Difference between revisions of "Promoters/Catalog/Anderson"

(New page: __NOTOC__ __NOEDITSECTION__ Prof. J. Christopher Anderson. (Photo: Peg Skorpinski) ==Description== Members of the Anderson promoter collection a...)
 
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The sequences of the Anderson promoters can be found via the table below.  To obtain the physical DNA, we recommend two approaches - <br>
 
The sequences of the Anderson promoters can be found via the table below.  To obtain the physical DNA, we recommend two approaches - <br>
 
'''Via ''de novo'' synthesis''': Since the promoters are short sequences, they can be easily and cheaply ordered as two single-stranded complementary oligo's and annealed.  See [[Help:Promoters/Construction|here]] for a tutorial on how to construct short parts via oligo annealing.
 
'''Via ''de novo'' synthesis''': Since the promoters are short sequences, they can be easily and cheaply ordered as two single-stranded complementary oligo's and annealed.  See [[Help:Promoters/Construction|here]] for a tutorial on how to construct short parts via oligo annealing.
−
 
  
 
'''Via the Registry distribution''': The promoters are included in the Registry distribution.  All parts except <partinfo>J23119</partinfo> are present in plasmid <partinfo>J61002</partinfo>.  This places the RFP downstream of the promoter.  Part <partinfo>J23119</partinfo> is present in <partinfo>pSB1A2</partinfo>.
 
'''Via the Registry distribution''': The promoters are included in the Registry distribution.  All parts except <partinfo>J23119</partinfo> are present in plasmid <partinfo>J61002</partinfo>.  This places the RFP downstream of the promoter.  Part <partinfo>J23119</partinfo> is present in <partinfo>pSB1A2</partinfo>.
  
 
==Anderson promoter collection==
 
==Anderson promoter collection==
−
Insert Table
+
  J23112          1
 +
  J23103          17
 +
  J23113          21
 +
  J23109          106
 +
  J23117          162
 +
  J23114          256
 +
  J23115          387
 +
  J23116          396
 +
  J23105          623
 +
  J23110          844
 +
  J23107          908
 +
  J23106          1185
 +
  J23108          1303
 +
  J23118          1429
 +
  J23111          1487
 +
  J23101          1791
 +
  J23104          1831
 +
  J23102          2179
 +
  J23100          2547
 +
 
 +
 
 +
{|class="wikitable" style="border:3px solid black; width: 60%" align="center"  cellspacing="0"
 +
! style="background:#AAAAAA; color:black"  |Identifier
 +
! style="background:#AAAAAA; color:black"  |Sequence<sup>a</sup>
 +
! colspan="2" style="background:#AAAAAA; color:black"  |Predicted Strength<sup>b</sup>
 +
|-
 +
|style="background:#AAAAAA; color:black" |
 +
|style="background:#AAAAAA; color:black" |
 +
|style="background:#AAAAAA; color:black"  align="center"|Mean
 +
|style="background:#AAAAAA; color:black"  align="center" |CV
 +
|-
 +
|align="center"|<partinfo>J23100</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGG</font>GA<font color="red">CAA</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|1
 +
|-
 +
|align="center"|<partinfo>J23101</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CAG</font>GA<font color="red">CCC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.70
 +
|-
 +
|align="center"|<partinfo>J23102</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TCC</font>GA<font color="red">TGT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.86
 +
|-
 +
|align="center"|<partinfo>J23103</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TTA</font>GA<font color="red">CAA</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.01
 +
|-
 +
|align="center"|<partinfo>J23104</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">AGG</font>GA<font color="red">CAG</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.72
 +
|-
 +
|align="center"|<partinfo>J23105</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CAT</font>GA<font color="red">CGT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.24
 +
|-
 +
|align="center"|<partinfo>J23106</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TAG</font>GA<font color="red">GAC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.47
 +
|-
 +
|align="center"|<partinfo>J23107</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">AGA</font>GA<font color="red">CTC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.36
 +
|-
 +
|align="center"|<partinfo>J23108</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CGA</font>GA<font color="red">TAT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.51
 +
|-
 +
|align="center"|<partinfo>J23109</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CTG</font>GA<font color="red">GAC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.04
 +
|-
 +
|align="center"|<partinfo>J23110</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGC</font>GA<font color="red">ATT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.33
 +
|-
 +
|align="center"|<partinfo>J23111</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGC</font>GA<font color="red">TAC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.58
 +
|-
 +
|align="center"|<partinfo>J23112</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GGT</font>GA<font color="red">CAT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.00
 +
|-
 +
|align="center"|<partinfo>J23113</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GTG</font>GA<font color="red">AAA</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.01
 +
|-
 +
|align="center"|<partinfo>J23114</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">TGA</font>GA<font color="red">AGA</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.10
 +
|-
 +
|align="center"|<partinfo>J23115</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">AGG</font>GA<font color="red">TAC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.15
 +
|-
 +
|align="center"|<partinfo>J23116</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CAT</font>GA<font color="red">GGC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.16
 +
|-
 +
|align="center"|<partinfo>J23117</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">CAT</font>GA<font color="red">GTT</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.06
 +
|-
 +
|align="center"|<partinfo>J23118</partinfo>
 +
|<font face="Courier" size="+1"><font color="grey">TCTAGAG</font>AAAGA<font color="red">GAC</font>GA<font color="red">ATC</font><font color="grey">ACTAG</font><font color="green">ATG</font></font>
 +
|align="center"|0.56
 +
|-
 +
|}
 +
<sup>a</sup>The sequence of individual promoters are shown in black and red.  The grey nucleotides show the bracketing sequence that results from assembling the RBS with an upstream part and a downstream coding sequence.  The start codon of the downstream coding sequence is shown in green.
 +
<sup>b</sup>The relative strengths of these promoters were measured by Chris Anderson and the 2006 Berkeley iGEM team.  These measurements are explained in greater detail in the Characterization section below.
 +
 
