Biomod/2012/Harvard/BioDesign/protocols
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Clarity: Is the project description well-written and easy to understand? Does it include the background and motivation of the project, methods, results, and discussion? Are the figures easy to understand? (10 points)
Transparency: Are all of the raw experimental data and source files easily accessible? Would it be straightforward to attempt to reproduce the team's results? (5 points)
Small Canvas SST
How to Design
Small Canvas SST Sequence Files
In order to design and further manipulate the small canvas SST files, use the following tools:
DyNAMic Workbench is an online tool that we used for designing and manipulating our DNA sequences to anneal at specific temperatures.
- Login
- Click Tools -> DD
- Add sequences, and fix base positions - capital letters remain constant, lower case letters mutate (double click on sequence to edit)
- Select desired nucleotides to include in mutations (double click on composition and choose from scroll down menu)
- Hit mutate - the lower the score, the better
NUPACK is an online tool that we used for computing the temperature at which our SST structures would melt.
Settings:
- Compute melt
- Concentration: 1 μM
Oligo Analyzer is an online tool that we used for determining if any of our SST structures would bind complementary to themselves.
Settings:
- Target type: DNA
- Oligo Conc: 1 μM
- Na+ Conc: 0mM
- Mg++ Conc: 10mM
- dNTPs Conc: 0 mM
- Use Analyze and Self-Dimer to optimize
Sequence Massager
Sequence Massager is an online tool that we used for reversing or finding the complement strands for our SST sequences.
- Click Reverse and Complement as needed
MFold is an online tool that we used for determining the temperatures at which our SST structures would form.
Settings:
- Na+: 0 mM
- Mg++: 10 mM
- Folding temperature: 25°C
How to Make
How to Analyze
DNA Origami
How to Design
- Download Cadnano2 and follow installation directions
- Watch the tutorials on YouTube
- Download and manipulate DNA Origami file and generate DNA sequences. Edit and add sequences as needed.
- Order strands via Integrated DNA Technologies or a similar DNA synthesis company
