Team:Paris Bettencourt/Notebook/Drug Screening/Monday 10th June.html

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<a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Drug_Screen" target="_blank" class="tbnotelogo DSlogo"> ASDF </a>
<a href="https://2013.igem.org/Team:Paris_Bettencourt/Project/Drug_Screen" target="_blank" class="tbnotelogo DSlogo"> ASDF </a>
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<h3>Day Number<sup>suffix</sup> Month</h3>
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<h3>Monday 10<sup>th</sup> June</h3>
<p><b><em>
<p><b><em>
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-
Design of SirA, FdrA, and FdxC genes for synthesis
+
Design of SirA genes for synthesis
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<br>Primers:
<br>Primers:
<br>TBsirA F &nbsp;&nbsp;&nbsp;&nbsp; GGAATTCCATATGTCCGCGAAGGAGAACCCC
<br>TBsirA F &nbsp;&nbsp;&nbsp;&nbsp; GGAATTCCATATGTCCGCGAAGGAGAACCCC
-
<br>TBsirA R &nbsp;&nbsp;&nbsp;&nbsp; AAGGAAAAAAGCGGCCGCTCATCGCAGGTCGTCCTCCTCGGCCCGGAT
+
<br>TBsirA R &nbsp;&nbsp;&nbsp;&nbsp; AAGGAAAAAAGCGGCCGCTCATCGCAGGTCGTCCTCCTCGGCCCGGAT <br>
We blasted the above primers used to clone sirA from M. tuberculosis into E. coli.  We then extracted the sequence from genbank to retrieve the following sequence which includes the restriction sites introduced by Pinto et al.</p>
We blasted the above primers used to clone sirA from M. tuberculosis into E. coli.  We then extracted the sequence from genbank to retrieve the following sequence which includes the restriction sites introduced by Pinto et al.</p>
-
<p>Ggaattccat atgtccgcga aggagaaccc ccaaatgacc actgcacgtc ccgccaaggc tcgaaatgag
+
<p style="font-family: courier">ggaattccat atgtccgcga aggagaaccc ccaaatgacc actgcacgtc <br>ccgccaaggc tcgaaatgag
-
ggccagtggg cgctgggaca tcgcgagcca ctcaacgcca acgaagagct gaagaaggcc
+
ggccagtggg cgctgggaca tcgcgagcca <br>ctcaacgcca acgaagagct gaagaaggcc
-
ggcaacccgc tcgacgtgcg ggagcgcatc gaaaacatct acgccaaaca gggtttcgac
+
ggcaacccgc tcgacgtgcg <br>ggagcgcatc gaaaacatct acgccaaaca gggtttcgac
-
agcatcgaca agaccgacct gcgagggcgc tttcgctggt ggggcctgta cacccagcgt
+
agcatcgaca <br>agaccgacct gcgagggcgc tttcgctggt ggggcctgta cacccagcgt
-
gagcagggct acgacggcac ctggaccggt gacgacaaca tcgacaagct cgaggccaaa
+
<br>gagcagggct acgacggcac ctggaccggt gacgacaaca tcgacaagct <br>cgaggccaaa
-
tacttcatga tgcgggtgcg ttgcgacggc ggcgcgctct cggctgccgc gctgcgcacg
+
tacttcatga tgcgggtgcg ttgcgacggc ggcgcgctct <br>cggctgccgc gctgcgcacg
-
ctgggccaga tctcgacgga gttcgcgcgc gataccgccg atatctccga ccggcagaac
+
ctgggccaga tctcgacgga gttcgcgcgc <br>gataccgccg atatctccga ccggcagaac
-
gtgcaatacc actggatcga agtggaaaac gtccctgaaa tctggcgacg gttagacgat
+
gtgcaatacc actggatcga <br>agtggaaaac gtccctgaaa tctggcgacg gttagacgat
-
gtcggactgc agaccaccga ggcgtgcggt gactgcccgc gggtagtgct gggctcgccg
+
gtcggactgc <br>agaccaccga ggcgtgcggt gactgcccgc gggtagtgct gggctcgccg
-
ttggccggcg agtcgctcga cgaagtgctc gacccgacct gggcgatcga ggagatcgtg
+
<br>ttggccggcg agtcgctcga cgaagtgctc gacccgacct gggcgatcga <br>ggagatcgtg
-
cgtcgctaca tcggcaagcc cgacttcgcc gacttgccgc gcaagtacaa gaccgccatc
+
cgtcgctaca tcggcaagcc cgacttcgcc gacttgccgc <br>gcaagtacaa gaccgccatc
-
tctggcctgc aggacgtcgc gcacgagatc aacgacgtcg ccttcatcgg cgtcaaccat
+
tctggcctgc aggacgtcgc gcacgagatc <br>aacgacgtcg ccttcatcgg cgtcaaccat
-
cccgagcacg gaccaggcct ggatctgtgg gtgggcggtg gactgtcgac caacccgatg
+
cccgagcacg gaccaggcct <br>ggatctgtgg gtgggcggtg gactgtcgac caacccgatg
-
ctggcccagc gggtcggcgc ctgggttcca ctgggcgaag tgcccgaggt gtgggcggcg
+
ctggcccagc <br>gggtcggcgc ctgggttcca ctgggcgaag tgcccgaggt gtgggcggcg
-
gtcacctcgg tgtttcgcga ctacggctac cggcgactgc gcgccaaggc ccggctgaaa
+
<br>gtcacctcgg tgtttcgcga ctacggctac cggcgactgc gcgccaaggc <br>ccggctgaaa
-
tttctgatca aagactgggg catagcgaag ttccgcgaag tgctcgaaac cgagtacctc
+
tttctgatca aagactgggg catagcgaag ttccgcgaag <br>tgctcgaaac cgagtacctc
