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<h2>[<span class="_togglegroup _toggle _toggler">April 30th, 2007: Project Proposal Presentations</span><span class="_toggle _toggler" style="display:none;">Close Project Proposals</span>]</h2>
<h2>April 30th, 2007: Project Proposal Presentations</h2>
<div class="_toggle" style="display:none;">
[<span class="_togglegroup _toggle _toggler">show </span><span class="_toggle _toggler" style="display:none;">hide </span>]
<h3>[<span class="_togglegroup _toggle _toggler">Bacterial Magnetosomes</span><span class="_toggle _toggler" style="display:none;">Close Bacterial Magnetosomes</span>]</h3>
<div class="_toggle" style="display:none;">
<div class="_toggle" style="display:none;">
<h3>Bacterial Magnetosomes</h3>
<table|left>
<table|left>
<tr>
<tr>
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</tr>
</table>
</table>
</div>
<h3>Biogenic Nanotubes</h3>
<h3>[<span class="_togglegroup _toggle _toggler">Biogenic Nanotubes</span><span class="_toggle _toggler" style="display:none;">Close Biogenic Nanotubes</span>]</h3>
<div class="_toggle" style="display:none;">
<font face ="Tahoma">
<font face ="Tahoma">
Disclaimer: It turns out this presentation was looking under the wrong name,
Disclaimer: It turns out this presentation was looking under the wrong name,
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</tr>
</table>
</table>
</div>
</div>
</div>
<h2>[<span class="_togglegroup _toggle _toggler">May 30th, 2007: Project Proposal Presentation</span><span class="_toggle _toggler" style="display:none;">Close Project Proposal</span>]</h2>
<h2>May 30th, 2007: Project Proposal Presentation</h2>
[<span class="_togglegroup _toggle _toggler">show </span><span class="_toggle _toggler" style="display:none;">hide </span>]
<div class="_toggle" style="display:none;">
<div class="_toggle" style="display:none;">
<h3>'''Bio-Dosimetry'''</h3>
<h3>'''Bio-Dosimetry'''</h3>
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</div>
<h2>[<span class="_togglegroup _toggle _toggler">June 4th, 2007: Lab Meeting Presentation</span><span class="_toggle _toggler" style="display:none;">Close Presentation</span>]</h2>
<h2>June 4th, 2007: Lab Meeting Presentation</h2>
[<span class="_togglegroup _toggle _toggler">show </span><span class="_toggle _toggler" style="display:none;">hide </span>]
<div class="_toggle" style="display:none;">
<div class="_toggle" style="display:none;">
<h3>'''iGEM Meeting'''</h3>
<h3>'''iGEM Meeting'''</h3>
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</table>
</div>
</div>
<h2>[<span class="_togglegroup _toggle _toggler">June 13th, 2007: XylR biobricks and primers</span><span class="_toggle _toggler" style="display:none;">Close Biobricks</span>]</h2>
<h2>June 13th, 2007: XylR Biobricks and Primers</h2>
[<span class="_togglegroup _toggle _toggler">show </span><span class="_toggle _toggler" style="display:none;">hide </span>]
<div class="_toggle" style="display:none;">
<div class="_toggle" style="display:none;">
Note: Start codons are in green, stop codons are in read, translational terminators are in blue
Note: Start codons are in green, stop codons are in read, translational terminators are in blue.
