Wiki/Team:Warsaw/primers

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<h1>Primers</h1>
<h1>Primers</h1>
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<h2>One-armed bandit preparation</h2>
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<h2>'One-armed bandit' strain preparation</h2>
<h4>AID and T7 cloning</h4>
<h4>AID and T7 cloning</h4>
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<pre>
<pre>
<a name="pZCseqL">pZCseqL</a>    5' CTTGACCCGCAGTTGCAAAC 3'
<a name="pZCseqL">pZCseqL</a>    5' CTTGACCCGCAGTTGCAAAC 3'
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<a name="pZCseqP">pZCseqP</a>    5' CCCAACTGATCTTCAGCATC 3'
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<a name="pZCseqR">pZCseqR</a>    5' CCCAACTGATCTTCAGCATC 3'
</pre>
</pre>
<h4>Sequencing of the T7 polymerase gene</h4>
<h4>Sequencing of the T7 polymerase gene</h4>
<pre>
<pre>
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<a name="T7Rseq">T7Rseq</a>     5' GCTTCAACCGCAGCTACCAC 3'
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<a name="T7-2seq">T7-2seq</a>  5' AGGTGCGCTGGCTGGCATC 3'
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<a name="T7-3seq">T7-3seq</a>  5' AAGGAAGGTTACTACTGGCT 3'
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<a name="T7-4seq">T7-4seq</a>  5' CAAAGAGTTCGGCTTCCGTC 3'
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<a name="T7Rseq">T7Rseq</a>   5' GCTTCAACCGCAGCTACCAC 3'
</pre>
</pre>
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<h2>Hunter and prey </h2>
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<h2>'Hunter and prey' strain preparation</h2>
<h4>Fusion of protein A and ompA and alpha or omega part of beta-lactamase</h4>
<h4>Fusion of protein A and ompA and alpha or omega part of beta-lactamase</h4>
<pre>
<pre>
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<a name="AlphaL_link">alphaL+link14+homo (alphaL_link)</a>         5' CAGTGGTGGAAGCGGTGGC GGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGT CACCCAGAAACGCTGGTGAAAG 3'
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<a name="AlphaL_link">alphaL_link</a> 5' CAGTGGTGGAAGCGGTGGCGGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGTCACCCAGAAACGCTGGTGAAAG 3'
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<a name="AlphaP_XB">alphaP+STOP+XbaI+BamHI (alphaP_XB)</a>       5' GG GGATCC GG TCTAGA TTA TTCGCCAGTTAATAGTTTGCG 3'
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<a name="AlphaP_XB">alphaP_XB</a>   5' GG GGATCCGGTCTAGATTATTCGCCAGTTAATAGTTTGCG 3'
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<a name="OmegaL_link">omegaL+link14+homo (omegaL_link)</a>         5' CAGTGGTGGAAGCGGTGGC GGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGT CTACTTACTCTAGCTTCCCGG 3'
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<a name="OmegaL_link">omegaL_link</a> 5' CAGTGGTGGAAGCGGTGGCGGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGTCTACTTACTCTAGCTTCCCGG 3'
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<a name="OmegaP_EPB">omegaP+STOP+EcoRI+PstI+BamHI (omegaP_EPB)</a> 5' AAGGATCCAACTGCAGAAGAATTC TTACCAATGCTTAATCAGTG 3'
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<a name="OmegaP_EPB">omegaP_EPB</a>   5' AAGGATCCAACTGCAGAAGAATTCTTACCAATGCTTAATCAGTG 3'
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<a name="OmpaL_N">OmpAL+NdeI (ompaL_N)</a>                     5' CATATGAAAGCTACTAAACTGGTACTGGG 3'
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<a name="OmpaL_N">ompaL_N</a>     5' CATATGAAAGCTACTAAACTGGTACTGGG 3'
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<a name="OmpaP_link">OmpAP+link8+SacI+NotI+homo (ompaP_link)</a>  5' GCCACCGCTTCCACCACT GCGGCCGC CA GAGCTC CCTCCTCCAGAACCTCC GCCGTTGTCCGGACGAGTGCCGATG 3'
