Biomod/2011/IITM/AcidArtists/Reference papers: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
Line 387: Line 387:
== Paper 7 ==
== Paper 7 ==


=== Title ===
=== DNA Robots ===
=== Summary ===
=== Summary ===
==== To Do ====
==== eMail ====


Paper 7 is an article on DNA robots. In the initial part it tells how this field emerged. They have already given up on making DNA computers for computational work because DNA computers are slow, error-prone, and difficult to scale up to perform millions of operations. But these DNA computers can process information inside organisms where conventional computer chips can’t go. DNA robot works on a very simple principle. The robots’ legs are DNA strands that bind to specific complementary DNAs on a predesigned surface. a specific DNA snippet,known as a “fuel” strand was added. Each fuel strand acts like a computer command telling the walker what to do next. The first fuel strand binds the site on the track holding the back “leg” of a two-legged walker, causing it to unbind from its DNA partner on the surface, and then bind to another DNA sequence past the front leg. Another snippet is then added to move the second leg forward, and so on.
Paper 7 is an article on DNA robots. In the initial part it tells how this field emerged. They have already given up on making DNA computers for computational work because DNA computers are slow, error-prone, and difficult to scale up to perform millions of operations. But these DNA computers can process information inside organisms where conventional computer chips can’t go. DNA robot works on a very simple principle. The robots’ legs are DNA strands that bind to specific complementary DNAs on a predesigned surface. a specific DNA snippet,known as a “fuel” strand was added. Each fuel strand acts like a computer command telling the walker what to do next. The first fuel strand binds the site on the track holding the back “leg” of a two-legged walker, causing it to unbind from its DNA partner on the surface, and then bind to another DNA sequence past the front leg. Another snippet is then added to move the second leg forward, and so on.

Revision as of 23:46, 2 November 2011

<html> <head> <style> /*

  1. bodyContent{text-align:center;}
  • /

ul.polaroids { width: 970px; margin: 0 0 18px -30px; } ul.polaroids li { display: inline; } ul.polaroids a{display: inline; float: left; margin: 0 0 27px 30px; width: auto; padding: 10px 10px 15px; text-align: center; font-family: "Marker Felt", sans-serif; text-decoration: none; color: #333; font-size: 18px; -webkit-transform: rotate(-2deg); -webkit-transition: -webkit-transform .15s linear; -moz-transform: rotate(-2deg); } ul.polaroids img { display: block; width: 300px; margin-bottom: 12px; -webkit-transform: rotate(-2deg); -webkit-transition: -webkit-transform .15s linear; -moz-transform: rotate(-2deg); }

  1. content{

color:#111; background:none; border:none; } .portlet .pBody { border:none; background:none; z-index:-1; } .portlet a{color:#white;} .pBody a{color:#white;}

  1. footer{background:none; border:none;}
  2. footer li{color:#333;;}
  3. footer li a {color:#333;;}


h1, h2, h3, h4, h5, h6, p, a, pre{color:#333;; font-family: 'Trebuchet MS', Helvetica, sans-serif;}

  1. menu ul{list-style:none;}
  2. menu ul li{float:left; width:125px; text-align:center; background:#234ade; margin:5px; cursor:pointer}
  1. content_container{width:1%;height:10px; background:#333; position:absolute; top:260px; display:none; left:495%; opacity:0.8;

border-radius:20px;-moz-border-radius:20px;-webkit-border-radius:20px; border:1px #AAA solid; }

  1. close_container{position:absolute;left:98.5%;top:5px;,cursor:pointer;}

.contents{float:none; position:absolute; width:89%; text-align:justify; top:280px; display:none; height:316px; overflow:auto; padding:16px;}

.slide_show_pic{ position:absolute; top:-40px; left:160px; display:none; height:400px; }