All sequences are shown without biobrick restriction sequences
<h3>XylR with promoter and rbs and terminator (right)</h3>
<h3>XylR with promoter, rbs and terminator (Forward )</h3>
<html><pre>GCAACCAAAC GCCGTTCTTG ATTTTGATAA AAATTTTCTC AAAGCCGGTT ACGTATTACC
<html><pre>GCAACCAAAC GCCGTTCTTG ATTTTGATAA AAATTTTCTC AAAGCCGGTT ACGTATTACC
Line 164:
Line 173: *TmC 63,78
*TmC 63,78
<h3>XylR with promoter and rbs (left)</h3>
<h3>XylR with promoter, rbs and terminator (Reverse )</h3>
<html><pre>ATTGCATTTC CTTG<font color=blue>AGCCTT ATCCGACTTG TCAGTCGGAT AAGGCT</font>TTTT ACTTTGTCTC
<html><pre>ATTGCATTTC CTTG<font color=blue>AGCCTT ATCCGACTTG TCAGTCGGAT AAGGCT</font>TTTT ACTTTGTCTC
Line 201:
Line 210: *TmC 63,80
*TmC 63,80
<h3>XylR open reading frame (right)</h3>
<h3>XylR open reading frame (Forward )</h3>
<html><pre><font color=green>ATG</font>TTTACTA AACGTCACCG CATCACATTA CTGTTCAATG CCAATAAAGC CTATGACCGG
<html><pre><font color=green>ATG</font>TTTACTA AACGTCACCG CATCACATTA CTGTTCAATG CCAATAAAGC CTATGACCGG
Line 234:
Line 243: *TmC 62,77
*TmC 62,77
<h3>XylR open reading frame (left)</h3>
<h3>XylR open reading frame (Reverse )</h3>
<html><pre><font color=red>CTA</font>CAACATG ACCTCGCTAT TTACATCGCG ATACTCTTTT GGCGTCGTGT CATATGCTTT
<html><pre><font color=red>CTA</font>CAACATG ACCTCGCTAT TTACATCGCG ATACTCTTTT GGCGTCGTGT CATATGCTTT
Line 260:
Line 269: <h4>Primers:</h4>
<h4>Primers:</h4>
ggaattcgcggccgcttctagag CTACAACATG ACCTCGCTAT TTACAT left side
ggaattcgcg gccgcttcta gag CTACAACATG ACCTCGCTAT TTACAT left side
Sequence for operations: ggaattcgcggccgcttctagagCTACAACATGACCTCGCTATTTACAT
Sequence for operations: ggaattcgcggccgcttctagagCTACAACATGACCTCGCTATTTACAT
*TmC 62,78
*TmC 62,78
ctgcagcggccgctactagta ATGTTTACTA AACGTCACCG CATCA right side
ctgcagcggc cgctactagt a ATGTTTACTA AACGTCACCG CATCA right side
Sequence for operations: ctgcagcggccgctactagtaATGTTTACTAAACGTCACCGCATCA
Sequence for operations: ctgcagcggccgctactagtaATGTTTACTAAACGTCACCGCATCA
*TmC 65,78
*TmC 65,78
</div>
<h2> June 28th, 2007: Lambda Biobricks and Primers</h2>
[<span class="_togglegroup _toggle _toggler">show</span><span class="_toggle _toggler" style="display:none;">hide</span>]
<div class="_toggle" style="display:none;">
<h3>Lambda control region (O<sub>R</sub>)</h3>
*Contains O<sub>R</sub>1, O<sub>R</sub>2, and O<sub>R</sub>3, shown in reverse order (i.e. the leftmost binding region below is O<sub>R</sub>3)
*Bi directional promoter
**in the lambda phage, CI is to the left(P<sub>RM</sub>), cro is to the right(P<sub>R</sub>)
*recognized by cro, CI
**cro binding affinities: O<sub>R</sub>3, O<sub>R</sub>2 ~ O<sub>R</sub>1 (O<sub>R</sub>1 is slightly less)
**CI binding affinites: O<sub>R</sub>1, O<sub>R</sub>2 ~ O<sub>R</sub>3 (O<sub>R</sub>3 is slightly less)
*CI acts as a positive regulator for P<sub>RM</sub> when bound to O<sub>R</sub>2, but and a negative regulator for P<sub>R</sub> when bound to O<sub>R</sub>3
<html><pre>ACGTTA<font color=cyan>AATC </font><font color= blue>TA</font><font color=green>TCACCGCA AGGGATA</font>AA<font color=cyan>T ATC</font><font color = blue>TA</font><font color = green>ACACC GTGCGTG</font><font color =blue>TTG</font><font color=cyan> ACT</font>ATTT<font color=green>TAC
CTCTGGCGGT </font><font color=blue>GATA</font><font color=cyan>AT</font>GGTT GC</pre></html>
Cro and CI binding regions are depicted in <font color = green>green</font>, -10 and -35 sequences in <font color = cyan>cyan</font>, and shared regions are in <font color = blue>blue</font>
<h4>Primers</h4>
Readable primer:ggaattcgcg gccgcttcta gag ACGTTAAATC TATCACCGC (left side)
Primer sequence:ggaattcgcggccgcttctagagACGTTAAATCTATCACCGC
*Mp: 57,77
Readable primer:ctgcagcggc cgctactagt a GCAACCATTA TCACCGC (right side)
Primer sequence:ctgcagcggccgctactagtaGCAACCATTATCACCGC
