IGEM:Harvard/2006/DNA nanostructures/Container Design 3: Difference between revisions
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====Outward apatmers==== | ====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 (46 bp): | |||
1* 019 02 020 02 020 01 | |||
TTTATCC TCTTTCC AGAGCCT TTT GGTTGGTGTGGTTGG | |||
====To do==== | ====To do==== |
Revision as of 09:23, 6 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)
- 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 (46 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.