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<a name="OmpaP_link">ompaP_link</a>  5' GCCACCGCTTCCACCACTGCGGCCGCCAGAGCTCCCTCCTCCAGAACCTCCGCCGTTGTCCGGACGAGTGCCGATG 3'
</pre>
</pre>
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<h4>Mutagenesis of the A protein</h4>
<h4>Mutagenesis of the A protein</h4>
<pre>
<pre>
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<a name="AmutDelecjaL+KpnI">AmutDelecjaL+KpnI</a>   5' AGGTACCCATGTAAGATCTCATAGAACGCG  3'
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<a name="ADelL+KpnI">ADelL+KpnI</a> 5' AGGTACCCATGTAAGATCTCATAGAACGCG  3'
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<a name="AmutDelecjaP">AmutDelecjaP</a>   5' AACTTAAACGAAGAACAACGAAACGCC  3'
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<a name="ADelP">AdelP</a>       5' AACTTAAACGAAGAACAACGAAACGCC  3'
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<a name="AmutMniejL+KpnI">AmutMniejL+KpnI</a>   5' AGTTAGGTACCGGTGAGATCTCATAGGACGCGTTTTGTTGTTCTTTGTTG 3'
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<a name="AmutL+KpnI">AmutL+KpnI</a>  5' TCGTTTAAGTTAGGTACCGGTGAGATCTCAGAGGACGCGTTTTGTTGTTCTTTGTTG  3'
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<a name="AmutMniejP">AmutMniejP</a>  5' TAAACGAAGAACAAGGAAACGCCTTCATCCAAAGTTTAAAAGATGACCC  3'
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<a name="AmutP">AmutP</a>       5' AGAACAAGGAAACGCCTTCGCCCAAAGTTTAGCAGATGACCCAAGCCAAAGCGC  3'
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<a name="AmutWiecejL+KpnI">AmutWiecejL+KpnI</a>  5' TCGTTTAAGTTAGGTACCGGTGAGATCTCAGAGGACGCGTTTTGTTGTTCTTTGTTG  3'
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<a name="AmutWiecejP">AmutWiecejP</a>   5' AGAACAAGGAAACGCCTTCGCCCAAAGTTTAGCAGATGACCCAAGCCAAAGCGC  3'
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</pre>
</pre>
<h4>Fusion of the A protein with the OmpaA protein and the alpha/omega part of beta-lactamase protein</h4>
<h4>Fusion of the A protein with the OmpaA protein and the alpha/omega part of beta-lactamase protein</h4>
<pre>  
<pre>  
-
<a name="AL+link10+homo2">AL+link10+homo2</a>   5' TCTGGAGGTGGAGGTAGCGG GGGTGGGGGTGGTTCGGGTGGAGGTGGT AAAACCGCGGCTCTTGCGC 3'
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<a name="AL+link10+homo2">AL+link10+homo2</a>     5' TCTGGAGGTGGAGGTAGCGGGGGTGGGGGTGGTTCGGGTGGAGGTGGTAAAACCGCGGCTCTTGCGC 3'
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<a name="AlphaP+link10+homo2">AlphaP+link10+homo2</a>   5' CCGCTACCTCCACCTCCAGA ACCACCTCCTCCGCTTCCTCCGCCACC TTCGCCAGTTAATAGTTTGCG 3'
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<a name="AlphaP+link10+homo2">AlphaP+link10+homo2</a> 5' CCGCTACCTCCACCTCCAGAACCACCTCCTCCGCTTCCTCCGCCACCTTCGCCAGTTAATAGTTTGCG 3'
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<a name="OmegaP+link10+homo2">OmegaP+link10+homo2</a>   5' CCGCTACCTCCACCTCCAGA ACCACCTCCTCCGCTTCCTCCGCCACC CCAATGCTTAATCAGTGAGGC 3'
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<a name="OmegaP+link10+homo2">OmegaP+link10+homo2</a> 5' CCGCTACCTCCACCTCCAGAACCACCTCCTCCGCTTCCTCCGCCACCCCAATGCTTAATCAGTGAGGC 3'
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<a name="AL+SacI">AL+SacI</a>   5' GG GAGCTC T AAAACCGCGGCTCTTGCGCAAC 3'
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<a name="AL+SacI">AL+SacI</a>             5' GG GAGCTCTAAAACCGCGGCTCTTGCGCAAC 3'
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<a name="AP+NotI">AP+NotI</a>   5' AA GCGGCCGC C GGTTGACTTCCCCGCGGAATTC 3'
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<a name="AP+NotI">AP+NotI</a>             5' AA GCGGCCGCCGGTTGACTTCCCCGCGGAATTC 3'
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<a name="AlphaL+SacI">AlphaL+SacI</a>   5' GG GAGCTC T CACCCAGAAACGCTGGTGAAAG 3'