*Mp: 58,78
<h3>Lambda Repressor (CI)</h3>
*Forms dimers
**Dimers associate to form tetramers, octamers etc
*Binds to O<sub>L</sub> and O<sub>R</sub> operators in bacteriophage genome
*Cleaved by activated RecA protein (activates with ssDNA exposure)
<html><pre><font color=green>ATG</font>AGCACAA AAAAGAAACC ATTAACACAA GAGCAGCTTG AGGACGCACG TCGCCTTAAA
GCAATTTATG AAAAAAAGAA AAATGAACTT GGCTTATCCC AGGAATCTGT CGCAGACAAG
ATGGGGATGG GGCAGTCAGG CGTTGGTGCT TTATTTAATG GCATCAATGC ATTAAATGCT
TATAACGCCG CATTGCTTGC AAAAATTCTC AAAGTTAGCG TTGAAGAATT TAGCCCTTCA
ATCGCCAGAG AAATCTACGA GATGTATGAA GCGGTTAGTA TGCAGCCGTC ACTTAGAAGT
GAGTATGAGT ACCCTGTTTT TTCTCATGTT CAGGCAGGGA TGTTCTCACC TGAGCTTAGA
ACCTTTACCA AAGGTGATGC GGAGAGATGG GTAAGCACAA CCAAAAAAGC CAGTGATTCT
GCATTCTGGC TTGAGGTTGA AGGTAATTCC ATGACCGCAC CAACAGGCTC CAAGCCAAGC
TTTCCTGACG GAATGTTAAT TCTCGTTGAC CCTGAGCAGG CTGTTGAGCC AGGTGATTTC
TGCATAGCCA GACTTGGGGG TGATGAGTTT ACCTTCAAGA AACTGATCAG GGATAGCGGT
CAGGTGTTTT TACAACCACT AAACCCACAG TACCCAATGA TCCCATGCAA TGAGAGTTGT
TCCGTTGTGG GGAAAGTTAT CGCTAGTCAG TGGCCTGAAG AGACGTTTGG C<font color=red>TGA</font></pre></html>
Start codon is in <font color=green>green</font> and stop codon is in <font color=red>red</font>
<h4>Primers</h4>
Readable Primer:ggaattcgcg gccgcttcta gag ATGAGCACAA AAAAGAAACC (left side)
Primer sequence:ggaattcgcggccgcttctagagATGAGCACAAAAAAGAAACC
*Mp: 56,77
Readable primer:ctgcagcggc cgctactagt a TCAGCCAAAC GTCTCTTC (right side)
Primer sequence:ctgcagcggccgctactagtaTCAGCCAAACGTCTCTTC
*Mp: 58,78
<h3>Lambda Repressor (CI) with degredation tag (LVA)</h3>
Part [http://parts.mit.edu/registry/index.php/Part:BBa_C0051 BBa_C0051] on MIT's parts registry
*same as CI repressor, but with degredation tag on the N terminus to promote degredation
<h3>Lambda AntiRepressor (Cro)</h3>
*Binds to O<sub>R</sub> and O<sub>L</sub> operators
*transcriptional activator, repressor
*favors lytic pathway in lambda bacteriophage
<html><pre><font color=green>ATG</font>GAACAAC GCATAACCCT GAAAGATTAT GCAATGCGCT TTGGGCAAAC CAAGACAGCT
AAAGATCTCG GCGTATATCA AAGCGCGATC AACAAGGCCA TTCATGCAGG CCGAAAGATT
TTTTTAACTA TAAACGCTGA TGGAAGCGTT TATGCGGAAG AGGTAAAGCC CTTCCCGAGT
AACAAAAAAA CAACAGCA<font color=red>TA A</font></pre></html>
Start codon is in <font color=green>green</font> and stop codon is in <font color=red>red</font>
<h4>Primers</h4>
Readable primer:ggaattcgcg gccgcttcta gag ATGGAACAAC GCATAACC (left side)
Primer sequence:ggaattcgcggccgcttctagagATGGAACAACGCATAACC
*Mp: 57,78
Readable primer:ctgcagcggc cgctactagt a TTATGCTGTT GTTTTTTTGT TACT (right side)
Primer sequence:ctgcagcggccgctactagtaTTATGCTGTTGTTTTTTTGTTACT
*Mp: 58,75
<h2>Oligo Order results:</h2>
*Primer 260 LBOrL 75.48 nm, 1046.19 ug, 100nM
*Primer 261 LBOrR 79.09 nm, 991.83 ug, 100nM
*Primer 262 LBClL 73.48 nm, 1042.71 ug, 100nM
*Primer 263 LBClR 79.76 nm, 1026.56 ug, 100nM
*Primer 264 LBCroL 79.42nm, 1074.55 ug, 100nM
*Primer 265 LBCroR 81.02 nm, 1206.56 ug, 100nM
</div>
<h2>June 30th, 2007: Competency Transformations</h2>
[<span class="_togglegroup _toggle _toggler">show</span><span class="_toggle _toggler" style="display:none;">hide</span>]
<div class="_toggle" style="display:none;">
<table|left>
<tr>
<td>'''Transformations of frozen competent cells'''</td>
</tr>
<tr>
<td>[[Image:GFL DB 31 puc 6 30.png|thumb|DB3.1 with puc19]]</td>
<td>[[Image:GFL DB 31 neg 6 30.png|thumb|DB3.1 negative control]]</td>
<td>[[Image:GFL DH5a puc 6 30.png|thumb|DH5alpha with puc19]]</td>
</tr>
<tr>
<td>[[Image:GFL DH5a puc close 6 30.png|thumb|DH5alpha with puc19 closeup]]</td>
<td>[[Image:GFL DH5a neg 6 30.png|thumb|DH5alpha negative control]]</td>
</tr>
</table>
Note that all images above have had their contrast levels adjusted in photoshop to highlight colonies, for originals contact [[user:tachyon60|me]].
