User:NUS Dnamazing: Difference between revisions
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==3. Why are we interested in creating DNAmazing?== | ==3. Why are we interested in creating DNAmazing?== | ||
Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch as Rothermund did | Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, in the beginning our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch for this purpose as Rothermund did in 3 months before he invented the technique of DNA Origami. | ||
==4. What are the goals and our achievements in this project?== | ==4. What are the goals and our achievements in this project?== | ||
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<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="#page_2">Home</a></li> <li class="nav2"><a href="#page_3">Mission</a></li> <li class="nav3"><a href="#page_4">Process</a></li> <li class="nav4"><a href="#page_5">Results</a></li> <li class="nav5"><a href="#page_6">Contacts</a></li> </ul> </nav> </header> <!--header end-->
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Everything you need to know about DNAmazing in 5 minutes
1. What is DNAmazing?
DNAmazing is a software dedicated for the design of DNA Origami structures. Like other CAD program in DNA Origami, such as caDNAnano, Nanoengineer, to name a few, DNAmazing helps designers determine the sequence of DNA strands.
2. Why another CAD program while there are several good ones?
Besides the basic functions of a CAD program in DNA Origami, DNAmazing was build on the vision of visualizing the applications of DNA Origami in the future: DNA motors operate on a complicated traffic system made by DNA Origami, complex nanoelectric circuits build from DNA Origami molds, and the organization of metal nanoparticles on DNA Origami platforms. These future DNA Origami designs are usually too complex to get the footprint done manually (the generation of the folding path, the determination of crossover positions, and the merging of staple sequences. Furthermore, these systems must find a way to interact with external devices, particles and environment. The best way may be the fabrication of sticky ends which act as connection sites. To our best knowledge, these features are not well focused in current CAD programs though we believe they are crucial in the future development of DNA Origami. Thus, CAD programs DNAmazing is expected to fulfill these gaps.
3. Why are we interested in creating DNAmazing?
Firstly, we conceive that a good DNA Origami structure must start from the good design, in other words a good CAD program. Furthermore, in the beginning our group had an idea of creating a complex traffic system on which DNA "motorcycles" operated. As mentioned above, this idea requires both the complexity of the system and the design of sticky ends as steps for DNA motorcycles. Hence, we decided to develop a CAD program from scratch for this purpose as Rothermund did in 3 months before he invented the technique of DNA Origami.
4. What are the goals and our achievements in this project?
Goals: DNAmazing was expected to
- Automatically generate folding path
- Automatically determine crossover position
- Automatically generate DNA staple sequence
- Design of sticky ends
- Basic chemical toolkits to determine the chemical properties of stick ends
Achievements:
DNAmazing is able to
- Automatically generate the folding of small and medium DNA Origami structures with arbitrary holes and shapes. Larger structures may take longer time to compute the possible folding paths.
- Select the most suitable folding paths for DNA Origami
- Automatically determine crossover position
- Automatically generate DNA staple sequence
- Design of sticky ends
- Basic chemical toolkits to determine the chemical properties of stick ends
- Bonus: Provide basic user-friendly interface.
5. What are DNAmazing features?
- Lithography-like Inputting
- "One-click" to results (Automatic generation of folding path, crossover positions, and staple sequence)
- Sticky ends generation
- Computational Toolkits
- User-friendly interface
- No programming required
- Free and Open Source
6. How can I run the DNAmazing?
It is easy to run and experience the program. Download it here.
