====== DNA Nanostructures ======

** 14th of September - William Shih (Wyss Institute) **
[[http://connectmedia.waag.org/AcadeMany/bio-2016/09/14/index.html|Recordings]]
{{vimeo>182727450?medium}}
{{vimeo>182729831?medium}}

=== PDF slides ===
  * [[https://www.dropbox.com/s/x15jlaspyy29exl/160914_htgaa.pdf?dl=0]]

=== Reading assignment to prepare for lecture ===
  * [[http://www.nature.com/nnano/journal/v6/n12/full/nnano.2011.187.html]]
  * [[http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-060308-102244]]

=== Reading useful for the homework assignment ===
  * [[http://www.nature.com/nature/journal/v440/n7082/abs/nature04586.html]]
  * [[http://www.nature.com/nature/journal/v459/n7245/full/nature08016.html]]
  * [[http://www.sciencemag.org/content/325/5941/725]]
  * [[http://nar.oxfordjournals.org/content/37/15/5001]]

=== Software needed for the homework assignment ===
  * [[http://cadnano.org/legacy]]
caDNAno and linux users:
  * [[https://github.com/cadnano/cadnano2.5]]

=== caDNAno software tutorials useful for the homework assignment ====
  * [[https://www.youtube.com/watch?v=cwj-4Wj6PMc&feature=youtu.be]]
  * [[https://www.youtube.com/watch?v=EabqNaYAI7o&feature=youtu.be]]

=== Homework assignment ===
  * Build flattened Rothemund rectangle in caDNAno; use square lattice (output: json file)
    * Color all staple strands light gray
    * [[https://www.dropbox.com/s/w2c6dld35ma2a79/160914_flat_rectangle.pdf?dl=0]]
  * Generate staple strand sequences in caDNAno (output: list of sequences in tab delimited text file)
  * Generate at least three examples of pixel art with six colors (output: svg files)
    * Use color palette of red, orange, yellow, green, blue, purple; for background, use light gray
    * [[https://www.dropbox.com/s/bup1p46rxfns4aw/160914_pixel_map.svg?dl=0]]
    * [[https://www.dropbox.com/s/gtqdndfqh803fcx/160914_pixel_art_example.png?dl=0]]
  * Generate at least three examples of pixel art with only one color (output: svg files)
    * Use black for on pixel, light gray for off pixel
  * Generate ASCII file representation of the images (output: text file)
    * [[https://www.dropbox.com/s/xm4nwnrrtk1vd68/150914_rectangle_pattern_empty.txt?dl=0]]
    * [[https://www.dropbox.com/s/gdpihkrt2qp24op/150914_rectangle_pattern_example.txt?dl=0]]

=== Extra-credit homework assignment (not required to pass the course) ===
    * Extra-credit (not required): write a script that converts from the svg file representation above to the ASCII representation below
  * [[https://www.dropbox.com/s/a8872vj86r2oqox/150830_extra_credit_files.zip?dl=0]]
  * Generate caDNAno-format json file encoding 24 strand flat rectangle from a Python script
  * Write a Python script that outputs the sequences in 96-well format according to pattern described by
    * [[https://www.dropbox.com/s/8wce2okbz08pg05/150830_empty_pipetting_rectangle.txt?dl=0]]
    * These are the pixels with value 0
  * Write a Python script that outputs the sequences with TTATACATCTAG appended to the end of each
    * These are the pixels with value P1