</div>
</div>
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April 30th, 2007: Project Proposal Presentations [show hide ]
Bacterial Magnetosomes <table|left>
Bacterial Magnetosomes Information
Slide 1 Slide 2 Slide 3 Slide 4 Slide 5 Slide 6 Slide 7 Biogenic Nanotubes
Disclaimer: It turns out this presentation was looking under the wrong name,
and thus is not an accurate portrayal of literature avaliability
<table|left>
Search for Biogenic Nanotubes
Slide 1 Slide 2 Slide 3 Slide 4 Slide 5
May 30th, 2007: Project Proposal Presentation [show hide ]
Bio-Dosimetry
<table|left>
Preliminary Dosimetry Feasibility Investigation
Slide 1 Slide 2 Slide 3 Slide 4 Slide 5 Slide 6
June 4th, 2007: Lab Meeting Presentation [show hide ]
iGEM Meeting <table|left>
June 13th, 2007: XylR Biobricks and Primers [show hide ]
Note: Start codons are in green, stop codons are in read, translational terminators are in blue.
All sequences are shown without biobrick restriction sequences
XylR with promoter, rbs and terminator (Forward) <html><pre>GCAACCAAAC GCCGTTCTTG ATTTTGATAA AAATTTTCTC AAAGCCGGTT ACGTATTACC
GGTTTTGAGT TTTTGCATGA TTCAGCAGGA AAAGAACC<font color=green>AT G</font>TTTACTAAA CGTCACCGCA
TCACATTACT GTTCAATGCC AATAAAGCCT ATGACCGGCA GGTAGTAGAA GGCGTAGGGG
AATATTTACA GGCGTCACAA TCGGAATGGG ATATTTTCAT TGAAGAAGAT TTCCGCGCCC
GCATTGATAA AATCAAGGAC TGGTTAGGAG ATGGCGTCAT TGCCGACTTC GACGACAAAC
AGATCGAGCA AGCGCTGGCT GATGTCGACG TCCCCATTGT TGGGGTTGGC GGCTCGTATC
ACCTTGCAGA AAGTTACCCA CCCGTTCATT ACATTGCCAC CGATAACTAT GCGCTGGTTG
AAAGCGCATT TTTGCATTTA AAAGAGAAAG GCGTTAACCG CTTTGCTTTT TATGGTCTTC
CGGAATCAAG CGGCAAACGT TGGGCCACTG AGCGCGAATA TGCATTTCGT CAGCTTGTCG
CCGAAGAAAA GTATCGCGGA GTGGTTTATC AGGGGTTAGA AACCGCGCCA GAGAACTGGC
AACACGCGCA AAATCGGCTG GCAGACTGGC TACAAACGCT ACCACCGCAA ACCGGGATTA
TTGCCGTTAC TGACGCCCGA GCGCGGCATA TTCTGCAAGT ATGTGAACAT CTACATATTC
CCGTACCGGA AAAATTATGC GTGATTGGCA TCGATAACGA AGAACTGACC CGCTATCTGT
CGCGTGTCGC CCTTTCTTCG GTCGCTCAGG GCGCGCGGCA AATGGGCTAT CAGGCGGCAA
AACTGTTGCA TCGATTATTA GATAAAGAAG AAATGCCGCT ACAGCGAATT TTGGTCCCAC
CAGTTCGCGT CATTGAACGG CGCTCAACAG ATTATCGCTC GCTGACCGAT CCCGCCGTTA
TTCAGGCCAT GCATTACATT CGTAATCACG CCTGTAAAGG GATTAAAGTG GATCAGGTAC
TGGATGCGGT CGGGATCTCG CGCTCCAATC TTGAGAAGCG TTTTAAAGAA GAGGTGGGTG
AAACCATCCA TGCCATGATT CATGCCGAGA AGCTGGAGAA AGCGCGCAGT CTGCTGATTT
CAACCACCTT GTCGATCAAT GAGATATCGC AAATGTGCGG TTATCCATCG CTGCAATATT
TCTACTCTGT TTTTAAAAAA GCATATGACA CGACGCCAAA AGAGTATCGC GATGTAAATA