-
aagcgtccgc tgatcgacgg tccggccccc gaaccggtca agcatccgat cgaccacgtc
+
aagcgtccgc tgatcgacgg tccggccccc <br>gaaccggtca agcatccgat cgaccacgtc
-
ggggtgcaac gactcaagaa cgggctcaac gccgtcggag tcgcccccat cgccgggcgg
+
ggggtgcaac gactcaagaa <br>cgggctcaac gccgtcggag tcgcccccat cgccgggcgg
-
gtatcgggca ccatcctcac ggcggtcgcc gacctgatgg cgcgggccgg ttccgaccgg
+
gtatcgggca <br>ccatcctcac ggcggtcgcc gacctgatgg cgcgggccgg ttccgaccgg
-
atccggttca ccccctacca gaagctggtc atcctcgaca ttccggacgc cttgctcgac
+
<br>atccggttca ccccctacca gaagctggtc atcctcgaca ttccggacgc <br>cttgctcgac
-
gacttgatcg ccggtctgga cgcgctgggg ctgcagtcgc gcccgtcgca ttggcgccgg
+
gacttgatcg ccggtctgga cgcgctgggg ctgcagtcgc <br>gcccgtcgca ttggcgccgg
-
aacttgatgg cgtgcagcgg gattgagttc tgcaagttgt cattcgccga aacccgggtt
+
aacttgatgg cgtgcagcgg gattgagttc <br>tgcaagttgt cattcgccga aacccgggtt
-
cgagcacagc atttggtgcc cgagctggaa cgccggcttg aggacatcaa ctcgcagctc
+
cgagcacagc atttggtgcc <br>cgagctggaa cgccggcttg aggacatcaa ctcgcagctc
-
gacgtaccga tcaccgtcaa catcaacggc tgcccgaact catgtgcgcg aattcaaatc
+
gacgtaccga <br>tcaccgtcaa catcaacggc tgcccgaact catgtgcgcg aattcaaatc
-
gccgacatcg gattcaaggg acagatgatc gacgacggac acggcggctc cgtcgaaggc
+
<br>gccgacatcg gattcaaggg acagatgatc gacgacggac acggcggctc <br>cgtcgaaggc
-
ttccaggtgc atctgggcgg acacctcggc ctggatgccg gattcggccg caaactgcgc
+
ttccaggtgc atctgggcgg acacctcggc ctggatgccg <br>gattcggccg caaactgcgc
-
cagcacaagg tcaccagtga cgaactcggc gactacatcg accgggtggt gcgcaacttc
+
cagcacaagg tcaccagtga cgaactcggc <br>gactacatcg accgggtggt gcgcaacttc
-
gtcaaacacc gcagcgaagg tgaacgcttc gcgcagtggg tcatccgggc cgaggaggac
+
gtcaaacacc gcagcgaagg <br>tgaacgcttc gcgcagtggg tcatccgggc cgaggaggac
-
gacctgcgat gagcggccgc ttttttcctt</p>
+
gacctgcgat <br>gagcggccgc ttttttcctt</p>
<p>This sequence was then inserted into Geneious.  The PstI and EcoRI sites were manually removed and replaced with silent mutations.  A NcoI site was inserted at the start codon and an extra glycine was added after the start codon for the NcoI site to function properly.  We chose glycine as it is small an unlikely to interfere with either polar or non-polar domains within the protein.  We used GGC as the codon as it is the highest used glycine codon in e. coli.  We also added an AvrII site on the 3’ end of the site.  We then added biobrick restriction sites on the ends of the sequence (EcoRI, XbaI, SpeI, PstI).  This will allow us to clone into our expression vector pACYCDuet-1 with NcoI and AvrII enzymes and into a biobrick registry with EcoRI and PstI.  The insertion into pACYCDuet-1 removes both protein tags and cuts out the second MCS resulting in vector pACYCDuet-TBsirA.  The resulting sequence for TB SirA follows:</p>
<p>This sequence was then inserted into Geneious.  The PstI and EcoRI sites were manually removed and replaced with silent mutations.  A NcoI site was inserted at the start codon and an extra glycine was added after the start codon for the NcoI site to function properly.  We chose glycine as it is small an unlikely to interfere with either polar or non-polar domains within the protein.  We used GGC as the codon as it is the highest used glycine codon in e. coli.  We also added an AvrII site on the 3’ end of the site.  We then added biobrick restriction sites on the ends of the sequence (EcoRI, XbaI, SpeI, PstI).  This will allow us to clone into our expression vector pACYCDuet-1 with NcoI and AvrII enzymes and into a biobrick registry with EcoRI and PstI.  The insertion into pACYCDuet-1 removes both protein tags and cuts out the second MCS resulting in vector pACYCDuet-TBsirA.  The resulting sequence for TB SirA follows:</p>
-
