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)
Tools for 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.
Tools for Making SST Structures
Thermal Cycler
The thermal cycler is a machine which we used to anneal our SST strands to form structures. It works by cycling tubes through predetermined temperatures and times.
Tools for Analyzing SST Structures
Agarose Gel Electrophoresis
Agarose Gel Electrophoresis is a method which we used in order to view our DNA SST structures separated by size. The agarose gel contains wells along the top in which one can place DNA samples. An electrical current pulls the negatively-charged DNA through the agarose gel. Smaller structures travel through the gel faster than larger structures.
