21.06.2012

• We have lab space ( 2 benches in B CUBE), we can also hang out there because they have a desk for us. Michael Schlierf already contacted a company with the funding. We should talk to the people of the Microscopy / TEM facility in BIOTEC, because these people know the companies very well and buy expensive equipments there… .
• GUV diameter is around 10 µm. In Schlierf´s lab they do LUVs with 100 nm -> which are stable
• Flat surface of the Origami after we induce the opening and get rid of the lid. Maybe have a little helix bundle as spacer between the surface so we have no sterical hindrance with the LUV,
• IDEA: If there would be a problem with the sterical hindrance of a stiff, flat Origami sheet we could add staples and linker strands which are longer and shorter in the middle.
• Tracking the opening of the DNA Origami: Using a quencher and a donor system which changes the fluorescence after conformational change, You can do up two colors. How would we stain Origami? Put in some fluorophores on staple strands, (10 fluorophores on the Origami, put them far away). There are Aptamers which can bind to ATP (we don´t expect to have ATP in our system) which seem to be pretty stable, they had to heat it up to 37°C, GC sequences which are usually more stable -> thermodynamically
• IDT: Online programme (Integrated DNA Technologies) is a quite good software to predict secondary structures … .
• Creation of LUVs with 100 nm can be in the range of 100 nm +- 20 nm;
• Problem of one LUV binding to several Origamis on a big GUV -> probably not an issue because of the curvature of the LUV,
• In the origami structure we maybe have to consider to use supporting strands which we get rid after the successful assembly of the structure.
• To find a proper aptamer we should go through the papers, and also look for papers who cite this paper (ATP Aptamer paper, which Michael gave to us),
• We want to use two Origami structures but there could be some problems:
• Because the dimensions need to fit really exactly, maybe we can use instead a single strand hinge and use the principle also used for the nanorobot (science
• Maybe the Origami is too complex, so we maybe should have a backup…just to attach an Origami to the GUV,
• Parallel approaches: Play with the Aptamer in solution if it binds correctly (characterizing it in experiments, identify it). How much does an aptamer with the fluorophores cost? Fluorophores order of 200 – 300 € , Order the DNA functionalized with a group and then attach the fluorophore using protocols already established in B CUBE.
• Bending of Origami is not 100 % controllable
• Papers about Aptamer:
  • “Structure-Switching Signaling Aptamers” – Razvan Nutiu and Yingfu Li (McMaster University)
  • “A DNA-Protein Nanoengine for “On-Demand” Release and Release and Precise Delivery of Molecules” – Razvan Nutiu and Yingfu Li