<p>CATGGAATTCTAGACCATGGGCTCCGCGAAGGAGAACCCCCAAATGACCACTGCACGTCCCGCCAAGGCTCGAAATGAGGGCCAGTGGGCGCTGGGACATCGCGAGCCACTCAACGCCAACGAAGAGCTGAAGAAGGCCGGCAACCCGCTCGACGTGCGGGAGCGCATCGAAAACATCTACGCCAAACAGGGTTTCGACAGCATCGACAAGACCGACCTGCGAGGGCGCTTTCGCTGGTGGGGCCTGTACACCCAGCGTGAGCAGGGCTACGACGGCACCTGGACCGGTGACGACAACATCGACAAGCTCGAGGCCAAATACTTCATGATGCGGGTGCGTTGCGACGGCGGCGCGCTCTCGGCTGCCGCGCTGCGCACGCTGGGCCAGATCTCGACGGAGTTCGCGCGCGATACCGCCGATATCTCCGACCGGCAGAACGTGCAATACCACTGGATCGAAGTGGAAAACGTCCCTGAAATCTGGCGACGGTTAGACGATGTCGGACTTCAGACCACCGAGGCGTGCGGTGACTGCCCGCGGGTAGTGCTGGGCTCGCCGTTGGCCGGCGAGTCGCTCGACGAAGTGCTCGACCCGACCTGGGCGATCGAGGAGATCGTGCGTCGCTACATCGGCAAGCCCGACTTCGCCGACTTGCCGCGCAAGTACAAGACCGCCATCTCTGGCCTTCAGGACGTCGCGCACGAGATCAACGACGTCGCCTTCATCGGCGTCAACCATCCCGAGCACGGACCAGGCCTGGATCTGTGGGTGGGCGGTGGACTGTCGACCAACCCGATGCTGGCCCAGCGGGTCGGCGCCTGGGTTCCACTGGGCGAAGTGCCCGAGGTGTGGGCGGCGGTCACCTCGGTGTTTCGCGACTACGGCTACCGGCGACTGCGCGCCAAGGCCCGGCTGAAATTTCTGATCAAAGACTGGGGCATAGCGAAGTTCCGCGAAGTGCTCGAAACCGAGTACCTCAAGCGTCCGCTGATCGACGGTCCGGCCCCCGAACCGGTCAAGCATCCGATCGACCACGTCGGGGTGCAACGACTCAAGAACGGGCTCAACGCCGTCGGAGTCGCCCCCATCGCCGGGCGGGTATCGGGCACCATCCTCACGGCGGTCGCCGACCTGATGGCGCGGGCCGGTTCCGACCGGATCCGGTTCACCCCCTACCAGAAGCTGGTCATCCTCGACATTCCGGACGCCTTGCTCGACGACTTGATCGCCGGTCTGGACGCGCTGGGGCTTCAGTCGCGCCCGTCGCATTGGCGCCGGAACTTGATGGCGTGCAGCGGGATTGAGTTCTGCAAGTTGTCATTCGCCGAAACCCGGGTTCGAGCACAGCATTTGGTGCCCGAGCTGGAACGCCGGCTTGAGGACATCAACTCGCAGCTCGACGTACCGATCACCGTCAACATCAACGGCTGCCCGAACTCATGTGCGCGAGTTCAAATCGCCGACATCGGATTCAAGGGACAGATGATCGACGACGGACACGGCGGCTCCGTCGAAGGCTTCCAGGTGCATCTGGGCGGACACCTCGGCCTGGATGCCGGATTCGGCCGCAAACTGCGCCAGCACAAGGTCACCAGTGACGAACTCGGCGACTACATCGACCGGGTGGTGCGCAACTTCGTCAAACACCGCAGCGAAGGTGAACGCTTCGCGCAGTGGGTCATCCGGGCCGAGGAGGACGACCTGCGATGAGCGGCCGCCTAGGACTACTAGTCTGCAGTTTTTCCTT</p>
+
<p style="font-family: courier">catggaattc tagaccatgg gctccgcgaa ggagaacccc caaatgacca <br>ctgcacgtcc cgccaaggct cgaaatgagg gccagtgggc gctgggacat <br>cgcgagccac tcaacgccaa cgaagagctg aagaaggccg gcaacccgct <br>cgacgtgcgg gagcgcatcg aaaacatcta cgccaaacag ggtttcgaca <br>gcatcgacaa gaccgacctg cgagggcgct ttcgctggtg gggcctgtac <br>acccagcgtg agcagggcta cgacggcacc tggaccggtg acgacaacat <br>cgacaagctc gaggccaaat acttcatgat gcgggtgcgt tgcgacggcg <br>gcgcgctctc ggctgccgcg ctgcgcacgc tgggccagat ctcgacggag <br>ttcgcgcgcg ataccgccga tatctccgac cggcagaacg tgcaatacca <br>ctggatcgaa gtggaaaacg tccctgaaat ctggcgacgg ttagacgatg <br>tcggacttca gaccaccgag gcgtgcggtg actgcccgcg ggtagtgctg <br>ggctcgccgt tggccggcga gtcgctcgac gaagtgctcg acccgacctg <br>ggcgatcgag gagatcgtgc gtcgctacat cggcaagccc gacttcgccg <br>acttgccgcg caagtacaag accgccatct ctggccttca ggacgtcgcg <br>cacgagatca acgacgtcgc cttcatcggc gtcaaccatc ccgagcacgg <br>accaggcctg gatctgtggg tgggcggtgg actgtcgacc aacccgatgc <br>tggcccagcg ggtcggcgcc tgggttccac tgggcgaagt gcccgaggtg <br>tgggcggcgg tcacctcggt gtttcgcgac tacggctacc ggcgactgcg <br>cgccaaggcc cggctgaaat ttctgatcaa agactggggc atagcgaagt <br>tccgcgaagt gctcgaaacc gagtacctca agcgtccgct gatcgacggt <br>ccggcccccg aaccggtcaa gcatccgatc gaccacgtcg gggtgcaacg <br>actcaagaac gggctcaacg ccgtcggagt cgcccccatc gccgggcggg <br>tatcgggcac catcctcacg gcggtcgccg acctgatggc gcgggccggt <br>tccgaccgga tccggttcac cccctaccag aagctggtca tcctcgacat <br>tccggacgcc ttgctcgacg acttgatcgc cggtctggac gcgctggggc <br>ttcagtcgcg cccgtcgcat tggcgccgga acttgatggc gtgcagcggg <br>attgagttct gcaagttgtc attcgccgaa acccgggttc gagcacagca <br>tttggtgccc gagctggaac gccggcttga ggacatcaac tcgcagctcg <br>acgtaccgat caccgtcaac atcaacggct gcccgaactc atgtgcgcga <br>gttcaaatcg ccgacatcgg attcaaggga cagatgatcg acgacggaca <br>cggcggctcc gtcgaaggct tccaggtgca tctgggcgga cacctcggcc <br>tggatgccgg attcggccgc aaactgcgcc agcacaaggt caccagtgac <br>gaactcggcg actacatcga ccgggtggtg cgcaacttcg tcaaacaccg <br>cagcgaaggt gaacgcttcg cgcagtgggt catccgggcc gaggaggacg <br>acctgcgatg agcggccgcc taggactact agtctgcagt ttttcctt</p>
<p><em>Mycobacterium smegmatis</em>
<p><em>Mycobacterium smegmatis</em>
<br>This reference also contains the cloning of sirA from T. smegmatis.  We used the primers below taken from Pinto et al, blasted against the T. smegmatis genome and extracted the sirA sequence from genbank as above.
