Biomod/2012/UCSD/tRiton Nano Architects/Brainstorm

From OpenWetWare
Jump to navigationJump to search

<html> <head> 

 <style>
  1. column-one { display:none; width:0px;}

.container{background-color: #ececec; margin-top:50px} .OWWNBcpCurrentDateFilled {display: none;}

  1. content {width: 0px; margin: 0 auto auto 0; padding: 1em 1em 1em 1em; align: center;}
  2. column-content {width: 0px; float: left; margin: 0 0 0 0;padding: 0;}

.firstHeading {display:none; width:0px;}

  1. globalWrapper{width:1280px; margin:auto}

body {background: #ececec!important;}

  1. column-one {display:none; width:0px;background-color: #ececec;}
  2. content{border:none;margin: 0 0 0 0; padding: 1em 1em 1em 1em; position: center; width: 800px;background-color: #ececec; }

.container{ width: 800px; margin: auto; background-color: #ececec; text-align:justify; font-family: helvetica, arial, sans-serif; color:#ececec; margin-top:25px; }

  1. bodyContent{ width: 1267px; align: center; background-color: #ececec;}
  2. column-content{width: 1280px;background-color: #ececec;}

.firstHeading { display:none;width:0px;background-color: #ececec;}

  1. header{position: center; width: 800px;background-color: #ececec;}
  2. footer{position: center; width:1280px;}
 </style>

</head> </html>

<html><center><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects'><img src=http://openwetware.org/images/a/a0/Trna_logo_with_title5.png width=1118px></a></center></html> <html><center><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects'><img src=http://openwetware.org/images/e/e5/Menuspacer2.png width=8px></a></center></html>

<html> <head> 

 <style type="text/css">

@import url(http://fonts.googleapis.com/css?family=Open+Sans:600);

/* Menu CSS */

  1. cssmenu, #cssmenu > ul{

background: url(http://openwetware.org/images/a/a0/Highlight-bg.png) repeat; padding-bottom: 3px; font-family: 'Open Sans', sans-serif; font-weight: 600;

}

  1. cssmenu:before, #cssmenu:after, #cssmenu > ul:before, #cssmenu > ul:after {

content: ''; display: table;

}


  1. cssmenu:after, #cssmenu > ul:after {

clear: both;

}

  1. cssmenu {

zoom:1;

}

  1. cssmenu > ul{

background: url(http://openwetware.org/images/0/04/Menu-bg2.png) repeat; margin: 0; padding: 0; position: relative;

}

  1. cssmenu > ul li{

margin: 0; padding: 0; list-style: none;

}

  1. cssmenu > ul > li{

float: left; position: relative;

}

  1. cssmenu > ul > li > a{

padding: 23px 26px; display: block; color: white; font-size: 13px; text-decoration: none; text-transform: uppercase; text-shadow: 0 -1px 0 #9e3825; text-shadow: 0 -1px 0 rgba(10, 12, 42, .70); line-height: 18px;

}


  1. cssmenu > ul > li:hover > a{

background: url(http://openwetware.org/images/4/48/Hover5.png) repeat; text-shadow: 0 -1px 0 #97321f; text-shadow: 0 -1px 0 rgba(32, 56, 112, .64);

}

  1. cssmenu > ul > li > a > span{

line-height: 18px;

}

  1. cssmenu > ul > li.active > a, #cssmenu > ul > li > a:active{

background: url(http://openwetware.org/images/b/b1/Active3.png) repeat;

}


/* Childs */

  1. cssmenu > ul ul{

opacity: 0; visibility: hidden; position: absolute; top: 120px; background: url(http://openwetware.org/images/a/a0/Highlight-bg.png) repeat; margin: 0; padding: 0; z-index: -1; -webkit-transition: all .35s .2s ease-in-out; -moz-transition: all .35s .2s ease-in-out; -ms-transition: all .35s .2s ease-in-out; transition: all .35s .2s ease-in-out;

}

  1. cssmenu > ul li:hover ul{

opacity: 1; visibility: visible; margin: 0; color: #000; z-index: 2; top:64px; left: 0;

}

  1. cssmenu > ul ul:before{

content: ''; position: absolute; top: -10px; width: 100%; height: 20px; background: transparent;

}


  1. cssmenu > ul ul li{

list-style: none; padding: 0; margin: 0; width: 100%;

}

  1. cssmenu > ul ul li a{

padding: 18px 26px; display: block; color: #393939; font-size: 13px; text-decoration: none; text-transform: uppercase; width: 150px; border-left: 4px solid transparent; -webkit-transition: all .35s ease-in-out; -moz-transition: all .35s ease-in-out; -ms-transition: all .35s ease-in-out; transition: all .35s ease-in-out; text-shadow: 0 1px 0 white;

}

  1. cssmenu > ul ul li a:hover{

border-left: 4px solid #0f2858; background: url(http://openwetware.org/images/a/a0/Highlight-bg.png) repeat; color: #20295C; text-shadow: 0 1px 0 black;

}

  1. cssmenu > ul ul li a:active{

background: url(http://openwetware.org/images/0/04/Menu-bg2.png) repeat;

} 

 </style type="text/css">

<div id='cssmenu'> <ul> 

  <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>

</ul> </div>

</head> </html>

<html><center><a href='http://openwetware.org/wiki/Biomod/2012/UCSD/tRiton_Nano_Architects'><img src=http://openwetware.org/images/a/ac/School.png width=1126px></a></center></html>

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 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.

Motion in liquid, magnetic steering, surface coating for biological camoflage

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

DNA, DNAzymes, electrodes Targeted Drug Delivery, error reduction upon recognition, close upon recognition of pathogen (through logic) 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 3 DNA Origami, Customizable 3D design. Stability/ tacking on other biological molecules text for row 1, column 3 text

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

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://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

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

DNA walker

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

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. ... 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

DNA lock box

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


Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2012/UCSD/tRiton_Nano_Architects/Brainstorm&oldid=637820"