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

 Project Overview Designs Notebook Protocols Presentations Literature  

 Design 1</li> Design 2</li> Design 3</li> Design 4</li> Design 5</li> Design 6</li> </ul> <br style = "clear:both">

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
 * [[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

 * 42 tubes (36.8 nm x 27.0 nm) x 84 bp strands (27.2 nm)
 * 6132 bp needed

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 014/015 to barrel strand 034
 * latch connecting lid strands 033/034 to barrel strand 015
 * 6612 bp needed

Top lid latch design
Linker (24 bp) between lid strand 014 and lid strand 015 (part of scaffold): 5'- GTAAATTCAGAG ACTGCGCTTTCC -3'

3' end (21 bp) of scaffold of strand 034: 5'- GATGTTATTA CTAATCAAAGA -3'

Scaffold-oligo-oligo-scaffold design:

5'- GGAAAGCGCAGT TTTT TTAGAATCAACCAG ATCGGTATGGCA -3' 5'- TCTTTGATTAG TTTT CTGGTTGATTCTAA TAGATGTGGCAA -3' Displacement strands (42 bp and 41 bp, respectively): 5'- TGCCATACCGAT CTGGTTGATTCTAA AAAA ACTGCGCTTTCC -3' 5'- TTGCCACATCTA TTAGAATCAACCAG AAAA CTAATCAAAGA -3'

Scaffold-oligo-staple-oligo-scaffold design:

5'- GGAAAGCGCAGT TTTT TTAGAAT CAACCAG -3' 5'- TCGTGAA ATTCTAA TGGCCCCAATAC -3' 5'- CTGGTTG GGATAGA GAGCTGTTCACC -3' 5'- TCTTTGATTAG TTTT TCTATCC  TTCACGA -3' Displacement strands (26 bp each): 5'- GTATTGGGGCCA TTAGAAT TTCACGA -3' 5'- GGTGAACAGCTC TCTATCC CAACCAG -3'

Old core oligo: 36 034 11  034 10  034 09  035 09  035 10  035 11       TCTTTGA TTAGTAA TAACATC TCCATCA CGCAAAT TAACCGT

New core oligo: 36*        034 10  034 09  035 09  035 10  035 11                   TAA TAACATC TCCATCA CGCAAAT TAACCGT

Bottom lid latch design
Linker (24 bp) between lid strand 035 and lid strand 036 (part of scaffold): 5'- GCCCTGTAGCGG CGCATTAAGCGC -3'

3' end (21 bp) of scaffold of strand 013: 5'- ATCCGCC TGGTACT GAGCAAA -3'

Scaffold-oligo-oligo-scaffold design:

5'- GCGCTTAATGCG TTTT AGACGTAGTATCAC ATGCTCCACCCG -3' 5'- <font color="#6666FF">TGCGAAT AGTACCA TTTT GTGATACTACGTCT GAGAAGATGTGC -3' Displacement strands (42 bp and 44 bp, respectively): 5'- CGGGTGGAGCAT GTGATACTACGTCT AAAA CGCATTAAGCGC -3' 5'- GCACATCTTCTC AGACGTAGTATCAC AAAA TGGTACT <font color="#6666FF">ATTCGCA -3'

Scaffold-oligo-staple-oligo-scaffold design:

5'- GCGCTTAATGCG  TTTT AGACGTA  GTATCAC -3' 5'- TCCTGCA TACGTCT ATGCTCCACCCG -3' 5'- GTGATAC TATCTAT GAGAAGATGTGC -3' 5'- <font color="#6666FF">TGCGAAT AGTACCA TTTT ATAGATA  TGCAGGA -3' Displacement strands (26 bp each): 5'- CGGGTGGAGCAT AGACGTA TGCAGGA -3' 5'- GCACATCTTCTC ATAGATA GTATCAC -3'

Old core oligo (42 bp): 1 010 01  011 01  011 02  012 02  012 01  013 01       ATTATAC CAAAAAA AAGGCTC AAGGAAT <font color="#6666FF">TGCGAAT  AGTACCA New core oligo (28 bp): 1* 010 01 011 01  011 02  012 02       ATTATAC CAAAAAA AAGGCTC AAGGAAT

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 (old) Matthewmeisel 12:51, 7 July 2006 (EDT)
 * 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 — done
 * divide oligos into the following categories: — done
 * see pre-working stocks below
 * order oligos!

Pre-working stocks

 * c3.2.1: core barrel oligos
 * c3.2.2: core top lid oligos
 * c3.2.3: core bottom lid oligos
 * c3.2.4: barrel oligos at inside apatamer locations -aptamers
 * c3.2.5: barrel oligos at outside aptamer locations -aptamers
 * c3.2.6: barrel oligos at inside apatamer locations +aptamers
 * c3.2.7: barrel oligos at outside aptamer locations +aptamers
 * c3.2.8: barrel oligos at latch locations -latches
 * c3.2.9: lid oligos at latch locations -latches (empty)
 * c3.2.10: barrel oligos at latch locations +latch1 +latch2
 * c3.2.11: latch oligos from barrel +latch1 -latch2
 * c3.2.12: latch oligos from barrel -latch1 +latch2
 * c3.2.13: lid oligos at latch locations +latch1 +latch2 (empty)
 * c3.2.14: latch oligos from lids +latch1 -latch2
 * c3.2.15: latch oligos from lids -latch1 +latch2
 * c3.2.16: latch staples +latch2
 * c3.2.17: displacement strands: latch1
 * c3.2.18: displacement strands: latch2

(mix 10 of each 50  stock ligand-oligos to make pre-working stocks)

Working stocks
list in progress

Final concentration of each oligo in working stocks is 250 nM.

Oligo list
link

Oligo "ligand" aptamers
on the July 31 notebook page

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.