<br>This reference also contains the cloning of sirA from T. smegmatis.  We used the primers below taken from Pinto et al, blasted against the T. smegmatis genome and extracted the sirA sequence from genbank as above.
<br>Primers: <br>smegsirA F &nbsp;&nbsp;&nbsp;&nbsp; TACAGCTGATGCTCGAAGACGAGTACTTCAT
<br>Primers: <br>smegsirA F &nbsp;&nbsp;&nbsp;&nbsp; TACAGCTGATGCTCGAAGACGAGTACTTCAT
<br>smegsirA R &nbsp;&nbsp;&nbsp;&nbsp; CCCAAGCTTTCACGTTGCCTACCTCAAATCCGCTTCGTC</p>
<br>smegsirA R &nbsp;&nbsp;&nbsp;&nbsp; CCCAAGCTTTCACGTTGCCTACCTCAAATCCGCTTCGTC</p>
-
<p>tacagctgat gctcgaagac gagtacttca tgctgcgcgt gcgctgcgat ggtggcgcgctgaccact
+
<p style="font-family: courier">
-
gcagcgctgc gcacgctcgg cggcatctcg accgagttcg cgcgcgacac cgccgacatc
+
tacagctgat gctcgaagac gagtacttca tgctgcgcgt gcgctgcgat  
-
tccgaccgcg agaacgtcca gtaccactgg atccaggtcg agaacatgcc cgagatctgg
+
<br>ggtggcgcgc tgaccactgc agcgctgcgc acgctcggcg gcatctcgac
-
aagcgcctcg acgccgtcgg cctgcagacc accgaggcgt gcggcgactg cccgcgtgtg
+
<br>cgagttcgcg cgcgacaccg ccgacatctc cgaccgcgag aacgtccagt
-
gtcctcggct cgccgctggc cggtgagtcc ctcgacgagg tgatcgacgg gacccccgcg
+
<br>accactggat ccaggtcgag aacatgcccg agatctggaa gcgcctcgac
-
atcgacgaga tcgtgcgccg ctacatcggc aagcccgagt actcgaacct gccgcgcaag
+
<br>gccgtcggcc tgcagaccac cgaggcgtgc ggcgactgcc cgcgtgtggt
-
ttcaagaccg cgatctcggg gcttcaggac gtggtccacg aggtcaacga cgtcgcgttc
+
<br>cctcggctcg ccgctggccg gtgagtccct cgacgaggtg atcgacggga
-
atcggcgtca accaccccga gcacggcccg ggcttcgacc tgtgggtcgg tggcggcctg
+
<br>cccccgcgat cgacgagatc gtgcgccgct acatcggcaa gcccgagtac
-
tcgaccaacc cgatgctggc ccagcgcgtc ggggtgtggg tgccgctcga cgaggtgccc
+
<br>tcgaacctgc cgcgcaagtt caagaccgcg atctcggggc ttcaggacgt
-
gacgtctggg agggcgtcgt cagcatcttc cgcgactacg gttaccggcg tctgcggtcg
+
<br>ggtccacgag gtcaacgacg tcgcgttcat cggcgtcaac caccccgagc
-
aaggcgcggc tgaagttcct gatcaaggac tggggcgtcg aaaagttcag ggaagtgctg
+
<br>acggcccggg cttcgacctg tgggtcggtg gcggcctgtc gaccaacccg
-
gaaaccgagt acctcaagcg ccccctgatc gacggcccgg cacccgaacc ggtgacccgc
+
<br>atgctggccc agcgcgtcgg ggtgtgggtg ccgctcgacg aggtgcccga
-
cccatcgacc acgtcggtgt gcagaagctc aagaacggcc tcaacgccgt gggcgtcgcc
+
<br>cgtctgggag ggcgtcgtca gcatcttccg cgactacggt taccggcgtc
-
ccgatcgcgg gtcgcgtctc gggcacgatc ctgaccaagg tggccgatct cgccgaggcc
+
<br>tgcggtcgaa ggcgcggctg aagttcctga tcaaggactg gggcgtcgaa
-
gccgggtccg accggatccg cttcacgccg taccagaagc tgatcatcct cgacgtgccc
+
<br>aagttcaggg aagtgctgga aaccgagtac ctcaagcgcc ccctgatcga
-
gacgacaaga tcgacgaact gcgcgctggc ctcgacgcgc tcggactgcc gtcgacgccg
+
<br>cggcccggca cccgaaccgg tgacccgccc catcgaccac gtcggtgtgc
-
tcgcactggc gccgcaacct catggcgtgc acgggtatcg agttctgcaa gctgagcttc
+
<br>agaagctcaa gaacggcctc aacgccgtgg gcgtcgcccc gatcgcgggt
-
gccgagaccc gcaagcgtgc ccaggtgctg gttcccgagc tggagaaacg gctcgacgac
+
<br>cgcgtctcgg gcacgatcct gaccaaggtg gccgatctcg ccgaggccgc
-
atcaacgccc agctcgacgt gcccatcacg gtcaacatca acggctgccc caactcgtgc
+
<br>cgggtccgac cggatccgct tcacgccgta ccagaagctg atcatcctcg
-
gcccgtatcc aggtcgccga catcgggttc aagggccaga tggtcgacga tggcaacggc
+
<br>acgtgcccga cgacaagatc gacgaactgc gcgctggcct cgacgcgctc
-
cccgaggagg gtttccaggt gcatctgggc ggcagcctgg gcctggacag cgggttcggc
+
<br>ggactgccgt cgacgccgtc gcactggcgc cgcaacctca tggcgtgcac
-
cgcaagctgc gccagcacaa ggtgctctcg tccgagctcg gcgactacat cgagcgcgtc
+
<br>gggtatcgag ttctgcaagc tgagcttcgc cgagacccgc aagcgtgccc