/*stack*/

.stack { position: fixed; bottom: 60px; right: 60px; } .stack > img { position: relative; cursor: pointer; padding-top: 35px; z-index: 2; left:20px;} .stack ul { list-style: none; position: absolute; top: 5px; cursor: pointer; z-index: 1; } .stack ul li { position: absolute; } .stack ul li img { border: 0; } .stack ul li span { display: none; } .stack .openStack li span { 

   font-family: "Lucida Grande", Lucida, Verdana, sans-serif;  
   display:block;  
   height: 14px;  
   position:absolute;  
   top: 17px;  
   right:60px;  
   line-height: 14px;  
   border: 0;  
   background-color:#000;  
   padding: 3px 10px;  
   border-radius: 10px;  
   -webkit-border-radius: 10px;  
   -moz-border-radius: 10px;  
   color: #fcfcfc;  
   text-align: center;  
   text-shadow: #000 1px 1px 1px;  
   opacity: .85;  
   filter: alpha(opacity = 85);

}

.stack img{width:50px;}

/* IE Fixes */ .stack { _position: absolute; } .stack ul { _z-index:-1; _top:-15px; } .stack ul li { *right:5px; }

/*stack close*/

  1. sidebar_bg{

width:150px; background:#000; opacity:0.6; height:830px; display:block; position:absolute; left:-156px; top:-50px; z-index:-100; }

.picture{width:200px;}

ul.polaroids a:after { content: attr(title); } 

   /* By default, we tilt all our images -2 degrees */
   ul.polaroids a {
   -webkit-transform: rotate(-2deg);
   -moz-transform: rotate(-2deg);
   }
    
   /* Rotate all even images 2 degrees */
   ul.polaroids li:nth-child(even) a {
   -webkit-transform: rotate(2deg);
   -moz-transform: rotate(2deg);
   }
    
   /* Don't rotate every third image, but offset its position */
   ul.polaroids li:nth-child(3n) a {
   -webkit-transform: none;
   -moz-transform: none;
   position: relative;
   top: -5px;
   }
    
   /* Rotate every fifth image by 5 degrees and offset it */
   ul.polaroids li:nth-child(5n) a {
   -webkit-transform: rotate(5deg);
   -moz-transform: rotate(5deg);
   position: relative;
   right: 5px;
   }
    
   /* Keep default rotate for every eighth, but offset it */
   ul.polaroids li:nth-child(8n) a {
   position: relative;
   top: 8px;
   right: 5px;
   }
    
   /* Keep default rotate for every eleventh, but offset it */
   ul.polaroids li:nth-child(11n) a {
   position: relative;
   top: 3px;
   left: -5px;
   }

   /* Scale the images on hover, add transitions for smoothing things out, and ensure the hover appears on top */
   ul.polaroids img:hover {
   -webkit-transform: scale(1.25);
   -moz-transform: scale(1.25);
   position: relative;
   z-index: 5;
   }

hr{width:80%;}

.stuff_contents{ position:fixed; top:8%; left:13%; display:none; width:80%; color:white; z-index:101; }

  1. contents_stuff p{width:80%; }

</style> <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.6.2/jquery.min.js"/></script> <script>

jQuery(function () { 

   // Stack initialize  
   var openspeed = 300;  
   var closespeed = 300;  
   $('.stack>img').toggle(function(){  
       //reverse above  
       var $el=$(this);  
       $el.next().removeClass('openStack').children('li').animate({top: '55px', left: '-10px'}, closespeed);  
       $el.next().find('li a>img').animate({width: '50px', marginLeft: '0'}, closespeed);  
       $el.animate({paddingTop: '35'});  
   },function(){  
       var vertical = 0;  
       var horizontal = 0;  
       var $el=$(this);  
       $el.next().children().each(function(){  
           $(this).animate({top: '-' + vertical + 'px', left: horizontal + 'px'}, openspeed);  
           vertical = vertical + 55;  
           horizontal = (horizontal+.75)*2;  
       });  
       $el.next().animate({top: '-50px', left: '10px'}, openspeed).addClass('openStack')  
          .find('li a>img').animate({width: '50px', marginLeft: '9px'}, openspeed);  
       $el.animate({paddingTop: '0'});  
   }); 
 
