Biomod/2012/UCSD/tRiton Nano Architects/Brainstorm
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<li class='active has-sub '><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects'><span>Home</span></a> <ul> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects#Abstract:_Fluorescent_DNA_Aptamer_for_lysozyme_detection'><span>Abstract</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects#Video'><span>Video</span></a></li> </ul> </li> <li class='has-sub '><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Project_introduction'><span>Project Introduction</span></a> <ul> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Project_introduction#Concepts'><span>Concepts</span></a></li> </ul> </li> <li class='has-sub '><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Experiment'><span>Experiment</span></a> <ul> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Experiment#Methods'><span>Methods</span></a></li> </ul> </li> <li class='has-sub '><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Resources'><span>Supplementary Resources</span></a> <ul> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Brainstorm#DNA_architecture_log'><span>DNA Architecture Log</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Brainstorm#Project_Ideas'><span>Project Ideas</span></a></li> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Literature'><span>Literature</span></a></li> </ul> </li> <li><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects/Team'><span>Team</span></a></li>
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DNA architecture log
The tRiton Nano Architect spent a large effort in brainstorming project ideas from April 2012 to July 2012. Our effort help us learn the process of DNA nanotechnology as well as the current research stage of DNA nanotechnology. We analyzed various scientific papers cited from the resource section of past BIOMOD 2011 teams. With this knowledge, the project scope and project budget was taken into consideration when selecting our actual project/abstract.
DNA Structures:
Architecture | Uses | Technique | Source |
---|---|---|---|
DNA box with lid |
1. Scaffold to encase nanosize cargo. 2. items for X-ray crystallography; Functionalize inside of box to trap pathogens (virus) then close | DNA Origami | http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html
http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d |
DNA tetrahedron |
1. Scaffold to encase nanosize cargo 2. items for X-ray crystallography | DNA Origami | http://pubs.rsc.org/en/Content/ArticleLanding/2004/CC/b402293a
http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d |
DNA octahedron |
1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography | DNA Origami | http://www.nature.com/nature/journal/v427/n6975/full/nature02307.html
http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d |
DNA bipyramid |
1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography | DNA Origami | http://pubs.acs.org/doi/abs/10.1021/ja071493b
http://pubs.rsc.org/en/Content/ArticleLanding/2010/NR/b9nr00246d |
DNA walker |
Motion w/ cargo delivery along designated tracks. | Creation of walker tracks, DNAzymes that move through the tracks | http://www.nature.com/nnano/journal/v5/n11/full/nnano.2010.190.html |
DNA dolphins with flexible tails |
Demonstration of unique DNA shapes; potentially a new propulsion system under high Reynolds number.
Motion in liquid, magnetic steering, surface coating for biological camoflage |
DNA Origami | http://pubs.acs.org/doi/abs/10.1021/nn800215j |
Biochemical Aptamers |
Biodetection of molecules or short oligos. | SELEX process | http://en.wikipedia.org/wiki/Aptamer, http://www.sciencedirect.com/science/article/pii/S0003269701951693 |
DNA computational circuits |
Targeted Drug Delivery, error reduction upon recognition, close upon recognition of pathogen (through logic) | Charging DNA with electricity between very thinly spaced electrodes | DNA attachment chemistry: http://journals.ohiolink.edu/ejc/article.cgi?issn=07437463&issue=v15i0019&article=6541_eirodfgu
DNA rings: http://www.pnas.org/content/105/14/5289 Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html |
DNA topological structures |
DNA 3D Origami, Customizable 3D design. DNA statues. | DNA origami | http://www.nature.com/nnano/journal/v5/n10/full/nnano.2010.193.html |
DNA shapes – curved and twisted |
DNA 3D Origami, Customizable 3D design. DNA gears/DNA rings. | DNA origami | http://www.sciencemag.org/content/325/5941/725.abstract |
Square Lattice |
DNA 3D Origami, Customizable 3D design. | DNA origami | http://pubs.acs.org/doi/abs/10.1021/ja906381y |
Liquid Crystal |
Biosensor material, DNA liquid crystal filtration. | Short oligos under various temperature and voltage. | http://www.pnas.org/content/early/2012/01/04/1117463109.abstract
http://www.nature.com/nmat/journal/v6/n12/full/nmat2010.html |
