Team:Freiburg bioware/oligos

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Oligo Name Ordered by... Length Sequence Description
Pimer forward CAT Sigma 64 GATCGCAATTGACCAACAAGGAGAAATCTAGATGGCCGGCGAGAAAAAAATCACTGGATATACC designed to get CAT-gene + Freigem restriction sites out of the lab vector no 258
Primer reverse CAT Sigma 58 GTGGCAGGGCGGGGCGACCGGTTAATACTAGTAGCGGCCGCCTGCAGAAGCTTGGGTA designed to get CAT-gene + Freigem restriction sites out of the lab vector no 258
Short Linker Sigma 18 CTAGAGGTGGTTCTGGTA GlySerGlyGly
Middle Linker Sigma 30 CTAGAGGTGGTTCTGGTACTAGAGGTGGTTCTGGTA GlySerGlyGlyx2
Long Linker Sigma 42 CTAGAGGTGGTTCTGGTACTAGAGGTGGTTCTGGTACTAGAGGTGGTTCTGGTA GlySerGlyGlyx3
Primer forward GenIII Sigma 52 GAATTCGCGGCCGCTTCTAGATGGCCGGCGATTTTGATTATGAAAAGATGGC Insert of GenIII(restriction sites RFC25) into M13DNA ,
Primer reverse GenIII Sigma 53 CTGCAGGCGGCCGCTACTAGTATTAACCGGTAGACTCCTTATTACGCAGTATG Insert of GenIII(restriction sites RFC25) into M13DNA ,
A4 AGO Sigma 21 AAGTTTTTTGGGGTCGAGGTG guide oligo complentary to target sequenz, the cutting event will be done after the tenth base 5'3'
A1 AGO Sigma 21 ACAACCATCGCCCACGCATAA guide oligo complentary to target sequenz, the cutting event will be done after the tenth base 5'3'.The M13ssDNA will be cut at position 3100
A2 AGO Sigma 21 GGTTTTACTCTGATTCTCTTC guide oligo complentary to target sequenz, the cutting event will be done after the tenth base of the oligo 5'3'.The M13ssDNA will be cut at position 550.
A3 AGO Sigma 21 TACCTTCGGGTACTCTTCTAA guide oligo complentary to target sequenz, the cutting event will be done after the tenth base 5'3'.The M13ssDNA will be cut at position 1280.
A5_Ago_pETfragment Sigma 21 AAGTTTTTTGGGGTCGAGGTG guide 
 oligo complentary to target sequenz, 
 the cutting event will be done
after the tenth base 5'3'.The M13ssDNA will be cut at position 100
Aa BB Primer Middle a Sigma 50 TCGTTCATTTTGAAATCCCCTGAACTCTTCTTCACCCACTCTTTTCAGTT deleted EcoRI site
Aa BB Primer Middle b Sigma 50 GGAAGGTGATATTATGTACTGGCTTTAATAATACTAGTAGCGGCCGCTGCAG deleted EcoRI site
Aa BB Primer Start Sigma 45 GGTTTAAAAGAGCTTCCTTTCCCATCTAGAAGCGGCCGCGAATTC Addon Tail to add Biobrick prefix
Aa BB Primer Back Sigma 52 AACTGAAAAGAGTGGGTGAAGAAGAGTTCAGGGGATTTCAAAATGAACGA Addon Tail to add Biobrick suffix
AGO-target _M13 Sigma 60 CTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTGTTGTCATTGTC 5'biotinylated olgio for phage display
AGO-guide-A1 5' Phos Sigma 21 [Phos]ACAACCATCGCCCACGCATAA phosporilised(5') for phage display assay with AGO protein
AGO-guide-A4 5' Phos Sigma 21 [Phos]AAGTTTTTTGGGGTCGAGGTG phosporilised(5') for phage display assay with AGO protein
Fok control 1 Sigma 40 TTCTACTAATAGTAGTAGCATTAACATCCAATAAATCATA 1669bp for the bond of gel elctrophoresis , the oligo hybridisized to the ssDNA enable Fok to cut
Fok control 2 Sigma 40 GTCATTTTTGCGGATGGCTTAGAGCTTAATTGCTGAATAT 1914bp for the bond of gel elctrophoresis, the oligo hybridisized to the ssDNA enable Fok to cut
Fok control 3 Sigma 40 TGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGT 786bp for the bond of gel elctrophoresis,the oligo hybridisized to the ssDNA enable Fok to cut