GCGAGGTCAT GTTG<font color = red>TAG</font>CGA TGATGAGAAT TGTCGGCGTC ACATCAGGTA ACGCTGCGTG
GTTGTCGGAT GCGGCGTGAA CGCCTTATCC GACCTACCCG CCAGGCATGA TAAAACGCAC
CAACAACGCT TCAGGCTCGT AGCTCAACTG CCTGAGACAA AGTAAAA<font color=blue>AGC CTTATCCGAC
TGACAAGTCG GATAAGGCT</font>C AAGGAAATGC AAT</pre></html>
Primers: ggaattcgcg gccgcttcta gag GCAACCAAAC GCCGTTCT (left side)
Sequence for operations: ggaattcgcggccgcttctagagGCAACCAAACGCCGTTCT
ctgcagcggc cgctactagt a ATTGCATTTC CTTGAGCCTT ATCC (right side)
Sequence for operations: ctgcagcggccgctactagtaATTGCATTTCCTTGAGCCTTATCC
XylR with promoter, rbs and terminator (Reverse) <html><pre>ATTGCATTTC CTTG<font color=blue>AGCCTT ATCCGACTTG TCAGTCGGAT AAGGCT</font>TTTT ACTTTGTCTC
AGGCAGTTGA GCTACGAGCC TGAAGCGTTG TTGGTGCGTT TTATCATGCC TGGCGGGTAG
GTCGGATAAG GCGTTCACGC CGCATCCGAC AACCACGCAG CGTTACCTGA TGTGACGCCG
ACAATTCTCA TCATCG<font color=red>CTA</font>C AACATGACCT CGCTATTTAC ATCGCGATAC TCTTTTGGCG
TCGTGTCATA TGCTTTTTTA AAAACAGAGT AGAAATATTG CAGCGATGGA TAACCGCACA
TTTGCGATAT CTCATTGATC GACAAGGTGG TTGAAATCAG CAGACTGCGC GCTTTCTCCA
GCTTCTCGGC ATGAATCATG GCATGGATGG TTTCACCCAC CTCTTCTTTA AAACGCTTCT
CAAGATTGGA GCGCGAGATC CCGACCGCAT CCAGTACCTG ATCCACTTTA ATCCCTTTAC
AGGCGTGATT ACGAATGTAA TGCATGGCCT GAATAACGGC GGGATCGGTC AGCGAGCGAT
AATCTGTTGA GCGCCGTTCA ATGACGCGAA CTGGTGGGAC CAAAATTCGC TGTAGCGGCA
TTTCTTCTTT ATCTAATAAT CGATGCAACA GTTTTGCCGC CTGATAGCCC ATTTGCCGCG
CGCCCTGAGC GACCGAAGAA AGGGCGACAC GCGACAGATA GCGGGTCAGT TCTTCGTTAT
CGATGCCAAT CACGCATAAT TTTTCCGGTA CGGGAATATG TAGATGTTCA CATACTTGCA
GAATATGCCG CGCTCGGGCG TCAGTAACGG CAATAATCCC GGTTTGCGGT GGTAGCGTTT
GTAGCCAGTC TGCCAGCCGA TTTTGCGCGT GTTGCCAGTT CTCTGGCGCG GTTTCTAACC
CCTGATAAAC CACTCCGCGA TACTTTTCTT CGGCGACAAG CTGACGAAAT GCATATTCGC
GCTCAGTGGC CCAACGTTTG CCGCTTGATT CCGGAAGACC ATAAAAAGCA AAGCGGTTAA
CGCCTTTCTC TTTTAAATGC AAAAATGCGC TTTCAACCAG CGCATAGTTA TCGGTGGCAA
TGTAATGAAC GGGTGGGTAA CTTTCTGCAA GGTGATACGA GCCGCCAACC CCAACAATGG
GGACGTCGAC ATCAGCCAGC GCTTGCTCGA TCTGTTTGTC GTCGAAGTCG GCAATGACGC
CATCTCCTAA CCAGTCCTTG ATTTTATCAA TGCGGGCGCG GAAATCTTCT TCAATGAAAA
TATCCCATTC CGATTGTGAC GCCTGTAAAT ATTCCCCTAC GCCTTCTACT ACCTGCCGGT
CATAGGCTTT ATTGGCATTG AACAGTAATG TGATGCGGTG ACGTTTAGTA AA<font color<font color=green>CAT</font>GGTTC
TTTTCCTGCT GAATCATGCA AAAACTCAAA ACCGGTAATA CGTAACCGGC TTTGAGAAAA
TTTTTATCAA AATCAAGAAC GGCGTTTGGT TGC</pre></html>
Primers: ggaattcgcg gccgcttcta gag ATTGCATTTC CTTGAGCCTT ATCC (right side)
Sequence for operations: ggaattcgcggccgcttctagagATTGCATTTCCTTGAGCCTTATCC
ctgcagcggc cgctactagt a GCAACCAAAC GCCGTTCT (left side)
