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| Line 46: |
Line 46: |
| *[[Media:lid2_7308_TC_62706.txt]] | | *[[Media:lid2_7308_TC_62706.txt]] |
| **Oligos for lid 2 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices) | | **Oligos for lid 2 (correct wordcount: 30lines, 30words, 1122chars (includes 30 carriage returns) for (96bp-12ssbp)*13helices) |
|
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|
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| ==Latches==
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| ===Two-Oligo Latch Sequences===
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| * Latch strands: Ts---any necessary additional bps---15bp overlap---12bp random toehold
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| * Displacement strands: 5'---12 bp pairing w/ toehold---15 bp pairing w/ rest of oligo, except the T spacers---3'
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|
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| <pre>
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| *latch1B1: barrel strand 10, oligo 60
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| TTTTTTT GTAACGAAGTTGCAC CACACAACGCTA
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|
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| *disp1B1: displaces latchB1
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| TAGCGTTGTGTG GTGCAACTTCGTTAC
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|
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|
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| *latch1L1: lid1 strand 6, oligo 2
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| TTTTTTT GTGCAACTTCGTTAC ACGAGTAATGCG
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|
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| *disp1L1: displaces latchL1
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| CGCATTACTCGT GTAACGAAGTTGCAC
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|
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| ---
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|
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| *latch1B2: barrel strand 24, oligo 43
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| TTTTTTTTTTTTTT GTACGCATGGCAAAT TACCACTCTAGC
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|
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| *disp1B2: displaces latchB2
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| GCTAGAGTGGTA ATTTGCCATGCGTAC
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|
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| *latch1L2: lid1 strand 7, oligo 29
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| TTTTTTTTTTTTTT ATTTGCCATGCGTAC CGGTTAGATAGC
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|
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| *disp1L2: displaces latchL2
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| GCTATCTAACCG GTACGCATGGCAAAT
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|
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| ---
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|
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| *latch1B3: barrel strand 10, oligo 21
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| TTTTTTTTTT TCGAGTTGACAAAGC TACCGGTTCAAG
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|
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| *disp1B3: displaes latchB3
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| CTTGAACCGGTA GCTTTGTCAACTCGA
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|
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| *latch1L3: lid2 strand 6, oligo 2
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| TTTTTTTTTTT GCTTTGTCAACTCGA ACTGGCCCTTAA
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|
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| *disp1L3: displaces latchL3
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| TTAAGGGCCAGT TCGAGTTGACAAAGC
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|
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| ---
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|
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| *latch1B4: barrel strand 24, oligo 27
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| TTTTTTTTTTTTTT CAGGATACCATCATC TACTAACCGGTG
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|
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| *disp1B4: displaces latchB4
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| CACCGGTTAGTA GATGATGGTATCCTG
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|
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| *latch1L4: lid2 strand 7, oligo 29
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| TTTTTTTTTTTTTT GATGATGGTATCCTG GTGGAGTAGTTG
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|
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| *disp1L4: displaces latchL4
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| CAACTACTCCAC CAGGATACCATCATC
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| </pre>
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|
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| ===Four-Oligo Latch Sequences===
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| *FIRST ATTACHED-to-BARREL OLIGO:
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| **5'---3Ts---Ts for spacers---7 rand bp (called '1A')---8 rand bp (called '1B')---3'
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| *FIRST ZIPPER OLIGO:
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| **5'---8bp complementing 2A---7 bp reverse complementing 1A--12 rand bp toehold---3'
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| *SECOND ZIPPER OLIGO:
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| **5'---8bp reverse complementing 1B---7 bp complementing 2B--12 rand bp toehold---3'
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| *SECOND ATTACHED-to-BARREL OLIGO:
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| **3'---8 rand bp (called '2A')---8 rand bp (called '2B')---Ts for spacers---3Ts---5'
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| *STRAND DISPLACERS FOR ZIPPER OLIGOS:
