Biomod/2012/Harvard/BioDesign/methods

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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)

Designing SST Structures

Cadnano2

Cadnano2 is software that we used for designing and visualizing DNA origami nanostructures.


DyNAMiC Workbench

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


NUPACK

NUPACK is an online tool that we used for computing the temperature at which our SST structures would melt.


Oligo Analyzer

Oligo Analyzer is an online tool that we used for determining if any of our SST structures would bind complementary to themselves.


Sequence Massager

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


MFold

MFold is an online tool that we used for determining the temperatures at which our SST structures would form.

Making SST Structures

Thermocycler 1-pot annealing 2-pot annealing

Analyzing SST Structures

Gel Electrophoresis Gel Imaging Gel Purification Centrifuge AFM

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