Biomod/2012/TU Dresden/Nanosaurs: Difference between revisions
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== Team Meetings == | == Team Meetings == | ||
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Mondays: 5:30 pm; Fridays: 4 pm (before beer Hour, Update of the week!!) | Mondays: 5:30 pm; Fridays: 4 pm (before beer Hour, Update of the week!!) | ||
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== Section2 == | == Section2 == | ||
Revision as of 03:04, 3 August 2012
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<li><a href="http://openwetware.org/wiki/Biomod/2012/TU_Dresden/Nanosaurs/Home">Home</a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2012/TU_Dresden/Nanosaurs/Team">Team</a></li>
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Team Meetings
probable meeting next week on Thursday at 5 pm at IPF
- Fereshteh Presented a Nanosaur for a special function (her idea);Environment is key --> Low Reynold's number. Reynolds number: Ratio of Inertial term to Viscosity term in Navier-Stokes Eq. Recommended book: Purcell et al: Life at Low Reynolds Number (1976)
- Brainstorm--> Control what sth. is doing. ATP is used as source of energy, how can it be supplied in a controlled fashion? At least 3 center of masses are necessary to have a nonreciprocal motion which leads to a pure displacement, at low Reynolds number. Aim: Build a little nano-swimmer to act autonomously in the body.
- Meeting with Dominik Kauert on Thursday at 4:30 pm in his office
- Santiago Presented Technische Universität München TUM NanU Project The TU Munich people made it possible to bend DNA origami structures pictures of us will be taken on Thursday.
- We talked about the lecture next Monday to officially present the Biomod Team.
End: 22:07
26.04.2012
BioMod Meeting in E05 in BioTec:
People: Mari, Ali, Agata, Santiago, Karen, Thomas, Svea, Sarah, Praveen
- Some thoughts about the meeting with Dominik Kauert:
- He has experience with DNA Origami and can tell us what is feasible and what´s not
- Works with bend DNA Origami and functionalize it with Cholesterol to attach a membrane and therefore force the bending of the membrane
- Nanopores on DNA Origami are possible
- caDNAno is a very nice tool and free to design DNA Oigami structures
- 12 cent per basepair
- Talk from Mari about MIT project: House shaped Origami -> targeted drug delivery:Roof could open using ph change: I-switch (ph switch).Ground floor can open due to light activation (azobenzene link in cis) -> so the “house” can open due to two different signals on two positions and therefore could have two different chambers in one origami.They evaluated the opening by using FRET measurements.
- Ali: DNA spiders -> CalTec: Principle of DNA spider--> 3 legs attached to body, DNA enzyme legs: they split the DNA single strands into shorter strands. Leaving a “burned” path.Molecular Spiders (paper):http://www.nature.com/nature/journal/v465/n7295/full/nature09012.html#/supplementary-information. Random walk: Pick cargos up and should deliver them to one specific site of the Origami.Nice and interesting project: but the problem is, that it might be not useful to work on a project, where there is no knowledge at TU Dresden.What we could use: Walking mechanism by partly complementary strands (useful to make something move, deliver sth. Idea of Ali to use a Jump mechanism for faster targeted delivery of the loads of the spiders.
- Karen: LMU Munich team: Modular nanoscopic drug delivery device with a ph sensitive opening mechanism (using DNA origami) I-motif is pH dependent: Uses cytosins, at low pH values it can pair to itself.
- Design DNA Origami: Using “caDNAno”: predict shape you want: and gives you the staple sequences. Company where you order the strands is MWG.
- G-quadruplex: needs an ion (dependent, metal ion: cation); cancer cells elongate the telomeres by the function of telomerase: a g-quadruplex at the end can prevent the function of the telomerase.
- Thomas: Danish Nano artists--> octahedron which can be used as drug delivery system and can itself work as drug by using RNA interference Why did they use RNA for the Origami? Only possibility to use the container itself for RNA interference and knockdown of genes.
- We need more brainstorm sessions before the tenth of Mai….Meeting on Monday: 7th after the lecture in cellular machines.
03.05.2012
Meeting with Leonid Ionov at the Institute for polymer research (IPF):
People: Varsha, Svea, Praveen, Ali, Santiago, Thomas
- Leonid Ionov works with smart polymers-> stimuli responsive polymers and they do a biomimetic approach and even try to do Origami folding techniques with Polymers.