-
gtgcgcaact tcgtgaaaca acgcgaggac ggcgagcgtt tcgcccagtg ggccgtgcgg
+
<br>aggtgctggt tcccgagctg gagaaacggc tcgacgacat caacgcccag
-
gccgacgaag cggatttgag gtaggcaacg tgaaagcttg gg</p>
+
<br>ctcgacgtgc ccatcacggt caacatcaac ggctgcccca actcgtgcgc
 +
<br>ccgtatccag gtcgccgaca tcgggttcaa gggccagatg gtcgacgatg
 +
<br>gcaacggccc cgaggagggt ttccaggtgc atctgggcgg cagcctgggc
 +
<br>ctggacagcg ggttcggccg caagctgcgc cagcacaagg tgctctcgtc
 +
<br>cgagctcggc gactacatcg agcgcgtcgt gcgcaacttc gtgaaacaac
 +
<br>gcgaggacgg cgagcgtttc gcccagtggg ccgtgcgggc cgacgaagcg
 +
<br>gatttgaggt aggcaacgtg aaagcttggg</p>
<p>As above, the sequence was imported into geneious, the biobrick restriction sites were manually removed from the sequence and restriction sites were added to the 5’ and 3’ ends in the same fashion as TB sirA.  This resulted in the following sequence for synthesis:</p>
<p>As above, the sequence was imported into geneious, the biobrick restriction sites were manually removed from the sequence and restriction sites were added to the 5’ and 3’ ends in the same fashion as TB sirA.  This resulted in the following sequence for synthesis:</p>
-
<p>
+
<p style="font-family: courier">
-
p {
+
tacagaattc tagaccatgg gcctcgaaga cgagtacttc atgctgcgcg
-
    text-transform: lowercase;
+
<br>tgcgctgcga tggtggcgcg ctgaccacta cagcgctgcg cacgctcggc
-
}
+
<br>ggcatctcga ccgagttcgc gcgcgacacc gccgacatct ccgaccgcga
-
TACAGAATTCTAGACCATGGGCCTCGAAGACGAGTACTTCATGCTGCGCGTGCGCTGCGATGGTGGCGCGCTGACCACTACAGCGCTGCGCACGCTCGGCGGCATCTCGACCGAGTTCGCGCGCGACACCGCCGACATCTCCGACCGCGAGAACGTCCAGTACCACTGGATCCAGGTCGAGAACATGCCCGAGATCTGGAAGCGCCTCGACGCCGTCGGCCTACAGACCACCGAGGCGTGCGGCGACTGCCCGCGTGTGGTCCTCGGCTCGCCGCTGGCCGGTGAGTCCCTCGACGAGGTGATCGACGGGACCCCCGCGATCGACGAGATCGTGCGCCGCTACATCGGCAAGCCCGAGTACTCGAACCTGCCGCGCAAGTTCAAGACCGCGATCTCGGGGCTTCAGGACGTGGTCCACGAGGTCAACGACGTCGCGTTCATCGGCGTCAACCACCCCGAGCACGGCCCGGGCTTCGACCTGTGGGTCGGTGGCGGCCTGTCGACCAACCCGATGCTGGCCCAGCGCGTCGGGGTGTGGGTGCCGCTCGACGAGGTGCCCGACGTCTGGGAGGGCGTCGTCAGCATCTTCCGCGACTACGGTTACCGGCGTCTGCGGTCGAAGGCGCGGCTGAAGTTCCTGATCAAGGACTGGGGCGTCGAAAAGTTCAGGGAAGTGCTGGAAACCGAGTACCTCAAGCGCCCCCTGATCGACGGCCCGGCACCCGAACCGGTGACCCGCCCCATCGACCACGTCGGTGTGCAGAAGCTCAAGAACGGCCTCAACGCCGTGGGCGTCGCCCCGATCGCGGGTCGCGTCTCGGGCACGATCCTGACCAAGGTGGCCGATCTCGCCGAGGCCGCCGGGTCCGACCGGATCCGCTTCACGCCGTACCAGAAGCTGATCATCCTCGACGTGCCCGACGACAAGATCGACGAACTGCGCGCTGGCCTCGACGCGCTCGGACTGCCGTCGACGCCGTCGCACTGGCGCCGCAACCTCATGGCGTGCACGGGTATCGAGTTCTGCAAGCTGAGCTTCGCCGAGACCCGCAAGCGTGCCCAGGTGCTGGTTCCCGAGCTGGAGAAACGGCTCGACGACATCAACGCCCAGCTCGACGTGCCCATCACGGTCAACATCAACGGCTGCCCCAACTCGTGCGCCCGTATCCAGGTCGCCGACATCGGGTTCAAGGGCCAGATGGTCGACGATGGCAACGGCCCCGAGGAGGGTTTCCAGGTGCATCTGGGCGGCAGCCTGGGCCTGGACAGCGGGTTCGGCCGCAAGCTGCGCCAGCACAAGGTGCTCTCGTCCGAGCTCGGCGACTACATCGAGCGCGTCGTGCGCAACTTCGTGAAACAACGCGAGGACGGCGAGCGTTTCGCCCAGTGGGCCGTGCGGGCCGACGAAGCGGATTTGAGGTAGGCAACGTGAAAGCCTAGGTACTAGTCTGCAGTGGG</p>
+
<br>gaacgtccag taccactgga tccaggtcga gaacatgccc gagatctgga
 +
<br>agcgcctcga cgccgtcggc ctacagacca ccgaggcgtg cggcgactgc
 +
<br>ccgcgtgtgg tcctcggctc gccgctggcc ggtgagtccc tcgacgaggt
 +
<br>gatcgacggg acccccgcga tcgacgagat cgtgcgccgc tacatcggca
 +
<br>agcccgagta ctcgaacctg ccgcgcaagt tcaagaccgc gatctcgggg
 +
<br>cttcaggacg tggtccacga ggtcaacgac gtcgcgttca tcggcgtcaa
 +
<br>ccaccccgag cacggcccgg gcttcgacct gtgggtcggt ggcggcctgt
 +
<br>cgaccaaccc gatgctggcc cagcgcgtcg gggtgtgggt gccgctcgac
 +