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<a name="AlphaL+SacI">AlphaL+SacI</a>         5' GG GAGCTCTCACCCAGAAACGCTGGTGAAAG 3'
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<a name="OmegaL+SacI">OmegaL+SacI</a>   5' GG GAGCTC G CTACTTACTCTAGCTTCCCGG 3'
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<a name="OmegaL+SacI">OmegaL+SacI</a>         5' GGGAGCTCGCTACTTACTCTAGCTTCCCGG 3'
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<a name="AlphaPlinkSac">AlphaPlinkSac</a>   5' TTGAGCTCCCTCCACCTCCGCTACCTCCACCAGAACCACCTCCTCCGCTTCCGGTACCTTCGCCAGTTAATAGTTTGC  3'
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<a name="AlphaPlinkSac">AlphaPlinkSac</a>       5' TTGAGCTCCCTCCACCTCCGCTACCTCCACCAGAACCACCTCCTCCGCTTCCGGTACCTTCGCCAGTTAATAGTTTGC  3'
</pre>
</pre>
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<h2>BioBricks Preparation</h2>
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<h2>Preparation of the BioBricks Standard Parts</h2>
<pre>
<pre>
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<a name="AIDpHSNP">AIDP_HindSpeNotPst</a>   5' AAACTGCAGCGGCCGCTACTAGTAAAGCTTTCAAAGTCCCAAAGTACGAAATG 3'
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<a name="AIDpSNP">AIDP_SpeNotPst</a>       5' AAACTGCAGCGGCCGCTACTAGTATCAAAGTCCCAAAGTACGAAATG 3'
<a name="AL_BNXNE">AL_BNXNE</a>            5' TAGAATTCGCGGCCGCTTCTAGAGGGCATATGGGATCCAAAACCGCGGCTCTTGCGCAAC  3'
<a name="AL_BNXNE">AL_BNXNE</a>            5' TAGAATTCGCGGCCGCTTCTAGAGGGCATATGGGATCCAAAACCGCGGCTCTTGCGCAAC  3'
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<a name="AlphaPSpe">AlfaPSpe</a>             5' GCACTAGTATTATTCGCCAGTTAATAGTTTGCG  3'
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<a name="AlphaPSpe">AlphaPSpe</a>           5' GCACTAGTATTATTCGCCAGTTAATAGTTTGCG  3'
<a name="APSacSpe">APSacSpe</a>            5' GGACTAGTAGAGCTCCCGTCTACTTTCGGCGCCTGAGC  3'
<a name="APSacSpe">APSacSpe</a>            5' GGACTAGTAGAGCTCCCGTCTACTTTCGGCGCCTGAGC  3'
<a name="LinLSXNE">LinLSXNE</a>            5' ATGAATTCGCGGCCGCTTCTAGAGGGAGCTCTGGTGGAAGCGGTGGCGGAGGATC  3'
<a name="LinLSXNE">LinLSXNE</a>            5' ATGAATTCGCGGCCGCTTCTAGAGGGAGCTCTGGTGGAAGCGGTGGCGGAGGATC  3'
<a name="LinP_BS">LinP_BS</a>              5' CCACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTAC  3'
<a name="LinP_BS">LinP_BS</a>              5' CCACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTAC  3'
 +
<a name="LinP_BS2">LinP_BS2</a>            5' ATACTAGTACCGGATCCAGAACCTCCTCCACCGCTACCTCCACCTCCAGAAC  3'
<a name="LinPBSNP">LinPBSNP</a>            5' AGCCTGCAGCGGCCGCTACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTACC  3'
<a name="LinPBSNP">LinPBSNP</a>            5' AGCCTGCAGCGGCCGCTACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTACC  3'
<a name="OmegPSpe">OmegPSpe</a>            5' GCACTAGTATTACCAATGCTTAATCAGTGAG  3'
<a name="OmegPSpe">OmegPSpe</a>            5' GCACTAGTATTACCAATGCTTAATCAGTGAG  3'
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<a name="PETt7L_XNE">pETt7L_XNE</a>          5' ATGAATTCGCGGCCGCTTCTAGAGATCCCGCGAAATTAATACG  3'
<a name="PETt7L_XNE">pETt7L_XNE</a>          5' ATGAATTCGCGGCCGCTTCTAGAGATCCCGCGAAATTAATACG  3'
<a name="PlacL_XNE">PlacL_XNE</a>            5' TAGAATTCGCGGCCGCTTCTAGAGCTGGCACGACAGGTTTCCC  3'
<a name="PlacL_XNE">PlacL_XNE</a>            5' TAGAATTCGCGGCCGCTTCTAGAGCTGGCACGACAGGTTTCCC  3'
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<a name="AP+XhoI+SpeI">AP+XhoI+SpeI</a>   5' AA ACTAGT CTCGAG GGTTGACTTCCCCGCGGAATTC 3'
+
<a name="AP+XhoI+SpeI">AP+0XhoI+SpeI</a>       5' AAACTAGTCTCGAGGGTTGACTTCCCCGCGGAATTC 3'
 +
<a name=AIDl>AIDl</a>                5' TATCTAGAACCATGGACAGCCTCTTG 3'
 +
<a name=AraCl>AraCl</a>                5' GCTCTAGATTATGACAACTTGACGGC 3'
</pre>
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Latest revision as of 21:45, 29 October 2008

