Biomod/2012/TU Dresden/Nanosaurs
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<div id="team-logo"> <p> TEAM LOGO </p> <p> :) :) :) :) :) :)</p> <p> :) :) :) :) :) :)</p> </div>
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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
24.04.2012
Start 19:45: People: Sarah, Svea, Praveen, Mari, Karen, Agata, Thomas, Fereshteh, Santiago, Varsha
First presentation of old projects:
- Praveen Presented Slovenia's old project: DNA origami add-ons, Zinc fingers: DNA specific can bind also proteins; site-specific functionalization of DNA origami. Is it possible to coat DNA Origami surfaces(with metals)? Nanolithography? Modification of single base pairs could be possible. It would be a nice idea to build a Diode by functionalizing a DNA origami.
- Thomas will contact main supervisors. Next week Monday at 1 pm we meet Ralf and Stefan to talk about their possible projects/research.
- Varsha contacted Prof. Büchner
- Thomas wrote to Leonid Ionov (smart polymers)--> 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
- Meeting with Dominik Kauert:
- He is very professional with DNA Origami and can tell us what is possible with Origami 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):
Attendants: 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 the 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 aim is to encapsulate cells into hydrogel and crosslink it. They were able to self-assemble tubes and used microparticles as clue 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 Presentation of Agata: Use motor proteins to sort things. Idea: 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 move 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 Tetraeder 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 tetraeder together to form a large extension. Meeting 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 o 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… o Could be possible to buy them in B-cube (might be cheaper); buy one couple it to different sites (hybridize the single one) o Add fluorescent labels to staples is cost-effective… o Facility usage: Write potential times up, so we can use it in BioTec without paying to much - Points: o Coupling of DNA Origami to membrane o Origami hybridization o Find a correct aptamer o Detection of transcription
Nanorockets:
- IFW is not really coupled to this place. - 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 o Binding of several antibodies to the end; maybe is not defined cutted end, but different length of the filaments… o Many conceptional questions…. - We need creativity, could be very difficult - 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? o 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: Hand work workshop stuff: Three parts: Workshop part: Applications for DNA Nanotechnology: Robots, Rockets Advertising for BioMod competition, Create a platform for donation. Stay 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
BioMod Meeting : People: Agata, Santiago, Thomas, Varsha, Karen, Maryam, Ali Advisors/Supervisors: Ralf, Michael, Dominik, Svea What do we have to do now? 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!)
- finalize 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 have 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) -> Michael knows about it (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
- People get smaller, explain the experiment and walk along
Meeting with supervisors Maybe 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
Meeting Tue: : People: Ali, Alexander (HiWi at Ralfs lab), Santiago, Praveen, Agata, Varsha, Thomas Description of the project to Alexander: 1. Coupling of DNA Origami to membrane and signaling (transcription activation) a. Dimerization process OR DNA transformer (opens the structure: transcription factor can bind) 2. Mimic integrins: that one GUV binds to another Webside: 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 told him that he might can work for this project (mainly). Main Origami design with caDNAno is quite fast. There is a Maya independent version of caDNAno Presentation of the CaDNAno program from Alexander Ohmann. 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, 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. Already proven structure? 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: goes more for the artificial cell system; transcription part is ready; motivation is not good enough; everything happens outside the cell; 1. The GUV attachment to each other: Idea of integrins: Step of vesicle fusion; 1. DNA Origami incorporated in the GUVs 2. Signal comes -> aptamer approach 3. Aptamer changes the conformation of our construct 4. small vesicles mimicking Integrins (detection with FRET) 5. Receptors Following a long discussion about the usefulness of either attaching the vesicles to each other without fusion! Or doing the artificial transcription outside of the GUV…. Karen modified the Text for Birte, Thomas will modify& 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
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), 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 Nanotechnology Our Project BioMod Info Thomas Mari Ali Karen Praveen Agata (ali) Varsha Santiago
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
Protocol BioMod Meeting Attendance: Ali, Praveen, Karen, Mari, Santiago, Alexander, Thomas, Varsha Origami Front: cadNANo is quite complex, 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; he 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 He 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 them for cancer targeting; Things to consider: final result we want to do 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: We need to ask her several questions: How to pay and to order; Maybe 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: is important 50% of the final mark, Santiago is working on it Video: Thomas met Shruti today: she is very experienced in Video design. She will be really helpful. 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 (Olec) about further experimental steps, ask him what we need to order. Alexander (Olec) will do LUVs next week; Karen and Praveen will join him;
Next Meeting Monday, 11.06.2012: 1:45 pm
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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"
