IGEM:Harvard/2006/DNA nanostructures/Container Design 3

Version 3.0

Version 3.0: top view, with cross sections of lids

• 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).

Version 3.0: schematic of DNA scaffold

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

Version 3.1 top view, with cross sections of lids

• 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)
• 6,468 bp needed

Version 3.2

Design changes

• lid linker sequences are 18 bp (4 bp previously)
• scaffold connector strands on lids are 24 bp (12 bp previously)
• one latch per lid (eight previously)
• 6612 bp needed

To do

• reprogram oligos using my program
  • use p8256
• check my program's output vs. OTP_ra (using Fifer's script)
• spot-check oligos against "flowed" scaffold using InDesign
• make modifications on latch design
• finalize aptamer locations
• divide oligos into the following categories:
  • core barrel oligos
  • core lid oligos
  • barrel oligos at inside apatamer locations
  • barrel oligos at outside aptamer locations
  • barrel oligos w/ inside apatmers
  • barrel oligos w/ outside aptamers
  • lid oligos at inside apatamer locations
  • lid oligos at outside aptamer locations
  • lid oligos w/ inside apatmers
  • lid oligos w/ outside aptamers
  • core oligos at latch locations
  • lid oligos at latch locations
  • core oligos w/ latches
  • lid oligos w/ latches
  • displacement strands

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.