- The change in the polymer is mostly due to swelling, how is it possible to engineer the swelling behavior upon specific stimulus--> In IPF they work with thermoresponsive polymers:
- Temperature low: swelling;
- temperature high: unswelling
- Different shapes were already used, for example they were able to create an envelope by a folding of the polymer. Alltogether the sizes are bigger: 10-100 µm
- One of their research aims is to encapsulate cells into hydrogel and crosslink it. They were able to self-assemble tubes and used microparticles as glue between rods.
- It is possible to anchor biomolecules inside hydrogels; fluorescent dyes pH sensitive polymers are also possible.
- IDEA: Put a Kinesin inside a polymer tube
- Leonid Ionov is willing to help us: he can provide a cryo TEM and a cryo SEM
- The ratio of swollen and not swollen state of the hydrogel is 1:10-> could be used as gate, but the problem is that the hydrogel gates are not tight! Molecules can diffuse through (slowly)
- Artificial organ culture with a 3D hydrogel network
- IDEA: Work with Nanoparticles in the range of 20 nm, not many people will work with that in the competition
- IDEA: Transition of one shape to another shape with DNA Origami (Aptamers)
- Two photon polymerization:
- Encapsulation of cells/bacteria into a hydrogel to create a living biofilm with demanded properties could be possible (e.g. a stent with a biofilm)
- Summary: Very interesting projects could be performed with polymers, but not really on the nanoscale it´s more on the Micro/milli scale…
09.05.2012
Internal Project discussion
Start: 8 pm People: Varsha, Praveen, Mari, Agata, Karen, Thomas, Santiago
- Thomas: Mimic an Artificial immune system using DNA origami boxes and a signal amplification. Bring up an example with the boxes using in cancer research. Create a DNA Transformer: Complex reformation of a shape on a nanoscale
- Agata: Use motor proteins to sort things. Problem with dimensions of DNA Origami and Microtubules/Motor Technology.In Schäffers group they investigate the fighting of Motor proteins, some go to the + end some to the – end. They use DNA Origami to connect the motors. Create caps and it can not further grow. Is it possible to add the Biotin to the ends. Coat surface with gold.
Bending abilities? How efficient is the microtubule system? Create a cap and connect the cap and therefore create a path for the Motors.
- Praveen: DNA Origami coupled with microtubule/kinesin system – biosensor. Distance movement is coupled to the amount of molecules you have. This is a very sensitive single molecule sensor. Correlation between amount of ATP you have and irregular movement. DNA Nanorockets coupled with DNA Origami and Smart Polymers: Drop boxes to a specific site.
- Karen: An artificial signaling cascade using DNA origami coupled to a membrane. Two Origamis on a membrane sheet. Brought together by an Aptamer clamp and the complementary strand would bind together to be able to form a double strand and do an artificial transcription system.
- Santiago: DNA piston Tetrahedron with Hairpin structure. Fuel with a hairpin and a handle at the end. Elongation of the structure -> creation of a spring (elongated-stretched-…). Fuel-Antifuel system. Idea use three tetrahedron together to form a large extension.
End: 10:45 pm
14.05.2012
Meeting at 1 pm
People: Ali, Agata, Santiago, Mari, Thomas
Projects List:
- Artificial Transcription System Membrane Bound:
- Three supervisors involved in the project: Ralf, Erik, Michael (Petra)
- Interesting and feasible project: coupling of Origami to membrane is very new and possible
- Possible to split into parts: DNA Origami coupling to membrane: Artificial transcription cascade: Bring the Origami at the membrane together
- Techniques used: Formation of lipid bilayer, FRET, DNA Origami, Selection of Aptamers/complementary strand system, assays for DNA transcription.
- Doing Origami inside of the cell.
- Does it fit into BioMod? Because it is not really an architecture … but already an application.
- What about the environmental conditions? The GUVs need exact conditions: a slight change in pH can disassemble the GUVs
- In solution FRET should be no problem
- Who would help? Possible supervisors: Alexander from Schwille lab, Dominik for DNA Origami
- T7-Polymerase: evaluation of the artificial transcription system: Svea? Sarah?
- Already established coupling of GUVs to DNA Origami
- Costs? Origami costs something if we have a special design; Cholesterol costs sth…
- Could be possible to buy them in B-cube (might be cheaper); buy one couple it to different sites (hybridize the single one)
- Add fluorescent labels to staples is cost-effective…
- Facility usage: Write potential times up, so we can use it in BioTec without paying to much
- Points:
- Coupling of DNA Origami to membrane
- Origami hybridization
- Find a correct aptamer
- Detection of transcription
- Nanorockets:
- IFW is not really coupled to Biotec.
