Oneclickfeature: Difference between revisions
| Line 71: | Line 71: | ||
The traditional algorithm of Hamiltonian circuit/circle was modified and adjusted for the finding of folding pathway in DNAmazing. | The traditional algorithm of Hamiltonian circuit/circle was modified and adjusted for the finding of folding pathway in DNAmazing. | ||
DNAmazing has been tested for various 2D structures with arbitrary shapes and holes. The positions of crossover are implicitly determined during the process of folding the scaffold strand and are not shown here. | DNAmazing has been tested for various 2D structures with arbitrary shapes and holes. The positions of crossover are implicitly determined during the process of folding the scaffold strand and are not shown here. | ||
These results can be easily reproduced by using the DNAmazing program in this report. | |||
==The generation of a 1 hole structure == | ==The generation of a 1 hole structure == | ||
Revision as of 21:27, 2 November 2011
<html><head> <style type="text/css"> .main { margin: 0 auto; width: 804px;border-style:solid; border-width:5px; }
- logo{ margin:10px 0 0 52px; display:block; background:url('http://openwetware.org/images/7/74/Banner20.png') 0 0 no-repeat; width:700px; height:200px; text-indent:-9999px;}
.navbox { position: relative; float: left; }
- menu{ background:url('http://openwetware.org/images/3/3f/Menu_bg.png') 0 0 no-repeat; width:643px; height:100px; margin:51px 0 0 78px; padding-top:100px}
- menu li{ float:left;}
- menu a{ font-size:30px; color:#000000; line-height:1.2em; text-decoration:none; letter-spacing:-1px;}
.nav1{ padding:26px 0 0 37px;} .nav2{ padding:16px 0 0 30px;} .nav3{ padding:36px 0 0 17px;} .nav4{ padding:16px 0 0 19px;} .nav5{ padding:26px 0 0 30px;}
- menu .nav1 a:hover{ color:#bb0e0e}
- menu .nav2 a:hover{ color:#ca6509}
- menu .nav3 a:hover{ color:#3f9711}
- menu .nav4 a:hover{ color:#0ca0ce}
- menu .nav5 a:hover{ color:#8606c5}
</style> </head>
<div class="extra"> <div id="page_1"> <div class="main" style="padding-top:10px; padding-bottom:10px"> <!--header --> <header> <a href="index.html" id="logo">DNAmazing asfsaf. Smart. Effective</a> <nav> <ul id="menu"> <li class="nav1"><a href="http://openwetware.org/wiki/User:NUS_Dnamazing">Home</a></li> <li class="nav2"><a href="http://openwetware.org/wiki/DNAmazingMission">Mission</a></li> <li class="nav3"><a href="http://openwetware.org/wiki/DNAmazingProcess">Process</a></li> <li class="nav4"><a href="http://openwetware.org/wiki/DNAmazingResult">Results</a></li> <li class="nav5"><a href="http://openwetware.org/wiki/DNAmazingResources">Resources</a></li> </ul> </nav> </header> <!--header end-->
</div>
</div>
</div> </html>
"One-click" feature to get the results
The DNAmazing program successfully
- Perform the automatic generation of possible scaffold folding paths from users' input and crossover positions for 2D DNA Origami structures
- Generate possible sticky end sequences
- Generate staple sequences with sticky ends which are necessary to conduct wet lab experiments for 2D DNA Origami structures.
With the "one-click" feature, the processing of DNA Origami design can be accelerated as users no longer have to do the raster filling (the folding path) manually which is definitely tedious for large and complex structure.
Automatic generation of possible folding paths and crossover positions
The traditional algorithm of Hamiltonian circuit/circle was modified and adjusted for the finding of folding pathway in DNAmazing.
DNAmazing has been tested for various 2D structures with arbitrary shapes and holes. The positions of crossover are implicitly determined during the process of folding the scaffold strand and are not shown here.
These results can be easily reproduced by using the DNAmazing program in this report.
The generation of a 1 hole structure
The generation of a 2 hole structure
The generation of a "smiling face" structure
Generate sticky end sequence
To support generation of sticky end, as well as, to ensure that the sticky end will not affect the scaffold folding, an additional component is provided. User can choose to manually input a DNA sequence, and the program can help to check for the most stabilizing binding position in the scaffold. The binding energy is also calculated for users’ reference.
User can also ask the program to generate the sticky end sequence with the defined length. DNA sequences with binding energy higher than a limit defined are given. The below image illustrates the output of sticky ends' sequence generation.