Sequence for operations: ctgcagcggccgctactagtaGCAACCAAACGCCGTTCT
XylR open reading frame (Forward) <html><pre><font color=green>ATG</font>TTTACTA AACGTCACCG CATCACATTA CTGTTCAATG CCAATAAAGC CTATGACCGG
CAGGTAGTAG AAGGCGTAGG GGAATATTTA CAGGCGTCAC AATCGGAATG GGATATTTTC
ATTGAAGAAG ATTTCCGCGC CCGCATTGAT AAAATCAAGG ACTGGTTAGG AGATGGCGTC
ATTGCCGACT TCGACGACAA ACAGATCGAG CAAGCGCTGG CTGATGTCGA CGTCCCCATT
GTTGGGGTTG GCGGCTCGTA TCACCTTGCA GAAAGTTACC CACCCGTTCA TTACATTGCC
ACCGATAACT ATGCGCTGGT TGAAAGCGCA TTTTTGCATT TAAAAGAGAA AGGCGTTAAC
CGCTTTGCTT TTTATGGTCT TCCGGAATCA AGCGGCAAAC GTTGGGCCAC TGAGCGCGAA
TATGCATTTC GTCAGCTTGT CGCCGAAGAA AAGTATCGCG GAGTGGTTTA TCAGGGGTTA
GAAACCGCGC CAGAGAACTG GCAACACGCG CAAAATCGGC TGGCAGACTG GCTACAAACG
CTACCACCGC AAACCGGGAT TATTGCCGTT ACTGACGCCC GAGCGCGGCA TATTCTGCAA
GTATGTGAAC ATCTACATAT TCCCGTACCG GAAAAATTAT GCGTGATTGG CATCGATAAC
GAAGAACTGA CCCGCTATCT GTCGCGTGTC GCCCTTTCTT CGGTCGCTCA GGGCGCGCGG
CAAATGGGCT ATCAGGCGGC AAAACTGTTG CATCGATTAT TAGATAAAGA AGAAATGCCG
CTACAGCGAA TTTTGGTCCC ACCAGTTCGC GTCATTGAAC GGCGCTCAAC AGATTATCGC
TCGCTGACCG ATCCCGCCGT TATTCAGGCC ATGCATTACA TTCGTAATCA CGCCTGTAAA
GGGATTAAAG TGGATCAGGT ACTGGATGCG GTCGGGATCT CGCGCTCCAA TCTTGAGAAG
CGTTTTAAAG AAGAGGTGGG TGAAACCATC CATGCCATGA TTCATGCCGA GAAGCTGGAG
AAAGCGCGCA GTCTGCTGAT TTCAACCACC TTGTCGATCA ATGAGATATC GCAAATGTGC
GGTTATCCAT CGCTGCAATA TTTCTACTCT GTTTTTAAAA AAGCATATGA CACGACGCCA
AAAGAGTATC GCGATGTAAA TAGCGAGGTC ATGTTG<font color=red>TAG</font></pre></html>
Primers: ggaattcgcg gccgcttcta gag ATGTTTACTA AACGTCACCG CATCA left side
Sequence without spaces: ggaattcgcggccgcttctagagATGTTTACTAAACGTCACCGCATCA
ctgcagcggc cgctactagt a CTACAACATG ACCTCGCTAT TTACAT right side
Sequence wihout spaces: ctgcagcggccgctactagtaCTACAACATGACCTCGCTATTTACAT
XylR open reading frame (Reverse) <html><pre><font color=red>CTA</font>CAACATG ACCTCGCTAT TTACATCGCG ATACTCTTTT GGCGTCGTGT CATATGCTTT
TTTAAAAACA GAGTAGAAAT ATTGCAGCGA TGGATAACCG CACATTTGCG ATATCTCATT
GATCGACAAG GTGGTTGAAA TCAGCAGACT GCGCGCTTTC TCCAGCTTCT CGGCATGAAT
CATGGCATGG ATGGTTTCAC CCACCTCTTC TTTAAAACGC TTCTCAAGAT TGGAGCGCGA
GATCCCGACC GCATCCAGTA CCTGATCCAC TTTAATCCCT TTACAGGCGT GATTACGAAT
GTAATGCATG GCCTGAATAA CGGCGGGATC GGTCAGCGAG CGATAATCTG TTGAGCGCCG
TTCAATGACG CGAACTGGTG GGACCAAAAT TCGCTGTAGC GGCATTTCTT CTTTATCTAA
TAATCGATGC AACAGTTTTG CCGCCTGATA GCCCATTTGC CGCGCGCCCT GAGCGACCGA
AGAAAGGGCG ACACGCGACA GATAGCGGGT CAGTTCTTCG TTATCGATGC CAATCACGCA
TAATTTTTCC GGTACGGGAA TATGTAGATG TTCACATACT TGCAGAATAT GCCGCGCTCG