 
==Characterization==
 
==Characterization==
 
[[Image:BerkiGEM2006-PromotersEppendorfs.jpg|300px|right]]
 
[[Image:BerkiGEM2006-PromotersEppendorfs.jpg|300px|right]]
 
===Measured strengths===
 
===Measured strengths===
 
Reported activities of the promoters are given as the relative fluorescence of these plasmids in strain TG1 grown in LB media to saturation.  See part J61002 for details on their use.
 
Reported activities of the promoters are given as the relative fluorescence of these plasmids in strain TG1 grown in LB media to saturation.  See part J61002 for details on their use.

Revision as of 04:38, 17 November 2008


Prof. J. Christopher Anderson. (Photo: Peg Skorpinski)

Description

Members of the Anderson promoter collection are suitable for general protein expression in E. coli and likely other prokaryotes. The collection is known to cover a range of activities so by testing a few promoters it should be possible to find a promoter activity that suits your application. The promoters were recovered from a library screen by Chris Anderson.

Parts J23100 through J23119 are a family of constitutive promoter parts isolated from a small combinatorial library. J23119 is the "consensus" promoter sequence and the strongest member of the family. The NheI and AvrII restriction sites present within these promoter parts make them a scaffold for further modification.

Obtaining Anderson promoter collection

PBca1020-r0040.jpg

The sequences of the Anderson promoters can be found via the table below. To obtain the physical DNA, we recommend two approaches -
Via de novo synthesis: Since the promoters are short sequences, they can be easily and cheaply ordered as two single-stranded complementary oligo's and annealed. See here for a tutorial on how to construct short parts via oligo annealing.

Via the Registry distribution: The promoters are included in the Registry distribution. All parts except BBa_J23119 are present in plasmid BBa_J61002. This places the RFP downstream of the promoter. Part BBa_J23119 is present in pSB1A2.

Anderson promoter collection

 J23112           1
 J23103           17
 J23113           21
 J23109           106
 J23117           162
 J23114           256
 J23115           387
 J23116           396
 J23105           623
 J23110           844
 J23107           908
 J23106           1185
 J23108           1303
 J23118           1429
 J23111           1487
 J23101           1791
 J23104           1831
 J23102           2179
 J23100           2547


Identifier Sequencea Predicted Strengthb
Mean CV
BBa_J23100 TCTAGAGAAAGAGGGGACAAACTAGATG 1
BBa_J23101 TCTAGAGAAAGACAGGACCCACTAGATG 0.70
BBa_J23102 TCTAGAGAAAGATCCGATGTACTAGATG 0.86
BBa_J23103 TCTAGAGAAAGATTAGACAAACTAGATG 0.01
BBa_J23104 TCTAGAGAAAGAAGGGACAGACTAGATG 0.72
BBa_J23105 TCTAGAGAAAGACATGACGTACTAGATG 0.24
BBa_J23106 TCTAGAGAAAGATAGGAGACACTAGATG 0.47
BBa_J23107 TCTAGAGAAAGAAGAGACTCACTAGATG 0.36
BBa_J23108 TCTAGAGAAAGACGAGATATACTAGATG 0.51
BBa_J23109 TCTAGAGAAAGACTGGAGACACTAGATG 0.04
BBa_J23110 TCTAGAGAAAGAGGCGAATTACTAGATG 0.33
BBa_J23111 TCTAGAGAAAGAGGCGATACACTAGATG 0.58
BBa_J23112 TCTAGAGAAAGAGGTGACATACTAGATG 0.00
BBa_J23113 TCTAGAGAAAGAGTGGAAAAACTAGATG 0.01
BBa_J23114 TCTAGAGAAAGATGAGAAGAACTAGATG 0.10
BBa_J23115 TCTAGAGAAAGAAGGGATACACTAGATG 0.15
BBa_J23116 TCTAGAGAAAGACATGAGGCACTAGATG 0.16
BBa_J23117 TCTAGAGAAAGACATGAGTTACTAGATG 0.06
BBa_J23118 TCTAGAGAAAGAGACGAATCACTAGATG 0.56

aThe sequence of individual promoters are shown in black and red. The grey nucleotides show the bracketing sequence that results from assembling the RBS with an upstream part and a downstream coding sequence. The start codon of the downstream coding sequence is shown in green. bThe relative strengths of these promoters were measured by Chris Anderson and the 2006 Berkeley iGEM team. These measurements are explained in greater detail in the Characterization section below.

Characterization

BerkiGEM2006-PromotersEppendorfs.jpg

Measured strengths

Reported activities of the promoters are given as the relative fluorescence of these plasmids in strain TG1 grown in LB media to saturation. See part J61002 for details on their use.