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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Our Brainstorming 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 Components Uses Technique Source

DNA box with lid

text for row 1, column 2 1. Scaffold to encase nanosize cargo. 2. items for X-ray crystallography; Functionalize inside of box to trap pathogens (virus) then close text for row 1, column 3 http://www.nature.com/nature/journal/v459/n7243/full/nature07971.html

DNA tetrahedron

text for row 2, column 2 1. Scaffold to encase nanosize cargo 2. items for X-ray crystallography text for row 1, column 3 http://pubs.rsc.org/en/Content/ArticleLanding/2004/CC/b402293a

DNA octahedron

text for row 2, column 2 1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography text for row 1, column 3 http://www.nature.com/nature/journal/v427/n6975/full/nature02307.html

DNA bipyramid

text for row 2, column 2 1. Scaffold to encase nanosize cargo 2.items for X-ray crystallography text for row 1, column 3 http://pubs.acs.org/doi/abs/10.1021/ja071493b

DNA walker

text for row 2, column 2 Motion w/ cargo delivery along designated tracks text for row 1, column 3 http://www.nature.com/nnano/journal/v5/n11/full/nnano.2010.190.html

DNA dolphins with flexible tails

text for row 2, column 2 Demonstration of unique DNA shapes; potentially a new propulsion system under high Reynolds number. text for row 1, column 3 http://pubs.acs.org/doi/abs/10.1021/nn800215j

Biochemical Aptamers

text for row 2, column 2 Biodetection of molecules or short oligos. text for row 1, column 3 http://en.wikipedia.org/wiki/Aptamer, http://www.sciencedirect.com/science/article/pii/S0003269701951693

DNA computational circuits

text DNA, DNAzymes, electrodes text 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

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

DNA shapes – curved and twisted

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

Liquid Crystal

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

DNA molecular robots [spider]

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

DNA origami tubes

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

Complex weaves

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3 text for row 1, column 3

Project Ideas:

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. While it was feasible, 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://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 Robotic Arm with Light-activated Joints and Tweezers as Hands

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3

DNA Art

creating 2D masterpieces out of colored/fluorescent nanomaterials on a DNA weave text for row 2, column 3 text for row 1, column 3

Nanophage

Function is to engulf target and prevent release, potential approach in pathology. Verification of target engulfed by luminescence. text for row 2, column 3 text for row 1, column 3 http://pubs.acs.org/doi/abs/10.1021/ja071493b

DNA walker

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3

Swimming DNA dolphins

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3

Nanodiamond tipped DNA Tweezers or Scissors

text for row 2, column 2 text for row 2, column 3 text for row 1, column 3


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