GGCGTCAGTA ACGGCAATAA TCCCGGTTTG CGGTGGTAGC GTTTGTAGCC AGTCTGCCAG
CCGATTTTGC GCGTGTTGCC AGTTCTCTGG CGCGGTTTCT AACCCCTGAT AAACCACTCC
GCGATACTTT TCTTCGGCGA CAAGCTGACG AAATGCATAT TCGCGCTCAG TGGCCCAACG
TTTGCCGCTT GATTCCGGAA GACCATAAAA AGCAAAGCGG TTAACGCCTT TCTCTTTTAA
ATGCAAAAAT GCGCTTTCAA CCAGCGCATA GTTATCGGTG GCAATGTAAT GAACGGGTGG
GTAACTTTCT GCAAGGTGAT ACGAGCCGCC AACCCCAACA ATGGGGACGT CGACATCAGC
CAGCGCTTGC TCGATCTGTT TGTCGTCGAA GTCGGCAATG ACGCCATCTC CTAACCAGTC
CTTGATTTTA TCAATGCGGG CGCGGAAATC TTCTTCAATG AAAATATCCC ATTCCGATTG
TGACGCCTGT AAATATTCCC CTACGCCTTC TACTACCTGC CGGTCATAGG CTTTATTGGC
ATTGAACAGT AATGTGATGC GGTGACGTTT AGTAAA<font color=green>CAT</font></pre></html>
Primers: ggaattcgcg gccgcttcta gag CTACAACATG ACCTCGCTAT TTACAT left side
Sequence for operations: ggaattcgcggccgcttctagagCTACAACATGACCTCGCTATTTACAT
ctgcagcggc cgctactagt a ATGTTTACTA AACGTCACCG CATCA right side
Sequence for operations: ctgcagcggccgctactagtaATGTTTACTAAACGTCACCGCATCA
June 28th, 2007: Lambda Biobricks and Primers [show hide ]
Lambda control region (OR ) Contains OR 1, OR 2, and OR 3, shown in reverse order (i.e. the leftmost binding region below is OR 3)
Bi directional promoter
in the lambda phage, CI is to the left(PRM ), cro is to the right(PR )
recognized by cro, CI
cro binding affinities: OR 3, OR 2 ~ OR 1 (OR 1 is slightly less)
CI binding affinites: OR 1, OR 2 ~ OR 3 (OR 3 is slightly less)
CI acts as a positive regulator for PRM when bound to OR 2, but and a negative regulator for PR when bound to OR 3 <html><pre>ACGTTA<font color=cyan>AATC </font><font color= blue>TA</font><font color=green>TCACCGCA AGGGATA</font>AA<font color=cyan>T ATC</font><font color = blue>TA</font><font color = green>ACACC GTGCGTG</font><font color =blue>TTG</font><font color=cyan> ACT</font>ATTT<font color=green>TAC
CTCTGGCGGT </font><font color=blue>GATA</font><font color=cyan>AT</font>GGTT GC</pre></html>
Cro and CI binding regions are depicted in green , -10 and -35 sequences in cyan , and shared regions are in blue
Primers Readable primer:ggaattcgcg gccgcttcta gag ACGTTAAATC TATCACCGC (left side)
Primer sequence:ggaattcgcggccgcttctagagACGTTAAATCTATCACCGC
Readable primer:ctgcagcggc cgctactagt a GCAACCATTA TCACCGC (right side)
Primer sequence:ctgcagcggccgctactagtaGCAACCATTATCACCGC
Lambda Repressor (CI) Forms dimers
Dimers associate to form tetramers, octamers etc
Binds to OL and OR operators in bacteriophage genome
