User:JeffreyLau/Notebook/2006-6-20

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Morning

  • Hetmann and I made glycerol stocks of our two R0010 + E0241 cultures from yesterday.
    • 100 µL 50% glycerol, 100 µL liquid culture
  • Hetmann and I made minipreps of our two cultures, following the Qiagen protocol.
  • Hetmann and I digested (with Xba and Pst1) our two R0010 + E0241 cultures from yesterday.
    1. Mix the following in each of the two tubes:
      • 8 µL DNA
      • 0.5 µL Xba + 0.5 µL Pst1 + 1 µL
        • 2 µL from a stock of 1 µL Xba + 1 µL Pst1 + 2 µL dH20
      • 0.25 µL BSA + 0.75 µL dH20
        • 1 µL from a stock of 1 µL BSA + 3 µL dH20
      • 2.5 µL buffer 3
      • 11.5 µL dH20 to bring the total volume to 25 µL
    2. Incubate at 37C for 1 hour (in reality, we incubated for about 4 hours since we broke for lunch and I went to a long meeting afterwards).

Afternoon

  • Several of us (David, Tiffany, Matt, Valerie, Katie, Lewis, and I, IIRC) had a meeting with Shawn to discuss designs for our DNA nanostructure.
    • Note: DNA helix width 2nm, helical turn every 3.4nm (10.5 bp). DNA gets floppy when longer than 50nm (~150bp).
    • We settled on a simple honeycomb cylinder, since we have high confidence we can make it, and it's not obvious which designs will perform better than others. At present, we will not design a honeycomb cube or a flat cube.
    • The biggest remaining challenge is to design the lid.
  • I made e-gels of Hetmann's and my digests. They didn't turn out very well (lanes 8 and 9). Now that I look back at my digest protocol, I realize that I forgot to heat shock our digests for 15 min at 80C.
    1. Combine 10 µL of each digest with 10 µL of dH20
    2. Insert into e-gel wells
    3. Run e-gel for 30 min
    • Results:

Image:Digest 6-20-06.jpg

  • I spent the rest of the day designing nanostructures with David, Tiffany, Matt, Katie, and Lewis. We made two designs based on a honeycomb cylinder: a large cylinder with two single-ply lids and a smaller cylinder with two double-ply lids. Our figures are written on the whiteboard in the 5th floor breakroom; I'll write them down tomorrow if no one else recorded them.
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