Biomod/2012/Harvard/BioDesign/SpringBrainstorming: Difference between revisions

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== Readings ==
== Readings ==


<br> Challenges and opportunities for structural DNA nanotechnology [http://www.nature.com/nnano/journal/v6/n12/abs/nnano.2011.187.html]
<br> A Logic-Gated Nanorobot for Targeted Transport of Molecular Payload [http://www.sciencemag.org/content/335/6070/831.abstract]
<br> Dynamic DNA nanotechnology using strand-displacement reactions [http://www.nature.com/nchem/journal/v3/n2/full/nchem.957.html]
<br> Organization of Intracellular Reactions with Rationally Designed RNA Assemblies [http://www.sciencemag.org/content/333/6041/470.short]
<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]
<br> Synthetic Biology Moving into the Clinic [http://www.sciencemag.org/content/333/6047/1248]
<br> A Tightly Regulated Molecular Motor Based upon T7 RNA Polymerase [http://www.cbp.pitt.edu/faculty/leuba/pdfs/pomerantz.pdf]
<br> Programming cells by multiplex genome engineering and accelerated evolution [http://www.nature.com/nature/journal/v460/n7257/full/nature08187.html]
<br> Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome [http://www.sciencemag.org/content/329/5987/52.abstract]


== Brainstorm (bolded ideas spurred positive discussion about feasiblity): ==
== Brainstorm (bolded ideas spurred positive discussion about feasiblity): ==

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Meeting #2 (4/29/12)

Readings


A Logic-Gated Nanorobot for Targeted Transport of Molecular Payload [1]
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies [2]
Synthetic Biology Moving into the Clinic [3]
A Tightly Regulated Molecular Motor Based upon T7 RNA Polymerase [4]
Programming cells by multiplex genome engineering and accelerated evolution [5]
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome [6]

Brainstorm (bolded ideas spurred positive discussion about feasiblity):

Conclusion

Meeting #1 (4/25/12)

Readings


Challenges and opportunities for structural DNA nanotechnology [7]
Dynamic DNA nanotechnology using strand-displacement reactions [8]
Harnessing biological motors to engineer systems for nanoscale transport and assembly [9]

Brainstorm (bolded ideas spurred positive discussion about feasiblity):


Competition is open to any ideas at molecular level
Should be DNA related in the end for the presentation
DNA/RNA can be much more useful than cells/proteins
Anything done with simple proteins can be very huge though.
People use DNA not because it’s the best but because it was just what was available
Decide what exactly we want to do by mid or late May. Meet every week?
Meet this time next week
Cascade of boxes
In vivo is potentially feasible
Use logic and/or gates to self-assemble at high accuracy
How did you decide on last year’s project?
Box on chalkboard



Ian
Use DNA to hook proteins together?
Assembly within a cell?
Nanoparticle assembly with help of DNA?
Pop up assembly?
Plate gridded DNA with nanoparticles? Semiconducting? Model after graphene?
Pathogen filter?
Use the accelerated high-throughput evolution to create bacteria that can make DNA for you.
Use phages
Use bacteria
Use mages - use sixty-base DNA and put into cells.
Replaces some of the okazaki fragments
Pierce
Use an interior red flag with fluorescent tag that shows when assembly failed?
Separate bad ones with filter?
Magnetic nanobeads? Use them? Or use them to speed up assembly?
UV crosslinking as a new method for DNA origami?
Potential damage
We want them to assemble complementary though
Make buckyballs out of DNA?
Use DNA AND RNA together?
ATPase + DNA = robot?
How do you make it?
What does it do?
Use DNA nanostructures for sequencing? Somehow?
Biosensors?
Nanopores/protein pores for sequencing?
Attach magnet to DNA nanocargos and use a super magnet above patient to localize only around tumors
What is the crucial capability that we can add?
Top-down construction/deconstruction
Mingjie - not our field's advantage
Nanopores
Use DNA boxes to eat bacteria
Make perpetual loop cascade
Problem of error
Need to add stuff to keep powering... use ATP?
Magnetic tracks for DNA robots?
Use cloud computing to screen for dynamics of crosstalk
Spear cells


Gina
PRINT DNA structures
Good for making libraries


Wesley
DNA walkers - what’s the application?
Can we use enzymes?
ATP?
Light?
Electricity?
The nice thing is that they are programmable
But the main drawback is that they are very, very slow
Can we speed it up?
Can we use heat?
We are talking about often is DNA replication
Rate limiting step is often the biased random walk
Temperature-mediated walk based on how similar the DNA strands are
Problem is that it isn’t sustainable


Valentina
Artificial immune system
Can we do stuff in the cell?
How do we measure the success of our final outcome?
Concretely: Can we see technically correct outcomes?
How do we know it actually worked?
Imaging neurons in a zebrafish - any applications?


Mark
Nanobots
Some scientists made a computer that would play tic tac toe with RNA


Ian
Interfering with the mRNA found in cancer cells


Valentina
How do DNA computers work?
Logic


Ian
Using stochastic motion to power DNA nanorobots

Conclusion


Next time, come with five or six big ideas
Come up with four good ideas
Pros
Cons
What do you think is the most difficult part?
Then come up with ten really bad ideas and explain!
Can we read a few more reviews because they really help catalyze ideas?
Shawn’s nanorobot paper
Wikipedia articles
Meet next week and present

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