- Only 3 months
- We would not have lab space
- We don´t have a real project so far.
- Supervisors only from that place
- Techniques: Roll up, chemical vapor deposition, photoresist, layer deposition techniques, protein assays
- Deposition of proteins into the tube
- Problem to transfer the protocols from one lab to another
- Difference in dimensions could be difficult
- All measurements would have to be done on single rockets
- Microtubule capping:
- Not splittable ( a bit): Build basket with antibody which could bind to the end of mts
- Binding of several antibodies to the end; maybe is not defined cutted end, but different length of the filaments…
- Many conceptual questions….
- Good Expertise with Microtubules in Dresden (Stefan Diez, Howart)
- Techniques: DNA Origami, FRET, Surface deposition,
- Many question marks
- Nucleate sth. from a DNA Origami; Create oriented arrays of MT;
- Signal amplification with Boxes:
- How tight are the boxes?
- Boxes itself already exist, not very new
- How do we get molecules inside
- Get the box should not be soo difficult: Use the published design: the staples
- Amplification system which opens and activates other little robots: Like the Paper of the DNA Nanorobot…
- Techniques?
- DNA Transformers:
- Much simpler structure needed (than a car…)
- We would need lots of TEM capacity
- Could be possible
- Goal to the end of month: Who is doing what, which deadlines do we want to have. Everything needs to be theoretically resolved. Recipe for everything.
- Long Night of Science: DNA Origami for dummies:
- Workshop--> Applications for DNA Nanotechnology: Robots, Rockets, advertising for BioMod competition, create a platform for donation.
- Say what BioMod is,explain also transcription.
- Poster Our project explanation; BioMod; DNA Applications in Nanotechnology: 3 posters
- Something for kids: building some Origami animals or DNA double helix origami
- Meeting with supervisors at 14.05.2012:
- Vote among ourselves:
- Which project would be the coolest?
- Which project would be the most reasonable?
21.05.2012
General Meeting:
People: Agata, Santiago, Thomas, Varsha, Karen, Maryam, Ali
Advisors/Supervisors: Ralf, Michael, Dominik, Svea
What do we have to do now? Ans=Divide the team for the individual parts:
- Who is dealing with the homepage? Santiago, Agata
- Who is dealing with the video? Ali + friends, Varsha (Shruti knows about video, they have a good camera), Thomas
- Who takes care about the lab work?
- Arrange a meeting with Dominik and Alexander (Agata will write to them this week!)
- Define the project idea
- Who wants to work with lipids? (Agata)
- Who works with caDNAno? And DNA Origami + FRET + Aptamer System (Santiago, Maryam)
- We want to ask Dominik + Alexander for papers about the theory behind the topic (maybe special papers) -> so everybody is at the same theoretical level: Everybody has to read it!! – short circle ten minutes presentations of the landmark papers
- Who wants to work with the transcription system? Detection system for the transcription? (Karen, Varsha, Praveen) -> Contact person Michael Schlierf (T7-Polymerase)
Tomorrow:
- Discuss about the Long Night of science? (7. of July)
- Who wants to do which poster? (do a little scetch) Competition, Applications DNA Nanotechnology, Our project + workshop for kids: how to fold DNA Origami^^
- Write in two languages a short abstract for tomorrow
- Write a general text to the people who want to support us
- Think of possible video ideas today (discuss them tomorrow)
Meeting every Monday 2 pm
Meeting tomorrow 5:30 pm
Meeting with supervisors:
- We should ask Petra to get more PhD students from her as advisors (maybe go to their group meeting, present the idea, the competition and ask if somebody is interested to further support us.
- Money + Funding:
- 2 pages of summary + write down all the expenses (include a figure in the project description)
- Contact Susann Fischer at DZNE!
- As soon as we have the description: supervisors could maybe contact some companies
- For lab space: we need a clear project description to contact other group leaders to get lab space
- Sum up the costs: we should write to get free access to confocal and Electron Microscopy at Technology Plattform of Biotec
- Maybe… Lab space in the Schwille lab (for vesicles) or B-cube (for FRET things or PCR machines)
- Short scetch about the project now: DNA Origami + lipids + transcription
- Include Dominik + Alexander in the mailing list (biomod-pr). Ask alexander for a short presentation
- If we go for the dimerization we can do cross-correlation to see that they get together
- Where should it happen? Maybe in GUVs it´s simpler,
- Alexander is a student worker in Ralf´s group and designs DNA Origami
- Aptamer guy: 1000 papers…. Itamar Willner, Friedrich Simmel about transcriptional oscillator
- Crucial point: how to get the switch between aptamer binding / conformational change to get the transcription to work.