Cleaved by activated RecA protein (activates with ssDNA exposure) <html><pre><font color=green>ATG</font>AGCACAA AAAAGAAACC ATTAACACAA GAGCAGCTTG AGGACGCACG TCGCCTTAAA
GCAATTTATG AAAAAAAGAA AAATGAACTT GGCTTATCCC AGGAATCTGT CGCAGACAAG
ATGGGGATGG GGCAGTCAGG CGTTGGTGCT TTATTTAATG GCATCAATGC ATTAAATGCT
TATAACGCCG CATTGCTTGC AAAAATTCTC AAAGTTAGCG TTGAAGAATT TAGCCCTTCA
ATCGCCAGAG AAATCTACGA GATGTATGAA GCGGTTAGTA TGCAGCCGTC ACTTAGAAGT
GAGTATGAGT ACCCTGTTTT TTCTCATGTT CAGGCAGGGA TGTTCTCACC TGAGCTTAGA
ACCTTTACCA AAGGTGATGC GGAGAGATGG GTAAGCACAA CCAAAAAAGC CAGTGATTCT
GCATTCTGGC TTGAGGTTGA AGGTAATTCC ATGACCGCAC CAACAGGCTC CAAGCCAAGC
TTTCCTGACG GAATGTTAAT TCTCGTTGAC CCTGAGCAGG CTGTTGAGCC AGGTGATTTC
TGCATAGCCA GACTTGGGGG TGATGAGTTT ACCTTCAAGA AACTGATCAG GGATAGCGGT
CAGGTGTTTT TACAACCACT AAACCCACAG TACCCAATGA TCCCATGCAA TGAGAGTTGT
TCCGTTGTGG GGAAAGTTAT CGCTAGTCAG TGGCCTGAAG AGACGTTTGG C<font color=red>TGA</font></pre></html>
Start codon is in green and stop codon is in red
Primers Readable Primer:ggaattcgcg gccgcttcta gag ATGAGCACAA AAAAGAAACC (left side)
Primer sequence:ggaattcgcggccgcttctagagATGAGCACAAAAAAGAAACC
Readable primer:ctgcagcggc cgctactagt a TCAGCCAAAC GTCTCTTC (right side)
Primer sequence:ctgcagcggccgctactagtaTCAGCCAAACGTCTCTTC
Lambda Repressor (CI) with degredation tag (LVA) Part BBa_C0051 on MIT's parts registry
same as CI repressor, but with degredation tag on the N terminus to promote degredation Lambda AntiRepressor (Cro) Binds to OR and OL operators
transcriptional activator, repressor
favors lytic pathway in lambda bacteriophage <html><pre><font color=green>ATG</font>GAACAAC GCATAACCCT GAAAGATTAT GCAATGCGCT TTGGGCAAAC CAAGACAGCT
AAAGATCTCG GCGTATATCA AAGCGCGATC AACAAGGCCA TTCATGCAGG CCGAAAGATT
TTTTTAACTA TAAACGCTGA TGGAAGCGTT TATGCGGAAG AGGTAAAGCC CTTCCCGAGT
AACAAAAAAA CAACAGCA<font color=red>TA A</font></pre></html>
Start codon is in green and stop codon is in red
Primers Readable primer:ggaattcgcg gccgcttcta gag ATGGAACAAC GCATAACC (left side)
Primer sequence:ggaattcgcggccgcttctagagATGGAACAACGCATAACC
Readable primer:ctgcagcggc cgctactagt a TTATGCTGTT GTTTTTTTGT TACT (right side)
Primer sequence:ctgcagcggccgctactagtaTTATGCTGTTGTTTTTTTGTTACT
Oligo Order results: Primer 260 LBOrL 75.48 nm, 1046.19 ug, 100nM
Primer 261 LBOrR 79.09 nm, 991.83 ug, 100nM
Primer 262 LBClL 73.48 nm, 1042.71 ug, 100nM
Primer 263 LBClR 79.76 nm, 1026.56 ug, 100nM
Primer 264 LBCroL 79.42nm, 1074.55 ug, 100nM
Primer 265 LBCroR 81.02 nm, 1206.56 ug, 100nM
June 30th, 2007: Competency Transformations [show hide ]