   // Stacks additional animation  
   $('.stack li a').hover(function(){  
       $("img",this).animate({width: '56px'}, 100);  
       $("span",this).animate({marginRight: '30px'});  
   },function(){  
       $("img",this).animate({width: '50px'}, 100);  
       $("span",this).animate({marginRight: '0'});  
   });

});

function open_menu(){ var openspeed = 300; 

   var closespeed = 300;

var vertical = 0; 

       var horizontal = 0;  
       var $el=$('.stack>img');  
       $el.next().children().each(function(){  
           $(this).animate({top: '-' + vertical + 'px', left: horizontal + 'px'}, openspeed);  
           vertical = vertical + 75;  
           horizontal = (horizontal+.75)*2;  
       });  
       $el.next().animate({top: '-50px', left: '10px'}, openspeed).addClass('openStack')  
          .find('li a>img').animate({width: '50px', marginLeft: '9px'}, openspeed);  
       $el.animate({paddingTop: '0'});

}

jQuery(document).ready(function(){ var name; $(".picture").click(function(){ name="#"+$(this).attr("title"); $("#data_container").fadeIn(); $(name).fadeIn(); });

$("#close_dialog").click(function(){ $("#data_container").fadeOut(); $(name).fadeOut(); });

});

</script> </head>

<body onload="open_menu()">


<div class="stack"> <img src="http://openwetware.org/images/9/9f/Stack.png" alt="stack"> <ul id="stack">

<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Protocols"><span>Protocols</span><img src="http://openwetware.org/images/7/7b/Protocols_pr1.gif" alt="Overveiw"></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Brain_storming"><span>Brain Stroming</span><img src="http://openwetware.org/images/3/3f/Brain.png" alt="Brain Storming"></a></li> <li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Work_diary"><span>Work Diary</span><img src="http://openwetware.org/images/2/2a/Diary.png" alt="Work diary"></a></li> 

<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists/Overveiw"><span>Overview</span><img src="http://openwetware.org/images/1/13/Papers.png" alt="Overveiw"></a></li>

<li><a href="http://openwetware.org/wiki/Biomod/2011/IITM/AcidArtists"><span>Home</span><img src="http://openwetware.org/images/f/f0/Home-sm.png" alt="Project"></a></li> </ul> </div>


<div id="menu_desc" style="position:fixed; right:-38px; width:200px; text-align:center; bottom:36px; color:white; cursor:pointer"><b>Menu</b></div>

<div id="edit_able_content"></html> Here are some of the papers that got us started with DNA Nanotechnology. We have had several discussions around them. These are raw, unedited discussions across groups, but can be a good starting point for anyone to begin with the subject.

You can access the original excel sheet here: https://docs.google.com/spreadsheet/ccc?key=0AksFSlQDSLnWdEw1bWxaOUZEeEU1TjZhNDN0MnlJRFE&hl=en_US#gid=0

(It contains our discussions in the form of answers to generalized questions.)

Paper 1

Title

Summary

To Do

  • Review
  • Expand

eMail

Paper one is a review of another paper on 3D nanostructures and self assembly by Douglas et al. The keyword here is 3D. The smiley faces that we have seen in DNA origami papers are 2D and have been made from techniques that have arisen from a different paradigm. Paradigm - a central concept that sprouts other supporting ideas. The paper outlines three different paradigms of DNA nanostructures and goes on to mention that Douglas et al.'s method produces intrinsically 3D structures. Exactly how this method produces INTRINSICALLY 3D structures is a subject dealt with in the main paper and not the review. Read on the second paper - the one on self assembly and DNA nanostructures by Douglas et. al.

Paper 2

Self-assembly of DNA into nanoscale three-dimensional shapes

Authors: Shawn M. Douglas, Hendrik Dietz, Tim Liedl, Bjo¨rn Ho¨gberg, Franziska Graf , & William M. Shih

Summary

To Do

  • Review
  • Complete entire summary
  • Provide Workable Information

eMail

the purpose is to get started and not make it perfect for archiving, so I start off with whatever I know.