- Getting DNA through membrane is difficult.
- Be clear about motivation to have a consistent story.
- In B-cube they can build 100 and 200 nm vesicles. Build up an artificial integrin system. Connect two vesicles…-> artificial cell adhesion system, vesicle fusion system: Michael knows…
- Find a natural system to mimic…. .
22.05.2012
General Meeting:
People: Ali, Alexander (HiWi at Ralfs lab), Santiago, Praveen, Agata, Varsha, Thomas
Description of the project to Alexander:
- Coupling of DNA Origami to membrane and signaling (transcription activation)
- Dimerization process OR DNA transformer (opens the structure: transcription factor can bind)
- Mimic integrins: that one GUV binds to another
Some key points for DNA origami:
- Website: cando--> Upload DNA Origami, they send a video what the Origami would look like
- Agata send Dominik and Alexander (Olek) an Email to meet them.
- We already had a GUV lab practical which could be useful.
- Ralf supports Alex participation in the group. Main Origami design with caDNAno is quite fast.
- Longer staples are also possible, short staples doesn’t work so good….up to 49 bp; too many scaffold crossings might not be so good. Skip bases can bend the structure. Online tutorials at the caDNAno page.
Usual Steps:
- Design construct
- Send it to cando to get idea if it could work
- Then order DNA Origami (1 week)
- Pipette together-> assemble it (fast routine: slow routine: 15 h : 72 h); heating and cooling down, then the structure can assemble.
- For already proven structures--> How long does it take to replicate structure? Usually in the supplementary data you can replicate it around 4 hours (maybe with a good computer: 2 hours);
Label sth. for example with a biotin. Book appointment at TEM.
Basic Idea:
- The transcription solution works better for the artificial cell system. Transcription part is ready. Motivation is not good enough. Everything happens outside the cel...
- The GUV attachment to each other--> Integrin's idea: Mimic one step of vesicle fusion;
- DNA Origami incorporated in the GUVs
- Signal comes -> aptamer approach
- Aptamer changes the conformation of our construct
- Small vesicles mimicking Integrins (detection with FRET)
- Receptors
- Discuss the utility of either attaching the vesicles to each other without fusion and/or doing the artificial transcription outside of the GUV….
- Karen modified the Text for Birte (Long Night of Science), Thomas will modify and translate it a little bit and then send it to Birte tonight.
- Project idea: Use a DNA Nanostructure to recognize via aptamers specific surface proteins on cancer cells and then opens the structure (Box/barrel like…). Inside we have functionalized invasin which induces endo/phagocytosis by the cancer cell. This DNA Nanostructure is attached to a vesicle which can be used as highly specific drug target delivery vesicle.
04.06.2012
General Meeting Time: 13:45
People: Varsha, Praveen, Thomas
Next steps:
- Lipid Front:
- Praveen is going to write Aleksander Czogalla (Schwille group) and asks him, when he is doing the experiment (Karen maybe can join?)
- Aptamer Front:
- Have to be discussed on the next meeting on Thursday, Please be prepared (!!!) what kind of Aptamer should be used and what kind of Origami, what should be the actual change!
- Origami Front:
- Varsha will email Alexander (Seidel group) for further progress in Origami design,
- Funding Front:
- Funding request sent to BioTec today…we will see. Thomas connected Kai Simmons to ask for funding and ideas, Thomas asked Oates and described the project, any suggestions or how to get funding from MPI; We need to meet Katrin Großer (Email already sent to her, waiting for reply). The letter should be officially sent (hardcopies) from BioTec with a signature from all of us + main supervisor (like Prof. Diez), Letters to companies should be sent in June,
- Video Front:
- Thomas wrote Shruti for asking how to do videos, Thomas will bring his laptop on Thursday and presents the animation program,
- Posters for long nigh of science:
- Respective groups should organize themselves:
| Application in Nanotech | Our Project | Biomod Info |
|---|---|---|
| Thomas | Karen | Varsha |
| Mari | Praveen | Santiago |
| Ali | Agata |
- Posters should be done by last week of June so everybody of the team can review it before we submit it to Birte (first week of July).
