Biomod/2011/NUS/DNAmazing

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(3. Why are we interested in creating DNAmazing?)
 
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[[Biomod/2011/NUS/DNAmazing|'''Home''']]=====[[About us|'''About us''']]=====[[DNAmazing 101|'''DNAmazing101''']]=====[[DNAmazing report| '''Our Report''']]
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<a href="index.html" id="logo">DNAmazing asfsaf. Smart. Effective</a>
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<li class="nav1"><a href="http://openwetware.org/wiki/User:NUS_Dnamazing">Home</a></li>
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<li class="nav2"><a href="http://openwetware.org/wiki/DNAmazingMission">Mission</a></li>
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<li class="nav3"><a href="http://openwetware.org/wiki/DNAmazingProcess">Process</a></li>
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<li class="nav4"><a href="http://openwetware.org/wiki/DNAmazingResult">Results</a></li>
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=      Everything you need to know about DNAmazing in 5 minutes=
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==1. What is DNAmazing?==
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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.
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==2. Why another CAD program while there are several good ones?==
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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.
 +
 
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==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. This is really a challenge as we have a different approach to design the CAD program compared to existing ones and none of our team members has been trained in computing science.
 +
 
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==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
 +
 
 +
<br>
 +
 
 +
'''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.
 +
[[DNAmazingResult]]
 +
==5. What are DNAmazing features and how are they compared to other developed CAD programs?==
 +
*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
 +
Be interested in how we develop the program, visit [[DNAmazingProcess]]
 +
==6. How can I run the DNAmazing?==
 +
It is easy to run and experience the program. Download it here.
 +
 
 +
==7. What are current limitations and future developments?==
 +
Problems:
 +
*The first version of DNAmazing may have long processing time to handle complicated or large structures.
 +
*There may be some exceptional structures which may not handled properly
 +
*The program is only used for 2D Origami
 +
*Due to the limitation of time, the results of DNAmazing which have been compared to other CAD programs have not been tested in wet lab experiments.
 +
Future developments:
 +
*Parallel computing or improvement on the algorithm may be considered to reduce the processing time
 +
*As the principles and layout has been developed for 2D, DNAmazing can be extended into the regime of 3D Origami with curved structures
 +
*More rigid computational tools can be included to analyze the chemical properties of sticky ends.
 +
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Current revision


Contents

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. This is really a challenge as we have a different approach to design the CAD program compared to existing ones and none of our team members has been trained in computing science.

4. What are the goals and our achievements in this project?

Goals: DNAmazing was expected to


  1. Automatically generate folding path
  2. Automatically determine crossover position
  3. Automatically generate DNA staple sequence
  4. Design of sticky ends
  5. Basic chemical toolkits to determine the chemical properties of stick ends


Achievements: DNAmazing is able to


  1. 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.
  2. Select the most suitable folding paths for DNA Origami
  3. Automatically determine crossover position
  4. Automatically generate DNA staple sequence
  5. Design of sticky ends
  6. Basic chemical toolkits to determine the chemical properties of stick ends
  7. Bonus: Provide basic user-friendly interface.

DNAmazingResult

5. What are DNAmazing features and how are they compared to other developed CAD programs?

  • 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

Be interested in how we develop the program, visit DNAmazingProcess

6. How can I run the DNAmazing?

It is easy to run and experience the program. Download it here.

7. What are current limitations and future developments?

Problems:

  • The first version of DNAmazing may have long processing time to handle complicated or large structures.
  • There may be some exceptional structures which may not handled properly
  • The program is only used for 2D Origami
  • Due to the limitation of time, the results of DNAmazing which have been compared to other CAD programs have not been tested in wet lab experiments.

Future developments:

  • Parallel computing or improvement on the algorithm may be considered to reduce the processing time
  • As the principles and layout has been developed for 2D, DNAmazing can be extended into the regime of 3D Origami with curved structures
  • More rigid computational tools can be included to analyze the chemical properties of sticky ends.
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