If you can take an overview, four figures form the main crux of the article.

1) Explaining the intricate 3D structure - starting from a planar representation of Staples and scaffolds to merging them in an intrinsically 3D structure. 2) Is the TEM analysis of the arranged particles. Of central importance are imaging the particles and also the intensity versus position graph. 3) and 4) I expect someone else to explain. If however, i find no reply in due time, I'll update myself.

Well, The summary I post right now is makeshift, so a perfect one needs some time. Anyways, you gotta make a start somewhere, right?

DNA is represented in cylindrical form by the color of the staple strand. XY plane to honeycomb lattice - this is something that needs to be done from the text of the article. Issues with staple lengths… To expand on the points: The first figure explains the making of a 3D (NOT 2D, see the paper 1 for a better understanding) nanostructure. The first section shows the proposed structure with staple and scaffold strands in XY plane. Note particularly how one type of staple turns into a different type of staple strand. For example, in the first section itself, we can see that a blue strand turns into a white one when a semicircular arc is complete.

The next two sections show the structure in half rolled and fully rolled forms. There is not much to note here, except the pitch and turn (read the paper) and also an obvious question : if the planar structure is folded over itself, then surely the semicircular arcs were symbolic and NOT representing any physical manifestation. Otherwise, we'd have an issue with the consistency of the length of the staple strands!

FIGURE TWO Starts off with projection and perspectives of all the expected particles.

What is not evident is the answer of the question : what do 5 different TEM pictures of the same type of particle do? Wouldn't one suffice? Answer is, ofcourse, in the article.

What are homogenous monodisperse fields? (These refer to a collection of 3D nanostructures in a gel like medium after the DNA has annealed!)

What is a monolith structure here?

Also, of note is the fact that we are now looking into DNA annealing and all other familiar details.

The type of medium required for TEM imaging has been described.

Two TEM images of a monolith particle, with an intensity profile have been shown. This is a way to analyze the fidelity of the structures with the proposed design. Obvious question, what physical parameter are we plotting when we plot "Intensity" versus the coordinates?

Other random points from my notes:

Experimental proofs? Intensity vs. expected grey intensity. How does a correlation between peak to peak distance and diameter come about? --> questionTwo types of analysis been plotted --> Intensity and peak indices. How was the second graph plotted? On the basis of what data? We are talking about h - the peak index versus the peak position What instrument was required for measuring the intensity profile? Then, what was it that made possible the exporting of the expected intensity profile?

Paper 3

Folding DNA into Twisted and Curved Nanoscale Shapes

Authors: Hendrik Dietz, Shawn M. Douglas, William M. Shih

Summary

To Do List

  • Insert Images
  • Review

eMail

One line summary: “targeted insertions and deletions of base pairs cause the DNA bundles to develop twist of either handedness, or to curve”.

The whole lattice [honey-comb lattice, in which each double stand has 3 nearest neighbours] is divided into cell arrays to simplify the visualization of this bending and curving. Each bundle [the pipe like str.] is joined to its nearest 3 neighbours at intervals of 21bp. Thus a connection occurs at each 7bp interval. If we imagine a planes, perpendicular to the helix axis, at all such connections then we get small pieces of ‘double stranded 7bp pipes’. This is called a cell. So now we talk about the whole structure as an array of such cells.

We assume that the DNA is in B-form [B-DNA are right handed helices, B-DNA has major and minor grooves of similar depths, & the bases are nearly perpendicular to the helical axis, which runs through the centre of each base pair.]

Now all the arrays are joined to each other at the 7th base pair.