- We will ask Alexander (from Seidel group) to be officially in our team. We would have to write Shawn Douglas if we can add a person. Varsha will ask Alexander if he wants.
- Next meeting: Thursday, 7.06.2012 at 7:45 pm in BioTec E05, I will ask Anne if she can reserve us the room.
07.06.2012
General Meeting
People: Ali, Praveen, Karen, Mari, Santiago, Alexander, Thomas, Varsha
- Origami Front:
- Alexander will send an email with an attachment/full Origami which can be opened with caDNAn o to Santiago to see how an official structure could look like.
- Alexander our new Expert for TEM will upload his phonenumber and schedule (he has time Thursday: 4 pm) for meetings with external people
- Origami people: please read the Douglas paper with the Nanorobot: http://www.sciencemag.org/content/335/6070/831.They uses a barrel structure which we could directly use and also the aptamer.
- We need to come up with two Origami structures: one for the GuVs, one for the LUVs;
- We need to meet the junior Group-leader (Zhang) in B-cube who can functionalize Origami-staples with cholesterol linkers.
- Praveen explains about aptamers, we could use them for cancer targeting;
- Things to consider--> final result we want to obtain should not interfere with the aptamer (vesicles?)
- Maybe a prism structure for the origami
- Funding:
- We meet Juliane Hoth 19.06.2012: 9:30 am at BioTec, she will be responsible for our account
- Key questions: How to pay and to order. Ask Susan Fischer if she can accompany us to Juliane. We would like her to sent the official Letter´s to the companies in German (with her address; name, email…). If it doesn´t work we could ask Prof. Diez or the Seidel group…we will discuss this on Monday with Stefan Diez in the cellular machines lecture.
- Wiki:
- 50% of the final mark, Santiago is working on it
- Video:
- Thomas met Shruti today--> She might be really helpful do to his media experience. We have already some ideas to catch people s attention. Important is to have a main theme in the video…like stars, water, ….
- GUV Front:
- Please ask Aleksander (Olek) about further experimental steps, ask him what we need to order.
- Aleksander (Olek) will do LUVs next week; Karen and Praveen will join him;
Next Meeting Monday, 11.06.2012: 1:45 pm
11.06.2012
General Meeting:
- Tuesday next week 19.06.2012: we meet the accountance person from BioTec. We need to ask a lot about the funding. How can we order things…
- Thursday 5:30 pm this week: we maybe meet in B-cube Mr. Zhang which makes the Origami coupling to cholesterol
- Origami shape:
- The group is still playing with the software. Maybe we want to do a 3dimensional triangular shape and couple it to the guv. ;
- GUVs: People meet Aleksander (Olec) to discuss about the further steps.
- Pictures of the team: Karen wrote a person which she knows; hopefully we can meet him soon: to make the pictures.
- Homepage:
Maybe should already have an order, like other teams already put their ideas on the wiki; Otherwise if we first upload the main things in august, we might be a little bit lost…We Should use the wiki as a lab-book… . BioMod is an open source competition, so we could already put everything on the wiki.
- Long night of Science:Posters need to be done.
- Video: Thomas tries to put the ideas into a simple video , effects could be further modified.
14.06.2012
Meeting with Dr. Zhang and discussion about the project
People: Alexander, Karen, Svea, Praveen, Ali, Santiago, Varsha, Agata, Thomas, Dr. Zhang Time: 17:30
- Alexander presented the Steps for the experiment--> Find presentation in the googlegroup
- We need three different cholesterol labelled oligos
- 9 connections to anchor the Origami on the outside of the GUV
- Ask Dominik to use the origami structure anchored to a guv (already in press in the paper);
- B CUBE has a pool of 30 different staples/oligos coupled to cholesterol;
- One cholesterol is added to one oligonucleotide: the big challenge is the solubility, with more cholesterols added
- There is no good method to purify it because the cholesterols would cluster together and the oligos stay outside, the cholesterol is added at the 3’ end; so the staples hanging out must be also complementary at the 3’ end.
- Origami coupling to the GUV: combining one anchor strand with a staple
- Discussion about getting rid of one of the lids, so we would not have the problem with a possible sterical hindrance, could be possible with different lock systems at the correct/proper places
- How many origamis? Coat the GUV with LUVs, so nearly coat the origami completely
- How much time is needed to synthetize the cholesterol coupled oligos?
