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

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)
• 6132 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)
  • latch connecting lid strands 012/013 to barrel strand 036
  • latch connecting lid strands 033/034 to barrel strand 015
• 6612 bp needed

Top lid latch design

Linker (24 bp) between lid strand 012 and lid strand 013 (part of scaffold):

5'- CTGGTGACGAAACTCAGTGTTACG -3'

3' end (21 bp) of scaffold of strand 036, followed by linker (12 bp) between lid strand 36 and 37 (part of scaffold):

5'- CCTCGACCCCAAAAAACTTGA TTTGGGTGATGG -3'

Scaffold-oligo-oligo-scaffold design:

5'- CGTAACACTGAG (poly-T) (14 bp) (toehold) -3'
5'- CCAAATCAAGTT (poly-T) (14 bp) (toehold) -3'

Old oligo:

38  036 11  036 10  036 09  037 09  037 10  037 11  
    TCAAGTT TTTTGGG GTCGAGG GGCGATG GCCCACT ACGTGAA 

New oligo:

38* 036 011 036 10  036 09  037 09  037 10  037 11  
    (latch) TTTTGGG GTCGAGG GGCGATG GCCCACT ACGTGAA 

Bottom lid latch design

Linker (24 bp) between lid strand 035 and lid strand 036 (part of scaffold):

5'- GCCCTGTAGCGGCGCATTAAGCGC -3'

Linker (12 bp) between strands 013 and 014, followed by 5' end of strand 014 (part of scaffold):

5'- ACCCCGCTAATC CTAATCCTTCTCTTGAGGAGT-3'

Scaffold-oligo-oligo-scaffold design:

5'- GCGCTTAATGCG (poly-T) (14 bp) (toehold) -3'
5'- GGATTAGGATTA (poly-T) (14 bp) (toehold) -3'

Old oligo:

17  015 00  014 00  
    AGCCACC GGATTAG 

New oligo:

17* 015 00  014 00  
    AGCCACC GGATTAG GATTA...

Inward aptamers

Old oligo (42 bp):

 1  013 08  014 08  014 07  015 07  015 08  016 08  
    GGAATAG GGAACCT ATTATTC ACCCTCA GAGCCAC TTTCATC 

New oligo (60 bp):

 1* 013 08  014 08  014 07  015 07  015 08  016 08  
    GGAATAG GGAACCT ATTATTC ACCCTCA GAGCCAC TTTCATC TTT GGTTGGTGTGGTTGG

Old oligo (42 bp):

 2  036 07  035 07  035 08  034 08  034 07  033 07  
    AAGCACT AGTAAAA GAGTCTG ACTTGCC TGAGTAG ACAGAGG 

New oligo (60 bp):

 2* 036 07  035 07  035 08  034 08  034 07  033 07  
    AAGCACT AGTAAAA GAGTCTG ACTTGCC TGAGTAG ACAGAGG TTT GGTTGGTGTGGTTGG

Old oligo (42 bp):

 1  004 03  004 02  004 01  005 01  005 02  005 03  
    AGTCAGA AGCAAAG CGGATTG GTAATAG TAAAATG TTTAGAC 

New oligo (53 bp):

 1* 004 03  004 02  004 01  005 01  005 02    
    AGTCAGA AGCAAAG CGGATTG GTAATAG TAAAATG TTT GGTTGGTGTGGTTGG

Outward apatmers

Old oligo (42 bp):

 1  010 07  011 07  011 08  012 08  012 07  013 07  
    GGCAAAA ATCAGCT TGCTTTC TTTCAAC AGTTTCA ATAGCCC 

New oligo (60 bp):

 1* 010 07  011 07  011 08  012 08  012 07  013 07  
    GGCAAAA ATCAGCT TGCTTTC TTTCAAC AGTTTCA ATAGCCC TTT GGTTGGTGTGGTTGG

Old oligo (42 bp):

 1  031 04  031 05  031 06  032 06  032 05  032 04  
    TCAGATG ATGGCAA TTCATCA CACCTTG CTGAACC TCAAATA 

New oligo (53 bp):

 1* 031 04  031 05  031 06  032 06  032 05    
    TCAGATG ATGGCAA TTCATCA CACCTTG CTGAACC TTT GGTTGGTGTGGTTGG

Old oligo (28 bp):

 1  019 02  020 02  020 01  020 00  
    TTTATCC TCTTTCC AGAGCCT AATTTGC 

New oligo (39 bp):

 1* 019 02  020 02  020 01  
    TTTATCC TCTTTCC AGAGCCT TTT GGTTGGTGTGGTTGG

To do

• reprogram oligos using my program — done
  • use p8256 — decided not to use, 7308 is sufficient for now, has no insert
• check my program's output vs. OTP_ra (using Fifer's script) — spot-check is successful. thank you Fifer!
• spot-check oligos against "flowed" scaffold using InDesign — wrote script instead of using InDesign, but spot-checking successful, and caught bug in program
• make modifications on latch design — done
• 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

Matthewmeisel 17:32, 3 July 2006 (EDT)

Design figures

• 

  Version 3.0: top view, with cross sections of lids

• 

  Version 3.0: schematic of DNA scaffold

• 

  Version 3.1 top view, with cross sections of lids

• 

  Version 3.1: schematic of DNA scaffold (Illustrator file)

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.