Biomod/2011/IITM/AcidArtists/Reference papers/Paper 1

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The beginning

Self Assembly Process mimicing has "entered" a new phase. DNA Nanotechnology is field that relies on the programmable molecular recognition and assembly. It all depends on Watson and Crick Base Pairing.

Three Strategies first of all:

  • 1) 1998 : Tile and Lattice Strategy. Holliday junctions with overhangs that bind to each other while cooling.
  • 2) 2006 : Scaffold with staple DNA. Sheets with any shape and pattern.
  • 3) 2009 : Layers, intrinsically 3D, Scaffold strand into a layer of helices. Anything which can be "Carved" out can be in principle made through this technique. Hollow thigns might not be made.

Another approach : Make sheets and connect them in different planes, making 3D structures out of intrinsically 2D sheets.


Conclusion :

  • 1) For Douglas et al's method :
    • a) Route the scaffold
    • b) Define enough junctions between adjacent helices. Adjacent is the keyword.
  • 2) Make hierarchical structures, consisting from several subunits - an already existing goal of nanotechnology. (Why is this a goal needs to be elucidated.)


We have been using caDNAno which uses the appraoch of Douglas et. al. described/reviewed in the paper. However, unlike the paper, we have used a square lattice. They have used a honeycomb lattice. The production of the icosahedron in the actual paper has to be seen.

Regarding Images

Question one

What do the images demonstrate?

  • DNA sculpture : Making objects out of DNA Double helices.
  • Tubes in honeycomb lattice ---> remove sections ----> One part of the tube is by routing a scaffold strand ---> held in place, crosslinked across tubes by "staple" strands ---> folding "directed" by staple strands.

Question Two

What are the keywords corresponding to the figure?

  • Scaffold Strand
  • Sculpture
  • Staple Strands
  • Folding Directed