- In B-cube (Dr. Zhang) they have already a lot of coupled oligos (in storage) and for the coupling you really need not many…
- Problem with connecting GUVs for the control (because no cholesterol labelled complementary strands): oligos can form hairpin structures so it should be possible; have a linker oligo
- We have to think about a partly double stranded structure to stabilize it
- Meeting tomorrow at noon: at B-cube (to discuss with Svea and Michael Schlierf about the control experiment and the attachment of the two GUVs )
- Karen will ask Dominik Kauert if he has any oligos left (stock solutions) which are labelled with cholesterol and which one for the sequence
21.06.2012
Meeting with Michael Schlierf: Start:17:30
- 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 paper).
- 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
28.06.2012
BIOMOD Meeting:
- We need to rearrange the groups, because the GUV group (Aptamer tests also included so far…) has lots of work to do and so far there are only molbioengineers in the group…Praveen, Agata, Karen…who wants to join this group from NanoBios? We want to establish a new group who is working with Aptamers + do the FRET experiments in B CUBE with Michael Schlierf.
- The GUV group works with Aleksander and he requires the people to be very well prepared, the paper has to be read, the calculations be done, the experiments planned…
| DNA Origami | GUV's | Aptamer |
|---|---|---|
| Design & the structure (mainly Alex) assembly of structure will be lots of pipetting work… | Agata, Praveen, Karen, Varsha, Santiago | Mari + (Praveen, Aga or Karen) |
| TEM (Alex and Ali for sample preparation) |
- Alex probably could need some help, for the TEM sample preparation -> Ali will help him and already joins him tomorrow (29.6.) for the TEM measurement (9-12),
- Varsha is going to the Long Night of Science meeting tomorrow for introduction at 10 am, in CRTD seminar room one
- The posters should be translated until Sunday evening, Thomas will take care that they are printed in time + reserve the printer time….(done)
- Thomas will give the names of the participating people to Birte for the badges (done).
- What kind of 3D model should we do for the long night to entertain the people and to explain our project?
- Build a box, with straws colour coded and attach GUV to GUV…. We should make the model entertaining…what kind of materials, please think a little bit more about the structure. We should get velcro, Big GUV with parts covered with sandwich velcros, LUVs with another Velcro but cannot attach to the sandwich, we have the aptamer ball (which mimics our aptamer key system) which takes away the top of the sandwich Velcro so the LUV with the fitting Velcro can attach. Question: where do we get the Velcro? For making the Origami structure we could use polystyrene->Alex will ask/look in the lab,
Everybody is expected to be in CRTD for the Long Night of Science…at least for a few hours, It starts at 6 officially, but we should be there at 4 or 5.
- Funding:
- We have more or less three accounts over which we can order things (BIOTEC, CRTD, DIGS-BB)-> we should not loose the overview. Therefore as soon as you order please state it in the Editgrid from which account you want to take it and contact the responsible person (BIOTEC: Juliane Hoth, CRTD: Ilona Kreher, DIGS-BB: Dana Jaster)
- Alex will be the responsible person for ordering over the DIGS-BB account-> Thomas will write an email to DIGS-BB (done)
- Unfortunately the Saxon Ministry of Science and Arts has no money for student projects…
- The letters have been put together by Thomas today and sent….let´s see what replies we will get.
02.07.2012
BIOMOD Meeting
- Long Night of science:
- Cardboard for the DNA Origami -> ask Birte or in the lab; Velcro for the GuVs , what are the smaller balls? Ping-Pong? Or tennis? Or sth. even bigger? Alex bought polystyrene balls, We need straws for the Origami-Oligos, We need double sided tape to attach the Velcro (the Velcro already has glue on one side…). -> we will put it together on Thursday. We need some candys ;)
- Alex will buy Velcro and Polystyrene spheres,
- Posters: We will make the photos on Wednesday at 5 pm!!!, also already for the homepage… . We have booked the printer on Thursday afternoon. Could all go over the posters and take a look please (look in Dropbox). Plese wear for the photoshooting: Jeans and T-Shirts with intense colours,
- Shifts of the Long Night of Science: 3 people for 2 ½ h. Be here already at 5 pm, Agata will make a doodle for the shifts.