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| **5'---12 bp pairing w/ toehold---15 bp pairing w/ the rest of the zipper oligo---3'
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|
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| <pre>
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| *latch2B1: barrel strand 10, oligo 60
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| TTTTTTT CCGGTGC AGAAGTTT
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| *latch2B1z: zipper oligo attached to latch2B1
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| GTATGGTC GCACCGG TGAGTACCGCTA
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|
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| *latch2L1: lid1 strand 6, oligo 2
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| TTTTTTT TAGAGAC GACCATAC
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| *latch2L1z: zipper oligo attached to latch2L1
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| AAACTTCT GTCTCTA TCTCTTCAGTCG
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|
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| *disp2B1z: displaces latch2B1z
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| TAGCGGTACTCA CCGGTGC GACCATAC
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| *disp2L1z: displaces latch2L1z
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| CGACTGAAGAGA TAGAGAC AGAAGTTT
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|
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| ---
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| *latch2B2: barrel strand 24, oligo 43
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| TTTTTTTTTTTTTT GGATCGG TACATTGT
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| *latch2B2z: zipper oligo attached to latch2B2
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| GTATTCGA CCGATCC GGACTTTCTAGG
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|
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| *latch2L2: lid1 strand 7, oligo 29
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| TTTTTTTTTTTTTT AGGCAAC TCGAATAC
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| *latch2L2z: zipper oligo attached to latch2L2
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| ACAATGTA GTTGCCT GGTTAAGGGTAC
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|
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| *disp2B2z: displaces latch2B2z
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| CCTAGAAAGTCC GGATCGG TCGAATAC
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| *disp2L2z: displaces latch2L2z
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| GTACCCTTAACC AGGCAAC TACATTGT
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|
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| ---
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|
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| *latch2B3: barrel strand 10, oligo 21
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| TTTTTTTTTT GGCACTC CTACAATT
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| *latch2B3z: zipper oligo attached to latch2B3
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| GTTGGTCT GAGTGCC GCACGGCAATAA
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| *latch2L3: lid2 strand 6, oligo 2
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| TTTTTTTTTTT GTAGTAG AGACCAAC
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| *latch2L3z: zipper oligo attached to latch2L3
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| AATTGTAG CTACTAC CGAAGGCTATTC
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| *disp2B3z: displaces latch2B3z
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| TTATTGCCGTGC GGCACTC AGACCAAC
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| *disp2L3z: displaces latch2L3z
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| GAATAGCCTTCG GTAGTAG CTACAATT
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|
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| ---
| |
|
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| *latch2B4: barrel strand 24, oligo 27
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| TTTTTTTTTTTTTT GACGATA GGGAAACA
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| *latch2B4z: zipper oligo attached to latch2B4
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| TGATCTTC TATCGTC GTTGTGAGCGAT
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| *latch2L4: lid2 strand 7, oligo 29
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| TTTTTTTTTTTTTT CCTACGA GAAGATCA
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| *latch2L4z: zipper oligo attached to latch2L4
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| TGTTTCCC TCGTAGG TCAGTGCTTGTG
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| *disp2B4z: displaces latch2B4z
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| ATCGCTCACAAC GACGATA GAAGATCA
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| *disp2L4z: displaces latch2L4z
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| CACAAGCACTGA CCTACGA GGGAAACA
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|
| |
| </pre>
| |
|
| |
| ===Latch-Including Schematics===
| |
| <gallery>
| |
| Image:latch_design4_barrel_schematic.gif|Barrel schematic showing where oligos need to be cut and latches added<br>([[Media:latch_design4_barrel_schematic.ai|ai file]])
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| Image:latch_design4_lid_schematic.gif|Lid schematic showing where oligos need to be cut and latches added<br>([[Media:latch_design4_lid_schematic.ai|ai file]])
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| Image:design4_updatedbarrel_schematic.gif|Updated barrel schematic showing latch position and oligo cutting<br>([[Media:Box4-revisedbarrel-schematic.ai|ai file]])
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| Image:design4_updatedlid-latch_schematic.gif|Updated lid schematic showing latch position and oligo cutting<br>([[Media:Box4_lid1or2_schematiclatch.ai|ai file]])
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| Image:design4_barrelfinal.jpg|Final barrel schematic with latch and aptamer positions<br>
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| Image:Box4_lid1or2final.jpg|Final lid 1 or 2 schematic with latch positions
| |
| </gallery>
| |
