Biomod/2011/IITM/AcidArtists/Reference papers/Paper 2

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Regarding Images

Question one

Figure One

  • Crossovers (Staple strands jumping helices) join adjacent helices. however, in the expanded and flattened two dimensional sheet, these crossovers do not seem to be at adjacent sections. This implies and points out the fact that adjacent helices may actually be very distant in terms of the DNA sequence of the scaffold strand.
  • The seven base pair equidistant potential crossovers have been shown in the cross section. Their relevance in the bend/twist paper is the torque that they can generate if the crossovers are not placed at the distance of 7 base pairs or a multiple. However, here they are merely introduced.

Figure Two

  • TEM micrographs of seven different shapes have been shown.
  • The conditions for imaging having been outlines (a useful reference)
  • It gives the impression of a charachterization procedure
  • Intensity perpendicular to the helical axis has been measured and superposed on an expected intensity profile. The intensity profile is plotted for a point which traverses distance along the line orthogonal to the Z axis ( Helical Axis).
  • In the example shown, the monolith particle has been charachterized. However, what is interesting in this otherwise dull particle is that the expected intensity profile has two "shoulders" near every peak which perhaps correspond to the "bumpy" surface of a honeycomb lattice.
  • The peak to peak distance can be correlated to the radius of the helical bundle. So, peak to peak distance should be a constant and the position of the peak with respect to their peak index should be a linear graph. This can be a very good way to judge the quality of annealing/self assembly.
  • The plot in this example has error bars at peak indices which correspond to width of the peak (ideally they should have been point like?)
  • Histogram of peak to peak distances has a very small standard deviation.
  • The expected intensity profile of a square nut is considerably different from a vanilla monolith particle.What do the two smaller peaks correspond to?

Figure Three

  • The title is self explanatory. The folding and it's quality is investigated through GEL analysis and TEM analysis.
  • Different "Thermal Annealing Ramps" were used with the intention of varying the time over which the annealing happens. There was a very short 1.2 h ramp that was used and then there were a series of longer ramps which reduced the temperature in two steps - one shorter step that reduced from 80 to 60 and then another step which reduced the temperature further at slower paces.
  • 16 mM MgCl2 concentration seems appropriate for folding while at this concentration of MgCl2, excess NaCl inhibits folding.

Figure Four

  • Polymerization of Stacked cross polymer has been demonstrated. This polymerization of the monomer happened in the presence of staple strands that functioned as the connector
  • Icosahedron was synthesized in a similar fashion, however it is important to note that the units were not all identical.