- We get 5 T-Shirts altogether and vouchers for a meal at the canteen, two bottles (one water, one apple juice) for the station -> so you should bring sth. for yourself I guess this is not enough for the whole evening
- Update about the lab work:
- The GUV group makes quite good progess in learning the techniques… Exam break for 2-3 weeks now…
- Visa: Please inform yourself about the length of the Visa process as soon as possible so we can estimate the time you need for the whole process
- We need to talk to the supervisors who will accompany us to Boston? Harvard University will pay for the accommodation…so they need to know how many people are going so they can arrange the rooms.
- Visa process: please don´t apply so far but gather the information what you need to get a visa and collect all the information (e.g. letter from BIOTEC that you are a student here….). Suggestion: the Visa application should be done then in the beginning of August as soon as we know how much money we approx. get from the companies (how supportive they are…) and so we know for how many people we can pay the flight.
30.07.2012
General "super" Meeting:
- Thomas will contact TU Dresden again to get the Money they promised as well as GSK Foundation
- Meeting this week with Juliane Hoth (Thursday or Friday: 8 am):
- Varsha and Praveen, Santiago will go with Thomas to get an overview over funding.
- Meeting with Supervisors beginning of next week (Aga will organize: maybe next monday):
- Money issue (what is process so far, contact of companies? Zeiss, Nikkon, JPK,….)
- Who is able to join us in the US?
- We have some companies who support us with Material, what kind of Material should we get, who needs what?
Aptamer group: Needs to work this week, exams are over!
- Questions to be answered this week about the aptamer group:
- Which Aptamer do we use? (Which Oligosequence?)
- How do we evaluate the opening of the Aptamer (Arrange a meeting with Michael: FRET!!)
- Experimental design – (PP – Presentation next week – merge with Origami group)
- What kind of FRET dyes do we need (Quencher – Donor), where can we buy it and how much, how is the labeling procedure (talk to Dominik)?
- GUV group:
- Order Oligos
- Use Oligos and stain them with Fluorophor
- Dominik has stains to label Oligos at 3-Prime (the one who is used for the linkage to the GUV…just without the cholesterol),
- A meeting needs to be arranged to get introduction to Microscopy! (Arrange meeting this week to be maybe next week or the week after: ask Aleksander (Olec) who is responsible)
- AIM: Work on your own, without supervisors look over the shoulders…soon!!
- Procedure: aleksander expects that the procedure will take a whole day.
- Sequence: Electroformation: at 9 am, Microscopy late in the afternoon.
- Check with the Fluorophores, Problem might be the Linker, couple Cholesterol with new Oligo or try everything out with the Structure itself,
- Maybe one can do TEM with the GUV coupled Origami
- Biolympics who takes care?
- Include some other class mates and Svea (Varsha will take care!)
- Wiki:
- Schedule: How to see the work until the abstract submission in September until end of the week, everybody!!
- Origami:
- Somebody should get an introductory course to work with TEM (additionally to Alex)
- Break:
- We can not afford to stop working due to vacation! We will modify the editgrid where everybody can put in when they work.
- Meeting with Opitz:
- He maybe can pay a flight, but has to talk to other directors at fraunhofer. He will get back to us in the middle of August.
- T-Shirts:
- Somebody has to design the T-Shirts (Middle of September…: Karen will design a CUTE Dinosaur^^),
- Application of our system to sell the story in the presentation. Meeting with Marino Zerial next week (Praveen),
- How many want to have a Matlab license?
- Santiago, Praveen, Varsha, Aga (one B CUBE computer: 5 Licenses: Santiago organizes it).
- Meeting with Transinsight:
- They will probably support us with 200 € and he (CEO: Michael Alvers) will support us with marketing hints (we should send him the presentation and present in front of him to get hints and shape the basic idea out, make it understandable and provoke questions); He will get back to us after the decision.
- VISA Photos: Thomas will send around where he did them – he knows visa requirements of USA,
- Questionnaire, Letter from BIOTEC that you are studying here, BIOTEC Transcript of records needed please contact Anne / Martina immediately
- Thomas will make Flowcharts for What happens if a company gives us money? What happens if I want to order sth?
- Regular Meetings:
Mondays: 5:30 pm; Fridays: 4 pm (before beer Hour, Update of the week!!)
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- Team Name:Dresden Nanosaurs
- Institution Name: TU Dresden
- Geographic Location: Dresden, Germany
Welcome to the Wiki of the Dresden Nanosaurs! During the next weeks and months we are going to update this page and post our progress of the project.
"Good, better, best. Never let it rest. 'Til your good is better and your better is best"
