IGEM:Harvard/2006/Container Design 4/Latch Sequences

 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">

 Design 4 Overview</li> Schematics</li> Scaffold</li> Code</li> Latches</li> Final Oligo List</li> </ul> <br style="clear:both">

Two-Oligo Latch Sequences

 * Latch strands: Ts---any necessary additional bps---15bp overlap---12bp random toehold
 * Displacement strands: 5'---12 bp pairing w/ toehold---15 bp pairing w/ rest of oligo, except the T spacers---3'

TTTTTTT GTAACGAAGTTGCAC CACACAACGCTA
 * latch1B1: barrel strand 10, oligo 60

TAGCGTTGTGTG GTGCAACTTCGTTAC
 * disp1B1: displaces latchB1

TTTTTTT GTGCAACTTCGTTAC ACGAGTAATGCG
 * latch1L1: lid1 strand 6, oligo 2

CGCATTACTCGT GTAACGAAGTTGCAC
 * disp1L1: displaces latchL1

---

TTTTTTTTTTTTTT GTACGCATGGCAAAT TACCACTCTAGC
 * latch1B2: barrel strand 24, oligo 43

GCTAGAGTGGTA ATTTGCCATGCGTAC
 * disp1B2: displaces latchB2

TTTTTTTTTTTTTT ATTTGCCATGCGTAC CGGTTAGATAGC
 * latch1L2: lid1 strand 7, oligo 29

GCTATCTAACCG GTACGCATGGCAAAT
 * disp1L2: displaces latchL2

---

TTTTTTTTTT TCGAGTTGACAAAGC TACCGGTTCAAG
 * latch1B3: barrel strand 10, oligo 21

CTTGAACCGGTA GCTTTGTCAACTCGA
 * disp1B3: displaes latchB3

TTTTTTTTTTT GCTTTGTCAACTCGA ACTGGCCCTTAA
 * latch1L3: lid2 strand 6, oligo 2

TTAAGGGCCAGT TCGAGTTGACAAAGC
 * disp1L3: displaces latchL3

---

TTTTTTTTTTTTTT CAGGATACCATCATC TACTAACCGGTG
 * latch1B4: barrel strand 24, oligo 27

CACCGGTTAGTA GATGATGGTATCCTG
 * disp1B4: displaces latchB4

TTTTTTTTTTTTTT GATGATGGTATCCTG GTGGAGTAGTTG
 * latch1L4: lid2 strand 7, oligo 29

CAACTACTCCAC CAGGATACCATCATC
 * disp1L4: displaces latchL4

Four-Oligo Latch Sequences

 * FIRST ATTACHED-to-BARREL OLIGO:
 * 5'---3Ts---Ts for spacers---7 rand bp (called '1A')---8 rand bp (called '1B')---3'
 * FIRST ZIPPER OLIGO:
 * 5'---8bp complementing 2A---7 bp reverse complementing 1A--12 rand bp toehold---3'
 * SECOND ZIPPER OLIGO:
 * 5'---8bp reverse complementing 1B---7 bp complementing 2B--12 rand bp toehold---3'
 * SECOND ATTACHED-to-BARREL OLIGO:
 * 3'---8 rand bp (called '2A')---8 rand bp (called '2B')---Ts for spacers---3Ts---5'
 * STRAND DISPLACERS FOR ZIPPER OLIGOS:
 * 5'---12 bp pairing w/ toehold---15 bp pairing w/ the rest of the zipper oligo---3'

TTTTTTT CCGGTGC AGAAGTTT GTATGGTC GCACCGG TGAGTACCGCTA
 * latch2B1: barrel strand 10, oligo 60
 * latch2B1z: zipper oligo attached to latch2B1

TTTTTTT TAGAGAC GACCATAC AAACTTCT GTCTCTA TCTCTTCAGTCG
 * latch2L1: lid1 strand 6, oligo 2
 * latch2L1z: zipper oligo attached to latch2L1

TAGCGGTACTCA CCGGTGC GACCATAC CGACTGAAGAGA TAGAGAC AGAAGTTT
 * disp2B1z: displaces latch2B1z
 * disp2L1z: displaces latch2L1z

--- TTTTTTTTTTTTTT GGATCGG TACATTGT GTATTCGA CCGATCC GGACTTTCTAGG
 * latch2B2: barrel strand 24, oligo 43
 * latch2B2z: zipper oligo attached to latch2B2

TTTTTTTTTTTTTT AGGCAAC TCGAATAC ACAATGTA GTTGCCT GGTTAAGGGTAC
 * latch2L2: lid1 strand 7, oligo 29
 * latch2L2z: zipper oligo attached to latch2L2

CCTAGAAAGTCC GGATCGG TCGAATAC GTACCCTTAACC AGGCAAC TACATTGT
 * disp2B2z: displaces latch2B2z
 * disp2L2z: displaces latch2L2z

---

TTTTTTTTTT GGCACTC CTACAATT GTTGGTCT GAGTGCC GCACGGCAATAA TTTTTTTTTTT GTAGTAG AGACCAAC AATTGTAG CTACTAC CGAAGGCTATTC TTATTGCCGTGC GGCACTC AGACCAAC GAATAGCCTTCG GTAGTAG CTACAATT
 * latch2B3: barrel strand 10, oligo 21
 * latch2B3z: zipper oligo attached to latch2B3
 * latch2L3: lid2 strand 6, oligo 2
 * latch2L3z: zipper oligo attached to latch2L3
 * disp2B3z: displaces latch2B3z
 * disp2L3z: displaces latch2L3z

---

TTTTTTTTTTTTTT GACGATA GGGAAACA TGATCTTC TATCGTC GTTGTGAGCGAT TTTTTTTTTTTTTT CCTACGA GAAGATCA TGTTTCCC TCGTAGG TCAGTGCTTGTG ATCGCTCACAAC GACGATA GAAGATCA CACAAGCACTGA CCTACGA GGGAAACA
 * latch2B4: barrel strand 24, oligo 27
 * latch2B4z: zipper oligo attached to latch2B4
 * latch2L4: lid2 strand 7, oligo 29
 * latch2L4z: zipper oligo attached to latch2L4
 * disp2B4z: displaces latch2B4z
 * disp2L4z: displaces latch2L4z