ð So if we delete 1 or 2bp, then there will be over-winding, resulting in a pull and a torque in the left hand thumb direction[fig C]

ð If we insert 2bp, there will be local underwinding, resulting in a push and a right hand thumb direction torque.[fig C second part]

Paper 4

Paper 5

Paper 6

DNA Nanotechnology Grows Up

Authors:Robert F. Service

Details

Summary

To Do

  • Abhinav - Eliminate Copy Paste Paragraphs
  • Paraphrase
  • Abhinav - Format the text.

eMail

This paper gives us a decent idea about the different applications of dna nanotech which have been done. The paper in the beginning is about how seeman came to idea of dna nanotech. While drinking in a pub he thought about making dna lattices(crystals) in whose voids proteins can be trapped came into his mind for determing the structure of protein and even in different conformations.(he worked in the field of protein crystallography)

Over the next few years,Seeman’s lab turned out triangles, squares,and other shapes. Then came the 1991 cube,and by 1998 Seeman’s team had figured out

how to assemble such parts into an extended two-dimensional array.

Paul Rothemund and colleagues developed a technique called DNA origami with viral genome and staple strands. In 2009, Seeman mapped out the structure of crystal lattice of a series of triangles with a resolution of 4 angstroms which was still smaller for protein structure.

william Shih (hms) reported that he had for the first time used DNA nanotech tools to map the structure of a previously unsolved protein, using nuclear magnetic resonance (NMR) spectroscopy. The technique works by identifying the magnetic signature of atoms in proteins relative to their neighbors. By knowing each atom’s neighbors, researchers can piece together the structure of an overall protein.

In 1997 some researchers spiked a protein-containing NMR solution with a compound that spontaneously forms liquid crystals, materials that flow but have a regular molecular orientation like a crystal in which the protein was trapped and the the NMR results showed to spot clues such as the angle between two atoms bonded in a protein. A big drawbackto the technique and later variations of it isthat many cell-membrane proteins can stay in solution only with the help of detergents, which often tear apart the liquid crystals. Shih and colleagues replaced liquid crystals with origami-based DNA nanotubes that weren’t affected by detergents.

DNA nanotech’s growth isn’t limited to mapping proteins. At Kyoto University in Japan, chemical biologist Hiroshi Sugiyama has turned to DNA nanotechnology to help him watch protein catalysts carry out reactions in real time. Biophysicists are also looking to DNA constructions to help them investigate molecules one at a time. Dietz reported that he and his colleagues are using DNA origami to improve a now-standard set of biophysics tools to see what happens to proteins and DNA as they are pulled apart. the standard way is to use laser, beads and linkers. But linkers are floppy so So Dietz and his colleagues replaced the usual fl oppy linkers with stiff rods made fromDNA origami containing as many as 18 helical tubes each to see changes in protein activity under tension.

Shawn Douglas, lab of George Church at HMS, is working on a DNA origami nanorobot designed to seek out and destroy cancer cells. Douglas’s “robot” looks more like a hollow cylinder some 60 nanometers long and 25 nanometers across. He built it from DNA origami and stapled it closed using DNA strands called aptamers, which in this case were designed to bind specifi cally to molecules specific to cancer cells.the cylinders are loaded with fl uorescent immune-system proteins that bind to cancer cells and induce apoptosis and added them to cancer cells in an in vitro assay. The loaded cylinders bound to their targets, released their cargo, and killed up to 40% of the cells.

Paper 7

DNA Robots

Summary

Paper 7 is an article on DNA robots. In the initial part it tells how this field emerged. They have already given up on making DNA computers for computational work because DNA computers are slow, error-prone, and difficult to scale up to perform millions of operations. But these DNA computers can process information inside organisms where conventional computer chips can’t go. DNA robot works on a very simple principle. The robots’ legs are DNA strands that bind to specific complementary DNAs on a predesigned surface. a specific DNA snippet,known as a “fuel” strand was added. Each fuel strand acts like a computer command telling the walker what to do next. The first fuel strand binds the site on the track holding the back “leg” of a two-legged walker, causing it to unbind from its DNA partner on the surface, and then bind to another DNA sequence past the front leg. Another snippet is then added to move the second leg forward, and so on.

<html></div>

</body> </html>

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2011/IITM/AcidArtists/Reference_papers&oldid=564019"