Biomod/2011/Harvard/HarvarDNAnos:LabNotebook Nick/2011/06/07

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 * style="background-color: #cdde95"|[[Image:owwnotebook_icon.png|128px]] Nick's Lab Notebook
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Tuesday (2011-06-07)

 * This morning I continued to work on my caDNAno file from yesterday, this time attempting to insure that all crossovers occurred after a minimum of 8 nucleotide lengths on any given helix (to insure stability). Given that this was nearly impossible, I decided to start again, this time designing a six-sided box with a hinged lid.
 * Later this morning, we made 2D rectangular DNA origami with materials already available in the Yin lab and attempted to photograph it on the AFM.
 * This afternoon we met with Tom and Wei, postdocs here in the Yin lab at the Wyss Institute. We discussed our initial box ideas and some new ones.  Here is what we learned/spoke about:
 * 1) For a five nanometer gold particle, the interior of any surface we design should have a diameter of at least 20 nm to account for a hydrodynamic shell present about the particle
 * 2) The m13 sequence (which we will be using for our origami) is 7,249 nucleotides long; any design we create in caDNAno should have a scaffold of no more than 7,249 nucleotides
 * 3) The possibility of designing a spherical "box" that could be opened along its equator
 * 4) The possibility of designing a box with a spring mechanism for opening a hinged lid