<br>gaggtgcccg acgtctggga gggcgtcgtc agcatcttcc gcgactacgg
 +
<br>ttaccggcgt ctgcggtcga aggcgcggct gaagttcctg atcaaggact
 +
<br>ggggcgtcga aaagttcagg gaagtgctgg aaaccgagta cctcaagcgc
 +
<br>cccctgatcg acggcccggc acccgaaccg gtgacccgcc ccatcgacca
 +
<br>cgtcggtgtg cagaagctca agaacggcct caacgccgtg ggcgtcgccc
 +
<br>cgatcgcggg tcgcgtctcg ggcacgatcc tgaccaaggt ggccgatctc
 +
<br>gccgaggccg ccgggtccga ccggatccgc ttcacgccgt accagaagct
 +
<br>gatcatcctc gacgtgcccg acgacaagat cgacgaactg cgcgctggcc
 +
<br>tcgacgcgct cggactgccg tcgacgccgt cgcactggcg ccgcaacctc
 +
<br>atggcgtgca cgggtatcga gttctgcaag ctgagcttcg ccgagacccg
 +
<br>caagcgtgcc caggtgctgg ttcccgagct ggagaaacgg ctcgacgaca
 +
<br>tcaacgccca gctcgacgtg cccatcacgg tcaacatcaa cggctgcccc
 +
<br>aactcgtgcg cccgtatcca ggtcgccgac atcgggttca agggccagat
 +
<br>ggtcgacgat ggcaacggcc ccgaggaggg tttccaggtg catctgggcg
 +
<br>gcagcctggg cctggacagc gggttcggcc gcaagctgcg ccagcacaag
 +
<br>gtgctctcgt ccgagctcgg cgactacatc gagcgcgtcg tgcgcaactt
 +
<br>cgtgaaacaa cgcgaggacg gcgagcgttt cgcccagtgg gccgtgcggg
 +
<br>ccgacgaagc ggatttgagg taggcaacgt gaaagcctag gtactagtct
 +
<br>gcagtggg
 +
</p>
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Latest revision as of 09:40, 13 August 2013

Drug Screening

Monday 10th June

Design of SirA genes for synthesis

SirA

Mycobacterium tuberculosis
Reference: Pinto et al. 2007. Sulfite Reduction in Mycobacteria doi: 10.1128/JB.00487-07
Primers:
TBsirA F      GGAATTCCATATGTCCGCGAAGGAGAACCCC
TBsirA R      AAGGAAAAAAGCGGCCGCTCATCGCAGGTCGTCCTCCTCGGCCCGGAT
We blasted the above primers used to clone sirA from M. tuberculosis into E. coli. We then extracted the sequence from genbank to retrieve the following sequence which includes the restriction sites introduced by Pinto et al.

ggaattccat atgtccgcga aggagaaccc ccaaatgacc actgcacgtc
ccgccaaggc tcgaaatgag ggccagtggg cgctgggaca tcgcgagcca
ctcaacgcca acgaagagct gaagaaggcc ggcaacccgc tcgacgtgcg
ggagcgcatc gaaaacatct acgccaaaca gggtttcgac agcatcgaca
agaccgacct gcgagggcgc tttcgctggt ggggcctgta cacccagcgt
gagcagggct acgacggcac ctggaccggt gacgacaaca tcgacaagct
cgaggccaaa tacttcatga tgcgggtgcg ttgcgacggc ggcgcgctct
cggctgccgc gctgcgcacg ctgggccaga tctcgacgga gttcgcgcgc
gataccgccg atatctccga ccggcagaac gtgcaatacc actggatcga
agtggaaaac gtccctgaaa tctggcgacg gttagacgat gtcggactgc
agaccaccga ggcgtgcggt gactgcccgc gggtagtgct gggctcgccg
ttggccggcg agtcgctcga cgaagtgctc gacccgacct gggcgatcga
ggagatcgtg cgtcgctaca tcggcaagcc cgacttcgcc gacttgccgc
gcaagtacaa gaccgccatc tctggcctgc aggacgtcgc gcacgagatc
aacgacgtcg ccttcatcgg cgtcaaccat cccgagcacg gaccaggcct
ggatctgtgg gtgggcggtg gactgtcgac caacccgatg ctggcccagc
gggtcggcgc ctgggttcca ctgggcgaag tgcccgaggt gtgggcggcg
gtcacctcgg tgtttcgcga ctacggctac cggcgactgc gcgccaaggc
ccggctgaaa tttctgatca aagactgggg catagcgaag ttccgcgaag
tgctcgaaac cgagtacctc aagcgtccgc tgatcgacgg tccggccccc
gaaccggtca agcatccgat cgaccacgtc ggggtgcaac gactcaagaa
cgggctcaac gccgtcggag tcgcccccat cgccgggcgg gtatcgggca
ccatcctcac ggcggtcgcc gacctgatgg cgcgggccgg ttccgaccgg
atccggttca ccccctacca gaagctggtc atcctcgaca ttccggacgc
cttgctcgac gacttgatcg ccggtctgga cgcgctgggg ctgcagtcgc
gcccgtcgca ttggcgccgg aacttgatgg cgtgcagcgg gattgagttc
tgcaagttgt cattcgccga aacccgggtt cgagcacagc atttggtgcc
cgagctggaa cgccggcttg aggacatcaa ctcgcagctc gacgtaccga
tcaccgtcaa catcaacggc tgcccgaact catgtgcgcg aattcaaatc
