Biomod/2011/IITM/AcidArtists/Reference papers/Paper 3

Details

• Title: Folding DNA into Twisted and Curved Nanoscale Shapes
• Authors: Hendrik Dietz, Shawn M. Douglas, William M. Shih
• Link: http://www.sciencemag.org/content/325/5941/725.short

From Images

Question one

What has been demonstrated in the picture?

Figure 1

• Possible crossover planes have been highlighted. These are placed at an interval of 7 base pairs. This is very similar to the observation made in the figure 1 of Douglas et. al.
• It has been proposed that teh section in between such planes can be viewed as a cell in an array.
• Cells that deviate from this standard length/interval experience strain due to the crossovers being inclined at an angle. This results in the cells exerting torque over other adjacent cells.
• <7 --> L Torque. >7 ---> R Torque
• "Global Bend Contributions", deletions for Left Handed, insertions for right handed and a combination of the two for "tunable" global bending with "cancellation of compensatory global twist contributions."""
• The pull and push also affect the neighboring strands and hence the size of the cells affect the overall shape of the helices!

Figure 2

• It's not about bending now so much as about twisting. And the keyword seems to be 10.5 bp per turn. Below it or above it and the 2D sheet itself twists.

• The DNA helix bundles migrate differently in a ethidium bromide agarose gel, depending on their twist and bp per turn.

• Half turns are not consistent in length but instead have a considerable standard deviation.

• A plot between global twist per turn and base pairs per turn is plotted. Standard deviation is again considerable nujmerically.

Figure 3

• First Glance : The most prominent figure seems to be the outcome of combinations of different radii of curvature and sectoral angle.

• These experiemnts were done on a 3 x 6 bundle of DNA.

• Some of the observed DNA bundles were marked faulty : Considering the fact that they did not have three (corresponding to 3x6 specification of the bundle) stripes at the corner. Or rather, the twist did not happen properly.

• There is a consistent standard deviation of around 5 degrees approximately for allbends of central angle from 30 - 90 degree in the experiement.

• Helical twist Density is measured in base pairs per turn and these vary across the layer of the bundle.

• The plot of the helical twist density versus layer is rather linear.

Figure 4

• One of the most amazing figures, with not much technical to observe.
• Very intricate figures have been made possible by identifying repeating units with bends and their subsequent <X>merization, <X> being greater than two.
• The combining of the repeating units happens through complementary ssDNA binding. This also points our attention to the fact that the repeating units are not entirely identical but differ slightly in their ssDNA overhangs and hence need to be made in separate chambers.
• Apart from the dimerizations and combinations, a spiral molecule has also been demonstrated. This is done merely by varying the twist density across the length.

Question two

What are the keywords and their relevance in the figures?

• Figure 1
  • Array Cells - defined as the section between two crossover planes (hypothetical or actual? min.. is 7 base pairs.). Manbipulations with their lengths results in the bending of DNA.
  • Insertions and deletions.
  • Strain and torque, L type, R Type

• Figure 2
  • BP/Turn
  • Helix Bundle
  • Twist Density
  • Standard Deviation

• Figure 3
  • Bend Angles : they are the central point of this figure
  • 3x6 helix bundle particles: Particles on whom the experiment is done.
  • TEM images :for charachterization
  • Double helical twist Density : The measurable parameter which affects the bend angles.

• Figure 4
  • Repeating Units and their combination through ssDNA binding.

Question 3

What are some of those words which are used prominently in the particular figure but are not central or core to the discussion?

• Figure 1
  • "Global Bend Contribution"

• Figure 2
  • Goniometer Angles
  • Node to Node Distance (?) (What exactly are Nodes?)
  • CCD (Charged Coupled Devices)
  • Goniometer Rotatio

• Figure 3
  • Radius of curvature

• Figure 4

Overview of the Paper

Question one

What does the paper suggest in the abstract?

Discussion

Two abilities of the DNA are suggested, twisting and beding. These are based on the number of base pairs per turn. These are observed in helix bundles of DNA. The degree of curvature can be controlled, and a twist can be of either handedness, but shows considerable standard deviation.

Question two

What conclusions are made towards the end?

Discussion

Complicated figures that involve curvatures have been synthesized.

Question Three

How can you make the jump from the abstract to the conclusion?

Discussion

Complicated figures are not synthesized in their etirety but single repeating unit with only one such feature are synthesized which are then combined with each other by the use of ssDNA complementary strands.

Question Four

• What is the relevance? (This might end up being a redundant question!)
• We need these techniques to make more intricate figures and shapes using DNA nanotech.