Given at Yin Lab Meeting
Notes [taken by Adam]:
- 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
- no need to include AFM images for failed sphere closings
- great description of the situation re possible things the locks can do
- william and peng suggest reducing the entropy of the open sphere state to make it easier to close again: "partially open sphere"
- asymmetric lock design: one side is 24 bases one is 8, for instance
- 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
- 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+
- 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
- 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
- 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
- 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)"
- actually there are pretty big differences between your box design and Wei's -- the main similarity is just the basic concept
- the lids on back, lids on side thing is probably some funky artifact of the grids or something ... ?
- opening closed boxes: awesome!
- photocleavage: awesome! this is a very versatile motif.
- attaching gold to lids slide: I really don't think those are lids :) -- probably just water spots
- 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
Given at Yin Lab Meeting: Media:11-07-14 Yin Lab Mtg Presentation Complete.zip
- 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
Given at Yin Lab Meeting: Media:11-06-23 Yin Lab Mtg Presentation Complete.pptx
- 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