gccgacatcg gattcaaggg acagatgatc gacgacggac acggcggctc
cgtcgaaggc ttccaggtgc atctgggcgg acacctcggc ctggatgccg
gattcggccg caaactgcgc cagcacaagg tcaccagtga cgaactcggc
gactacatcg accgggtggt gcgcaacttc gtcaaacacc gcagcgaagg
tgaacgcttc gcgcagtggg tcatccgggc cgaggaggac gacctgcgat
gagcggccgc ttttttcctt

This sequence was then inserted into Geneious. The PstI and EcoRI sites were manually removed and replaced with silent mutations. A NcoI site was inserted at the start codon and an extra glycine was added after the start codon for the NcoI site to function properly. We chose glycine as it is small an unlikely to interfere with either polar or non-polar domains within the protein. We used GGC as the codon as it is the highest used glycine codon in e. coli. We also added an AvrII site on the 3’ end of the site. We then added biobrick restriction sites on the ends of the sequence (EcoRI, XbaI, SpeI, PstI). This will allow us to clone into our expression vector pACYCDuet-1 with NcoI and AvrII enzymes and into a biobrick registry with EcoRI and PstI. The insertion into pACYCDuet-1 removes both protein tags and cuts out the second MCS resulting in vector pACYCDuet-TBsirA. The resulting sequence for TB SirA follows:

catggaattc tagaccatgg gctccgcgaa ggagaacccc caaatgacca
ctgcacgtcc cgccaaggct cgaaatgagg gccagtgggc gctgggacat
cgcgagccac tcaacgccaa cgaagagctg aagaaggccg gcaacccgct
cgacgtgcgg gagcgcatcg aaaacatcta cgccaaacag ggtttcgaca
gcatcgacaa gaccgacctg cgagggcgct ttcgctggtg gggcctgtac
acccagcgtg agcagggcta cgacggcacc tggaccggtg acgacaacat
cgacaagctc gaggccaaat acttcatgat gcgggtgcgt tgcgacggcg
gcgcgctctc ggctgccgcg ctgcgcacgc tgggccagat ctcgacggag
ttcgcgcgcg ataccgccga tatctccgac cggcagaacg tgcaatacca
ctggatcgaa gtggaaaacg tccctgaaat ctggcgacgg ttagacgatg
tcggacttca gaccaccgag gcgtgcggtg actgcccgcg ggtagtgctg
ggctcgccgt tggccggcga gtcgctcgac gaagtgctcg acccgacctg
ggcgatcgag gagatcgtgc gtcgctacat cggcaagccc gacttcgccg
acttgccgcg caagtacaag accgccatct ctggccttca ggacgtcgcg
cacgagatca acgacgtcgc cttcatcggc gtcaaccatc ccgagcacgg
accaggcctg gatctgtggg tgggcggtgg actgtcgacc aacccgatgc
tggcccagcg ggtcggcgcc tgggttccac tgggcgaagt gcccgaggtg
tgggcggcgg tcacctcggt gtttcgcgac tacggctacc ggcgactgcg
cgccaaggcc cggctgaaat ttctgatcaa agactggggc atagcgaagt
tccgcgaagt gctcgaaacc gagtacctca agcgtccgct gatcgacggt
ccggcccccg aaccggtcaa gcatccgatc gaccacgtcg gggtgcaacg
actcaagaac gggctcaacg ccgtcggagt cgcccccatc gccgggcggg
tatcgggcac catcctcacg gcggtcgccg acctgatggc gcgggccggt
tccgaccgga tccggttcac cccctaccag aagctggtca tcctcgacat
tccggacgcc ttgctcgacg acttgatcgc cggtctggac gcgctggggc
ttcagtcgcg cccgtcgcat tggcgccgga acttgatggc gtgcagcggg
attgagttct gcaagttgtc attcgccgaa acccgggttc gagcacagca
tttggtgccc gagctggaac gccggcttga ggacatcaac tcgcagctcg
acgtaccgat caccgtcaac atcaacggct gcccgaactc atgtgcgcga
gttcaaatcg ccgacatcgg attcaaggga cagatgatcg acgacggaca
cggcggctcc gtcgaaggct tccaggtgca tctgggcgga cacctcggcc
tggatgccgg attcggccgc aaactgcgcc agcacaaggt caccagtgac
gaactcggcg actacatcga ccgggtggtg cgcaacttcg tcaaacaccg
cagcgaaggt gaacgcttcg cgcagtgggt catccgggcc gaggaggacg
acctgcgatg agcggccgcc taggactact agtctgcagt ttttcctt

Mycobacterium smegmatis
This reference also contains the cloning of sirA from T. smegmatis. We used the primers below taken from Pinto et al, blasted against the T. smegmatis genome and extracted the sirA sequence from genbank as above.
