IGEM:Harvard/2006/DNA nanostructures/Container Design 3: Difference between revisions
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*Goal is easier and more regular lid attachment | *Goal is easier and more regular lid attachment | ||
*[[Media:Igemharv06_msm3.1.ai|Schematic of DNA scaffold (version 3.1)]] shows linker oligo locations (blue) and possible aptamer binding sites (green) | *[[Media:Igemharv06_msm3.1.ai|Schematic of DNA scaffold (version 3.1)]] shows linker oligo locations (blue) and possible aptamer binding sites (green) | ||
*[[Media:igemharv06_msm3_1.zip|code and output]] | |||
===Dimensions=== | ===Dimensions=== |
Revision as of 18:50, 1 July 2006
Version 3.0
- This is a top view with top and bottom (lids) unattached.
- Each tube is 84 turns (or 27.5 nm) long.
- The pleated sheets connected to the box by red lines are cross-sectional views of the top and bottom (lids).
- The red lines represent short single-stranded linker sequences in the scaffold.
- Notice that the scaffold strand first enters a lid on a positive coil and leaves it on a negative coil (or vice versa).
Dimensions
- 46 tubes (34.2 nm x 27.0 nm) x 84 bp strands (27.2 nm)
- each lid strand is connected to the adjacent barrel strand by a short single-strand linker
- each lid is 15 tubes wide (34.2 nm) x 84 bp (27.2 nm)
- total scaffold needed = 7116 bp
Version 3.1
- Structure is narrowed, ends are straightened
- Goal is easier and more regular lid attachment
- Schematic of DNA scaffold (version 3.1) shows linker oligo locations (blue) and possible aptamer binding sites (green)
- code and output
Dimensions
- 42 tubes (36.8 nm x 27.0 nm) x 84 bp strands (27.2 nm)
Notes about designs
- Calculating coil length: The distance between stacked base pairs is approximately (3.4 nm / turn) / (10.5 bp / turn) = 0.324 nm / bp.
- Calculating sheet length: The length of a "sheet" can be calculated using simple trigonometry, as demonstrated by the diagram below.
- The effective diameter of a coil is 3 nm according to Dr. Shih, but I'm not 100% sure that this figure is correct, so I will call it d until we can verify it.
Design details
based on n = 0.324 nm, d = 3.0 nm
Shape | Lid ply | Cylinder design | Lid design | Total scaffold length |
honeycomb rectangle | single | 46 tubes (34.2 nm x 27 nm) x (84+12)bp long (30.8 nm) | 15 tubes (34.2 nm) x (84+12)bp long (30.8 nm) | 7116 |