ==
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| <br>Competition is open to any ideas at molecular level
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| <br>Should be DNA related in the end for the presentation
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| <br>DNA/RNA can be much more useful than cells/proteins
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| <br>Anything done with simple proteins can be very huge though.
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| <br>People use DNA not because it’s the best but because it was just what was available
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| <br>Decide what exactly we want to do by mid or late May. Meet every week?
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| <br>Meet this time next week
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| <br>Cascade of boxes
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| <br>In vivo is potentially feasible
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| <br>Use logic and/or gates to self-assemble at high accuracy
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| <br>How did you decide on last year’s project?
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| <br>Box on chalkboard
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| <br>Ian
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| <br>Use DNA to hook proteins together?
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| <br>Assembly within a cell?
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| <br>Nanoparticle assembly with help of DNA?
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| <br>Pop up assembly?
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| <br>Plate gridded DNA with nanoparticles? Semiconducting? Model after graphene?
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| <br>Pathogen filter?
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| <br>Use the accelerated high-throughput evolution to create bacteria that can make DNA for you.
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| <br>Use phages
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| <br>Use bacteria
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| <br>Use mages - use sixty-base DNA and put into cells.
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| <br>Replaces some of the okazaki fragments
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| <br>Pierce
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| <br>Use an interior red flag with fluorescent tag that shows when assembly failed?
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| <br>Separate bad ones with filter?
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| <br>Magnetic nanobeads? Use them? Or use them to speed up assembly?
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| <br>UV crosslinking as a new method for DNA origami?
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| <br>Potential damage
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| <br>We want them to assemble complementary though
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| <br>Make buckyballs out of DNA?
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| <br>Use DNA AND RNA together?
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| <br>ATPase + DNA = robot?
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| <br>How do you make it?
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| <br>What does it do?
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| <br>Use DNA nanostructures for sequencing? Somehow?
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| <br>Biosensors?
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| <br>Nanopores/protein pores for sequencing?
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| <br>Attach magnet to DNA nanocargos and use a super magnet above patient to localize only around tumors
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| <br>What is the crucial capability that we can add?
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| <br>Top-down construction/deconstruction
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| <br> Mingjie - not our field's advantage
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| <br>Nanopores
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| <br>Use DNA boxes to eat bacteria
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| <br>Make perpetual loop cascade
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| <br>Problem of error
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| <br>Need to add stuff to keep powering... use ATP?
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| <br>Magnetic tracks for DNA robots?
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| <br>Use cloud computing to screen for dynamics of crosstalk
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| <br>Spear cells
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| <br>Gina
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| <br>PRINT DNA structures
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| <br>Good for making libraries
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| <br>Wesley
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| <br>DNA walkers - what’s the application?
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| <br>Can we use enzymes?
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| <br>ATP?
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| <br>Light?
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| <br>Electricity?
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| <br>The nice thing is that they are programmable
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| <br>But the main drawback is that they are very, very slow
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| <br>Can we speed it up?
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| <br>Can we use heat?
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| <br>We are talking about often is DNA replication
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| <br>Rate limiting step is often the biased random walk
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| <br>Temperature-mediated walk based on how similar the DNA strands are
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| <br>Problem is that it isn’t sustainable
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| <br>Valentina
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| <br>Artificial immune system
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| <br>Can we do stuff in the cell?
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| <br>How do we measure the success of our final outcome?
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| <br>Concretely: Can we see technically correct outcomes?
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| <br>How do we know it actually worked?
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| <br>Imaging neurons in a zebrafish - any applications?
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| <br>Mark
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| <br>Nanobots
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| <br>Some scientists made a computer that would play tic tac toe with RNA
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| <br>Ian
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| <br>Interfering with the mRNA found in cancer cells
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| <br>Valentina
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| <br>How do DNA computers work?
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| <br>Logic
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| <br>Ian
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| <br>Using stochastic motion to power DNA nanorobots
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| == Conclusion==
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| <br>Next time, come with five or six big ideas
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| <br>Come up with four good ideas
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| <br>Pros
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| <br>Cons
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| <br>What do you think is the most difficult part?
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| <br>Then come up with ten really bad ideas and explain!
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| <br>Can we read a few more reviews because they really help catalyze ideas?
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| <br>Shawn’s nanorobot paper
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| <br>Wikipedia articles
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| <br>Meet next week and present
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