5'fluo40bp Sigma 40 Test nucleotide for the in vivo assay
xbaI_RBS-Strep-Fok_a Sigma 40 GCTCTAGAGAAGGAGATATACTATGGCCGGCTGGAGCCAT Insert a RBS befor the StrepTag
StrepFoka_r Sigma 28 GAAGCTTCTGCAGCGGCCGCTACTAGTA Insert a RBS befor the StrepTag
XbaI_DsbAss_AgeI_2r Sigma 62 CCGGTCGCCGATGCGCTAAACGCTAAAACTAAACCAGCCAGCGCCAGCCAAATCTTTTTCAT olgio with xbaI and ageI ends , can linked on DsbA signalsequenz
pBAD-TOPO f Sigma 34 GTCCCCCCGGGAACCCCGCTTATTAAAAGCATTC add-on tail primer for pcr to remove the two AgeI sites of the vector and to introduce the bb-pre and suffix
pBAD-TOPO r Sigma 56 TCCCCCCGGGCTGCAGTATGAATTCACTCCTTCTTAAAGTTAAACAAAATTATTTC add-on tail primer for pcr to remove the two AgeI sites of the vector and to introduce the bb-pre and suffix
XbaI_NgoMIV_DsbA forward Sigma 19 CGCTTCTAGATGGCCGGCA add-on tail primer to generte a FOS-DsbA-Split-Fok_a part
DsbA-Fos Sigma 36 CGTTTAGCGCATCGGCGCACCATCACCACCACCATG add-on tail primer to generte a FOS-DsbA-Split-Fok_a part
Fos-SplitFok_a Sigma 38 GGAGTTCATCCTGGCAGCACGACCAGCCTGTAAGATTC add-on tail primer to generte a FOS-DsbA-Split-Fok_a part
SplitFok_a age_Spe_not_pst Sigma 17 AGCTCTGCAGCGGCCGC add-on tail primer to generte a FOS-DsbA-Split-Fok_a part
80mer Fok control Sigma 80 AGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAAT target oligonucleotide for Fok cleavage assay
80mer Fok control Sigma 80 [Cy3]AGTTCGGTTCCCTTATGATTGACCGTCTGCGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAAT target oligonucleotide for Fok cleavage assay with fluorescine mark
Standard 35 forward Sigma 25 CCGAATTCGCGGCCGCTTCTAGATG freiburg stadard primer (standard 25) to amplify insert
Standard 35 reverse Sigma 29 GCTCTGCAGCGGCCGCTACTAGTATTAAC freiburg stadard primer (standard 25) to amplify insert
pr_fwd_Xba_SDII_TorA Sigma 55 ATATAAATTCTAGATAACGAGGGCAAATCATGAACAATAACGATCTCTTTCAGGC Shine-Dalgarno sequence II TorA(signal sequence for periplasm transport)
ssDNA_prod_pET39b+ Sigma 23 CGGATCCGATATCGCCATGGTTG primer for modifies thermocycler protocoll to produce ssDNA
fokm_li_xbaI_ageI Sigma 90 CTAGATGGCCGGCGGTTCTGGTGGTGGTTCTGGCGGTGGTTCTGGAGGTAGTTCTGGCGGTGGATCTGGAGGCGGTTCTGGGTCAGGATC 36 GS linker wrong
fok_m_link_NgoMIV_HINFI_compl Sigma 91 CCGGCGGTGGTTCTGGTGGTGGTTCTGGCGGTGGTTCTGGAGGTAGTTCTGGCGGTGGATCTGGAGGCGGTTCTGGGTCAGGATCTGGTGATGGTTCTGGCTCTGGG 36 Gs linker wrong complement
o_diA1_5dig_site1 Purimex 16 CGGAACGAGGCGCAGA Modified oligonucleotid to guide the Fok-Complex to the target sequence via digoxigenin
o_diAB1_5fluo_site1 Purimex 16 CGGTCAATCATAAGGG Modified oligonucleotid to guide the Fok-Complex to the target sequence via fluorescin
o_diB1_15dig_site1 Purimex 30 CCATGTTACTTAGCCGGAACGAGGCGCAGA Modified oligonucleotid to guide the Fok-Complex to the target sequence via digoxigenin
o_mono1_3fluo_14dig_site1 Purimex 30 CATGTTACTTAGCCGGAACGAGGCGCAGAC Modified oligonucleotid to guide the Fok-Complex to the target sequence via digoxigenin and fluorecine
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