Biomod/2012/Harvard/BioDesign/protocols

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=Small Canvas SST=
=Small Canvas SST=
==How to Design==
==How to Design==
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'''[https://www.dropbox.com/sh/lahfbz85lqiumr0/Yg9EL0uf3u Small Canvas SST Sequence Files]'''
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In order to design and further manipulate the small canvas SST files, use the following tools:
In order to design and further manipulate the small canvas SST files, use the following tools:
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==How to Make==
==How to Make==
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==How to Analyze==
==How to Analyze==

Revision as of 23:40, 26 October 2012



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)



Contents

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

DyNAMic Workbench is an online tool that we used for designing and manipulating our DNA sequences to anneal at specific temperatures.

  1. Login
  2. Click Tools -> DD
  3. Add sequences, and fix base positions - capital letters remain constant, lower case letters mutate (double click on sequence to edit)
  4. Select desired nucleotides to include in mutations (double click on composition and choose from scroll down menu)
  5. Hit mutate - the lower the score, the better

Image: DyNAMiC Workbench.png

NUPACK

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

Image: NUPACK.png


Oligo Analyzer

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

Image: Oligo_Analyzer.png


Sequence Massager Sequence Massager is an online tool that we used for reversing or finding the complement strands for our SST sequences.

Image: Sequence_Massager.png

  • Click Reverse and Complement as needed


MFold

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

Image: MFold.png

How to Make

How to Analyze

DNA Origami

How to Design

  1. Download Cadnano2 and follow installation directions
  2. Watch the tutorials on YouTube
  3. Download and manipulate DNA Origami file and generate DNA sequences. Edit and add sequences as needed.
  4. Order strands via Integrated DNA Technologies or a similar DNA synthesis company

How to Make

How to Analyze

Large Canvas SST

How to Design

How to Make

==How to Analyze==
Personal tools