Biomod/2011/Harvard/HarvarDNAnos:Presentations

Presentations

2011-08-11

Given at Yin Lab Meeting

Notes [taken by Adam]:

1. for future presentations, you have much better afm images of gel-purified open spheres now -- make sure to include those when you introduce open spheres
2. no need to include AFM images for failed sphere closings
3. great description of the situation re possible things the locks can do
4. william and peng suggest reducing the entropy of the open sphere state to make it easier to close again: "partially open sphere"
5. asymmetric lock design: one side is 24 bases one is 8, for instance
6. there's a lot of emphasis on adding lock in one-pot with the sphere -- but the more important scenario is really a 2-step closing where you add lock to purified open sphere... so let's focus more on that
7. we should put magnesium in the PAGE gels in the future -- definitely we're getting some hybridization as it is, but it might be a lot better with Mg2+
8. TEM images of open spheres that Nick showed are very unlikely to actually be spheres - nice TEM image, but not spheres... :) so let's not include those
9. adding more sodium to the nanoparticles might be fine -- the Na+ outcompetes the Mg2+... the fact that both have positive charge kind of does not matter
10. no need to include much about the first Evan/Tom box -- let's just talk about Wei's box modification -- but I like how you presented this
11. nice description of Wei's box concept -- for acknowledgement you can just put on the slide, in big text, "Modified from design by Wei Sun (Yin lab, Harvard)"
12. actually there are pretty big differences between your box design and Wei's -- the main similarity is just the basic concept
13. the lids on back, lids on side thing is probably some funky artifact of the grids or something ... ?
14. opening closed boxes: awesome!
15. photocleavage: awesome! this is a very versatile motif.
16. attaching gold to lids slide: I really don't think those are lids :) -- probably just water spots
17. generally this gold to lids slide does not make sense -- you guys need more data on this attachment process in order to be able to say something conclusive

2011-07-14

Given at Yin Lab Meeting: Media:11-07-14 Yin Lab Mtg Presentation Complete.zip

Notes:

• Wei: 12.5 mM MgCl2 is not enough for 3D origami
• Shih: Recommends running a not-2% agarose gel of boxes to see if the box band and M13 scaffold just happen to run at the same rate in 2% agarose

2011-06-23

Given at Yin Lab Meeting: Media:11-06-23 Yin Lab Mtg Presentation Complete.pptx

Notes:

• thiolated nanoparticle strand needs to be distinct from the disulphide strand (to allow conjugation to gold without breaking the disulphide - gold itself can competitively reduce disulphides)
• use something other than DTT to cleave disulphide bonds if you want to NOT also cleave the thiol bond to gold
• box foldings with AuNP cargo should be 2-step not 1-step
• linking of 5' S-S strand directly to gold particle works with high efficiency. we have one of these for the 15-mer, but it is short, so gel separation won't be good. still, we can try it.
• look into conditions necessary for restriction enzyme activity and the two other options (i forgot the names) that were suggested that could cleave downstream of a recognition sequence given that peng thought we would need about ten bases of pre cutexcess (which is a lot more than I expected)
• caged DNA instead of azobenzene: impractical this summer since we have the azobenzene strand already
• use Type II restriction enzyme which is an "offset cutter" to cut close to origami while keeping cut site a reasonable distance away from the origami