Gallery Bricks Notebook Team Project Home


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Primers

'One-armed bandit' strain preparation

AID and T7 cloning

T7lLinkB   5' CGGATCCGGCGGTGGCGGTAGTGGAGGAGGTGGGTCTGGAGGCGGAGGGAACACGATTAACATCGCTAAGAAC  3'
T7lRBSHi   5' CACAAGCTTAGGAGGTGTACTAGATGAACACGATTAACATCGCTAAG  3'
T7pXbSal   5' TCTGTCGACTCTAGATTACGCGAACGCGAAGTCC  3'
AIDlNrH    5' CGTAAGCTTAGGAGGTGTAGACCATGGACAGCCTCTTGATG  3'
AIDpLinB   5' CCACTACCGCCACCGCCGGATCCGCCACCTCCGCTGCCTCCACCACCAAGTCCCAAAGTACGAAATGC  3'

Sequencing of pMPM-T5

pMPMT5seqF  5' CTACTGTTTCTCCATACCCG  3'
pMPMT5seqR  5' GAAAATCTTCTCTCATCCGC 3'
AIDseqP     5' GCTTCGGCGCATCCTTTTG 3'

Sequencing of β-galactosidase from pZC320

pZCseqL     5' CTTGACCCGCAGTTGCAAAC 3'
pZCseqR     5' CCCAACTGATCTTCAGCATC 3'

Sequencing of the T7 polymerase gene

T7-2seq   5' AGGTGCGCTGGCTGGCATC 3'
T7-3seq   5' AAGGAAGGTTACTACTGGCT 3'
T7-4seq   5' CAAAGAGTTCGGCTTCCGTC 3'
T7Rseq    5' GCTTCAACCGCAGCTACCAC 3'

'Hunter and prey' strain preparation

Fusion of protein A and ompA and alpha or omega part of beta-lactamase

alphaL_link  5' CAGTGGTGGAAGCGGTGGCGGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGTCACCCAGAAACGCTGGTGAAAG 3'
alphaP_XB    5' GG GGATCCGGTCTAGATTATTCGCCAGTTAATAGTTTGCG 3'
omegaL_link  5' CAGTGGTGGAAGCGGTGGCGGAGGATCTGGAGGAGGTGGTTCTGGAGGTGGAGGTCTACTTACTCTAGCTTCCCGG 3'
omegaP_EPB   5' AAGGATCCAACTGCAGAAGAATTCTTACCAATGCTTAATCAGTG 3'
ompaL_N      5' CATATGAAAGCTACTAAACTGGTACTGGG 3'
ompaP_link   5' GCCACCGCTTCCACCACTGCGGCCGCCAGAGCTCCCTCCTCCAGAACCTCCGCCGTTGTCCGGACGAGTGCCGATG 3'

Cloning of A and/or Z protein to expression vector (pET15b/pET24a)