Primers:
smegsirA F      TACAGCTGATGCTCGAAGACGAGTACTTCAT
smegsirA R      CCCAAGCTTTCACGTTGCCTACCTCAAATCCGCTTCGTC

tacagctgat gctcgaagac gagtacttca tgctgcgcgt gcgctgcgat
ggtggcgcgc tgaccactgc agcgctgcgc acgctcggcg gcatctcgac
cgagttcgcg cgcgacaccg ccgacatctc cgaccgcgag aacgtccagt
accactggat ccaggtcgag aacatgcccg agatctggaa gcgcctcgac
gccgtcggcc tgcagaccac cgaggcgtgc ggcgactgcc cgcgtgtggt
cctcggctcg ccgctggccg gtgagtccct cgacgaggtg atcgacggga
cccccgcgat cgacgagatc gtgcgccgct acatcggcaa gcccgagtac
tcgaacctgc cgcgcaagtt caagaccgcg atctcggggc ttcaggacgt
ggtccacgag gtcaacgacg tcgcgttcat cggcgtcaac caccccgagc
acggcccggg cttcgacctg tgggtcggtg gcggcctgtc gaccaacccg
atgctggccc agcgcgtcgg ggtgtgggtg ccgctcgacg aggtgcccga
cgtctgggag ggcgtcgtca gcatcttccg cgactacggt taccggcgtc
tgcggtcgaa ggcgcggctg aagttcctga tcaaggactg gggcgtcgaa
aagttcaggg aagtgctgga aaccgagtac ctcaagcgcc ccctgatcga
cggcccggca cccgaaccgg tgacccgccc catcgaccac gtcggtgtgc
agaagctcaa gaacggcctc aacgccgtgg gcgtcgcccc gatcgcgggt
cgcgtctcgg gcacgatcct gaccaaggtg gccgatctcg ccgaggccgc
cgggtccgac cggatccgct tcacgccgta ccagaagctg atcatcctcg
acgtgcccga cgacaagatc gacgaactgc gcgctggcct cgacgcgctc
ggactgccgt cgacgccgtc gcactggcgc cgcaacctca tggcgtgcac
gggtatcgag ttctgcaagc tgagcttcgc cgagacccgc aagcgtgccc
aggtgctggt tcccgagctg gagaaacggc tcgacgacat caacgcccag
ctcgacgtgc ccatcacggt caacatcaac ggctgcccca actcgtgcgc
ccgtatccag gtcgccgaca tcgggttcaa gggccagatg gtcgacgatg
gcaacggccc cgaggagggt ttccaggtgc atctgggcgg cagcctgggc
ctggacagcg ggttcggccg caagctgcgc cagcacaagg tgctctcgtc
cgagctcggc gactacatcg agcgcgtcgt gcgcaacttc gtgaaacaac
gcgaggacgg cgagcgtttc gcccagtggg ccgtgcgggc cgacgaagcg
gatttgaggt aggcaacgtg aaagcttggg

As above, the sequence was imported into geneious, the biobrick restriction sites were manually removed from the sequence and restriction sites were added to the 5’ and 3’ ends in the same fashion as TB sirA. This resulted in the following sequence for synthesis:

tacagaattc tagaccatgg gcctcgaaga cgagtacttc atgctgcgcg
tgcgctgcga tggtggcgcg ctgaccacta cagcgctgcg cacgctcggc
ggcatctcga ccgagttcgc gcgcgacacc gccgacatct ccgaccgcga
gaacgtccag taccactgga tccaggtcga gaacatgccc gagatctgga
agcgcctcga cgccgtcggc ctacagacca ccgaggcgtg cggcgactgc
ccgcgtgtgg tcctcggctc gccgctggcc ggtgagtccc tcgacgaggt
gatcgacggg acccccgcga tcgacgagat cgtgcgccgc tacatcggca
agcccgagta ctcgaacctg ccgcgcaagt tcaagaccgc gatctcgggg
cttcaggacg tggtccacga ggtcaacgac gtcgcgttca tcggcgtcaa
ccaccccgag cacggcccgg gcttcgacct gtgggtcggt ggcggcctgt
cgaccaaccc gatgctggcc cagcgcgtcg gggtgtgggt gccgctcgac
gaggtgcccg acgtctggga gggcgtcgtc agcatcttcc gcgactacgg
ttaccggcgt ctgcggtcga aggcgcggct gaagttcctg atcaaggact
ggggcgtcga aaagttcagg gaagtgctgg aaaccgagta cctcaagcgc
cccctgatcg acggcccggc acccgaaccg gtgacccgcc ccatcgacca
cgtcggtgtg cagaagctca agaacggcct caacgccgtg ggcgtcgccc
cgatcgcggg tcgcgtctcg ggcacgatcc tgaccaaggt ggccgatctc
gccgaggccg ccgggtccga ccggatccgc ttcacgccgt accagaagct
gatcatcctc gacgtgcccg acgacaagat cgacgaactg cgcgctggcc
tcgacgcgct cggactgccg tcgacgccgt cgcactggcg ccgcaacctc
atggcgtgca cgggtatcga gttctgcaag ctgagcttcg ccgagacccg
caagcgtgcc caggtgctgg ttcccgagct ggagaaacgg ctcgacgaca
tcaacgccca gctcgacgtg cccatcacgg tcaacatcaa cggctgcccc
aactcgtgcg cccgtatcca ggtcgccgac atcgggttca agggccagat
ggtcgacgat ggcaacggcc ccgaggaggg tttccaggtg catctgggcg
gcagcctggg cctggacagc gggttcggcc gcaagctgcg ccagcacaag
gtgctctcgt ccgagctcgg cgactacatc gagcgcgtcg tgcgcaactt
cgtgaaacaa cgcgaggacg gcgagcgttt cgcccagtgg gccgtgcggg
ccgacgaagc ggatttgagg taggcaacgt gaaagcctag gtactagtct
gcagtggg

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