DNA molecular robots [spider] |
Extension to the DNA walker | Functionalization of DNAzymes as legs and DNA arrays as tracks. | http://www.nature.com/nature/journal/v465/n7295/full/nature09012.html |
DNA origami tubes |
Scaffold for drug carriers, biodetection. | DNA origami | Initial reading - http://pubs.acs.org/doi/abs/10.1021/nl101079u
http://pubs.rsc.org/en/content/articlelanding/2012/SC/C2SC20446K |
Complex weaves/ Programmable 2D DNA arrays |
Scaffold for multifunctionalization using SAM (Self-assembled monolayers)/Biotin/other biolinkers to attach to functional groups/nanoparticles. | DNA origami | http://pubs.acs.org/doi/abs/10.1021/nl060994c
http://onlinelibrary.wiley.com/doi/10.1002/cphc.200600260/full http://www.sciencedirect.com/science/article/pii/S0959440X1000062X |
Project Ideas
Below is a selection from the multitude of ideas we considered before settling on our final project:
Idea | Concept | Uses | Reason Rejected | Sources |
---|---|---|---|---|
DNA sensing circuit with DNAzymes |
This idea utilizes DNAs conductivity. Many structural versions of this design were contemplated but the most popular structure was interlocking rings of DNA in a Y shape, which would be connected to two electrodes at one end and one at the other. On one of the Ys would contain aDNAzyme, so cleavage of that strand of DNA would occur when a trigger of a specific DNA sequence was added. | The idea was that this could be used in sensing. Once the target sequence of DNA (ie, a specific virus) was present, the DNAzyme would break, and the current across the chain would change.We would also attatch fluorophores and quenchers on opposite sides of the Y to enable us to verify whether the circuit was open or closed. | While it was a feasible concept, our mentor said this would be too hard to optimize in the given time due to the complexity of the interlocking rings and measuring the charges. | DNA attachment chemistry: http://pubs.acs.org/doi/abs/10.1021/la9905315
DNA rings: http://www.pnas.org/content/105/14/5289 Conductivity: http://www.nature.com/nature/journal/v403/n6770/full/403635a0.html |
DNA Robotic Arm with Light-activated Joints and Tweezers as Hands |
This idea was inspired by DNA walkers. We wanted to see if we can create the arms of a molecular robot, knowing that others have already designed the legs. Our robotic idea utilized DNA tweezers as hands and photoreceptive molecules that would change chemical conformation in order to bend the "shoulders", "elbows", and "wrists" of the DNA arms. We planned to test our project by attaching it to a platform and controlling it with light to pick up nanoparticles placed on certain locations. | This would have been a useful contribution to nanorobotics. | Based on our current skills, the idea was unfeasible. | http://www.ncbi.nlm.nih.gov/pubmed/18850700 |
DNA Art |
creating 2D masterpieces out of colored/fluorescent nanomaterials on a DNA weave. This could incorporate quantum dots or other materials that have differing colors at different sizes such as silver and gold. | This aesthetic use of nanomaterials to create a new artform could have had nano barcoding or labeling applications. | This was one of our more considered ideas if sensing hadn't taken a higher priority. | http://dx.doi.org/10.1016/j.sbi.2010.03.009, |
Nanophage |
Function is to engulf target and prevent release, potential approach in pathology. Verification of target engulfed by luminescence. | This could be useful in pathology and/or sensing. | This idea was judged by an advisor to be time consuming to optimize and too large of a project to expect results within the timeframe. | http://www.nature.com/nnano/journal/v5/n3/pdf/nnano.2010.5.pdf , http://pubs.rsc.org/en/content/articlepdf/2007/cp/b700410a |
Swimming DNA dolphins |
The idea of creating tiny nanodolphins from DNA was intriguing so we considered potential practical applications for them, even though it was originally a mechanism of showing the agility of DNA folding software. Attaching magnetic metal nanoparticles to the noses and/or tails of the dolphins and allowing them to be moved by magnetic fields and thereby "swim" was contemplated. | A modified dolphin could be able to used to demonstrate an artistic method of navigating DNA objects in fluids. | The practical applications of creating swiming nanodolphins didn't make the project worthwhile. | http://pubs.acs.org/doi/abs/10.1021/nn800215j |
Nanodiamond tipped DNA Tweezers or Scissors |
This idea mixed the nanorobotics concept with nanodiamonds, which are a relatively inexpensive material with interesting properties. It was brought up out of curiosity over what unique properties diamonds possess at the nanoscale. | Robotics, or nanoscale assembly. | Other ideas were more compelling. | pg 94+ http://www.mse.ncsu.edu/CompMatSci/pdf/full4.pdf |