AlphaP+link+Sac   5' GG GAGCTC CC ACCACCCCCACCCCCGCTACCTC  3'
AlphaL+Nde        5' CGGG CATATG CACCCAGAAACGCTGGTGAAAG  3'

Mutagenesis of the A protein

ADelL+KpnI  5' AGGTACCCATGTAAGATCTCATAGAACGCG  3'
AdelP       5' AACTTAAACGAAGAACAACGAAACGCC  3'
AmutL+KpnI  5' TCGTTTAAGTTAGGTACCGGTGAGATCTCAGAGGACGCGTTTTGTTGTTCTTTGTTG  3'
AmutP       5' AGAACAAGGAAACGCCTTCGCCCAAAGTTTAGCAGATGACCCAAGCCAAAGCGC  3'

Fusion of the A protein with the OmpaA protein and the alpha/omega part of beta-lactamase protein

 
AL+link10+homo2     5' TCTGGAGGTGGAGGTAGCGGGGGTGGGGGTGGTTCGGGTGGAGGTGGTAAAACCGCGGCTCTTGCGC  3'
AlphaP+link10+homo2 5' CCGCTACCTCCACCTCCAGAACCACCTCCTCCGCTTCCTCCGCCACCTTCGCCAGTTAATAGTTTGCG  3'
OmegaP+link10+homo2 5' CCGCTACCTCCACCTCCAGAACCACCTCCTCCGCTTCCTCCGCCACCCCAATGCTTAATCAGTGAGGC  3'
AL+SacI             5' GG GAGCTCTAAAACCGCGGCTCTTGCGCAAC  3'
AP+NotI             5' AA GCGGCCGCCGGTTGACTTCCCCGCGGAATTC  3'
AlphaL+SacI         5' GG GAGCTCTCACCCAGAAACGCTGGTGAAAG  3'
OmegaL+SacI         5' GGGAGCTCGCTACTTACTCTAGCTTCCCGG  3'
AlphaPlinkSac       5' TTGAGCTCCCTCCACCTCCGCTACCTCCACCAGAACCACCTCCTCCGCTTCCGGTACCTTCGCCAGTTAATAGTTTGC  3'

Preparation of the BioBricks Standard Parts

AIDP_SpeNotPst       5' AAACTGCAGCGGCCGCTACTAGTATCAAAGTCCCAAAGTACGAAATG  3'
AL_BNXNE             5' TAGAATTCGCGGCCGCTTCTAGAGGGCATATGGGATCCAAAACCGCGGCTCTTGCGCAAC  3'
AlphaPSpe            5' GCACTAGTATTATTCGCCAGTTAATAGTTTGCG  3'
APSacSpe             5' GGACTAGTAGAGCTCCCGTCTACTTTCGGCGCCTGAGC  3'
LinLSXNE             5' ATGAATTCGCGGCCGCTTCTAGAGGGAGCTCTGGTGGAAGCGGTGGCGGAGGATC  3'
LinP_BS              5' CCACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTAC  3'
LinP_BS2             5' ATACTAGTACCGGATCCAGAACCTCCTCCACCGCTACCTCCACCTCCAGAAC  3'
LinPBSNP             5' AGCCTGCAGCGGCCGCTACTAGTACCGGATCCCGAACCACCCCCACCCCCGCTACC  3'
OmegPSpe             5' GCACTAGTATTACCAATGCTTAATCAGTGAG  3'
OmegLNde             5' CAGCCATATGCTACTTACTCTAGCTTCCCGG  3'
OmpLNXNE             5' TAGAATTCGCGGCCGCTTCTAGAGGGCATATGAAAGCTACTAAACTGGTAC  3'
OmLNXNEB             5' ATTAGATCTGAATTCGCGGCCGCTTCTAGAGGGCATATGAAAGCTACTAAACTGGTAC  3'
pETt7L_XNE           5' ATGAATTCGCGGCCGCTTCTAGAGATCCCGCGAAATTAATACG  3'
PlacL_XNE            5' TAGAATTCGCGGCCGCTTCTAGAGCTGGCACGACAGGTTTCCC  3'
AP+0XhoI+SpeI        5' AAACTAGTCTCGAGGGTTGACTTCCCCGCGGAATTC  3'
AIDl                 5' TATCTAGAACCATGGACAGCCTCTTG 3'
AraCl                5' GCTCTAGATTATGACAACTTGACGGC 3'


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