Latest revision as of 22:06, 4 October 2013

Description

This is a page containing a synthetic promoter library (SPL) of pBAD promoters made by [http://2013.igem.org/Team:DTU-Denmark 2013 DTU iGEM team]. The library can be used to make and arabinose inducible system with very low leakiness, or tune the the promoter strength of the system when it's turned on.

A tight inducible system can be a very useful tool to express lethal or growth inhibiting proteins in E.coli. It can also be necessary with a non leaky expression system if you would like to visualize the expression of GFP SF in E.coli (see [http://2013.igem.org/Team:DTU-Denmark/HelloWorld link]).

The library

Here is a complete list of the sequences and their relative leakiness and strength:

Identifier	Sequence^a	Induced Strength	Leakiness	Inducibility^b
Col. 02	CTGACGACGCCCCTCTCCGCCCCTTAAAATGTCCA	14.2	0.203	69.9
Col. 03	CTGACGTAATCATACCGCCGAAAGTATTATCATTA	16.6	0.426	39
Col. 04	CTGACGCGACAACATTGCGTCCTATAAAATGCCGA	14.2	0.345	41
Col. 05	CTGACGGCCCGCCCCCGATGCGCATAAAATACCAA	17.7	0.424	41.6
Col. 12	CTGACGCGTATCGCGAGCGGGCGTTATTATACGCA	13.6	0.414	32.9
Col. 10	CTGACGCCCCGAATCAGTAGTATTTATTATCTAGA	18	0.462	38.8
Col. 09	CTGACGCCACCCCCCCCCCCGGCGTATAATTCCCA	16.1	0.530	30.4
Col. 08	CTGACGCCCTACCGCTCGCCCCCCTATTATACCCA	13.4	0.211	63.4
Col. 13	CTGACGCCCCCCCCGTCCACCCCCTAATATCCCGA	10.9	0.096	113.6
Col. 15	CTGACGTGCGCCTGCCGTCCAAAGTAATATCCTTA	15.5	0.235	65.8
Col. 18	CTGACGCCCCGAATCAGTAGTATTTATTATCTAGA	19.8	0.524	37.8
Col. 19	CTGACGCTCGCACCGGCGACCCGATAATATCCATA	18.0	0.315	57
Col. 31	CTGACGCCCCCCCTCCCCCGACCTAAAATATCCAG	3.8	0.161	23.6
Col. 29	CTGACGCCGCTGCACCCGTCCCCCTATTATAGCAA	14.8	0.301	49.2
Col. 26	CTGACGCCGATCCTATCTCCCTATTAAAATTTTTA	13.8	0.292	47.2
Col. 22	CTGACGCCCCGAATCAGTAGTATTTATTATCTAGA	16.8	0.466	36.1
Col. 33	CTGACGCCAGCTTCCTACTTCAAATATAATCCGTA	14.4	1.01	14.3
Col. 34	CTGACGTCCCTCTTCCGCGCCCCCTAAAATACCCA	12.4	0.187	65.9
Col. 35	CTGACGCCCAACCCGACACAGCGATATAATAATGA	18.4	0.89	20.7

^a The sequence of each pBAD promoter characterized. To use this simply produce a primer with the promoter sequence you wish in a tail. Replace the old promoter in your system e.g. Part:BBa_K808000 with the new and see the chance. For more information go to ([http://2013.igem.org/Team:DTU-Denmark/pBAD_SPL link]).

^b Inducibility = Induced Strength divided by leakiness.

Characterization

We did a characterization by running growth experiments in parallel on a BioLector ([http://2013.igem.org/Team:DTU-Denmark/pBAD_SPL see more]). Below diagram sums up our results:

Conclusion

The pBAD SPL contain promoters to the arabinose inducible system that will enable low leakiness but still maintain a reasonable promoter strength when turned on. This verifies that the SPL standard ([http://dspace.mit.edu/handle/1721.1/60080 RFC 63]) also can be used to produce promoters for inducible systems.

@@ Line 1: / Line 1: @@
-Here the DTU iGEM team will present their work on characterizing a SPL of pBAD promoters.
+=Description=
+This is a page containing a synthetic promoter library (SPL) of pBAD promoters made by [http://2013.igem.org/Team:DTU-Denmark 2013 DTU iGEM team]. The library can be used to make and arabinose inducible system with very low leakiness, or tune the the promoter strength of the system when it's turned on.
-List of sequences:
+A tight inducible system can be a very useful tool to express lethal or growth inhibiting proteins in ''E.coli''. It can also be necessary with a non leaky expression system if you would like to visualize the expression of GFP SF in ''E.coli'' (see [http://2013.igem.org/Team:DTU-Denmark/HelloWorld link]).
+=The library=
+Here is a complete list of the sequences and their relative leakiness and strength:
-==DTU pBAD SPL==
 {|class="sortable" style="border:3px solid black; width: 70%" align="center"  cellspacing="0"
 ! style="background:#AAAAAA; color:black"  |Identifier
 ! style="background:#AAAAAA; color:black"  |Sequence<sup>a</sup>
 ! style="background:#AAAAAA; color:black"  |Induced Strength
-! colspan="2" style="background:#AAAAAA; color:black"  |Leakyness
+! style="background:#AAAAAA; color:black"  |Leakiness
+! colspan="3" style="background:#AAAAAA; color:black"  |Inducibility<sup>b</sup>
 |-
-|align="center"|Col. 2
+|align="center"|Col. 02
-|<font face="Courier" size="+1">CTGACGACGCCCCTCTCCGCCCCTTAAAATGTCCA</font>
+|<font face="Courier" size="+1" class=">CTGACGACGCCCCTCTCCGCCCCTTAAAATGTCCA</font>
 |align="center"|14.2
 |align="center"|0.203
+|align="center"|69.9
 |-
-|align="center"|Col. 3
+|align="center"|Col. 03
 |<font face="Courier" size="+1">CTGACGTAATCATACCGCCGAAAGTATTATCATTA</font>
 |align="center"|16.6
 |align="center"|0.426
+|align="center"|39
 |-
-|align="center"|Col. 4
+|align="center"|Col. 04
 |<font face="Courier" size="+1">CTGACGCGACAACATTGCGTCCTATAAAATGCCGA</font>
 |align="center"|14.2
 |align="center"|0.345
+|align="center"|41
 |-
-|align="center"|Col. 5
+|align="center"|Col. 05
 |<font face="Courier" size="+1">CTGACGGCCCGCCCCCGATGCGCATAAAATACCAA</font>
 |align="center"|17.7
 |align="center"|0.424
+|align="center"|41.6
 |-
 |align="center"|Col. 12
@@ Line 35: / Line 45: @@
 |align="center"|13.6
 |align="center"|0.414
+|align="center"|32.9
 |-
 |align="center"|Col. 10
@@ Line 40: / Line 51: @@
 |align="center"|18
 |align="center"|0.462
+|align="center"|38.8
 |-
-|align="center"|Col. 9
+|align="center"|Col. 09
 |<font face="Courier" size="+1">CTGACGCCACCCCCCCCCCCGGCGTATAATTCCCA</font>
 |align="center"|16.1
 |align="center"|0.530
+|align="center"|30.4
 |-
-|align="center"|Col. 8
+|align="center"|Col. 08
 |<font face="Courier" size="+1">CTGACGCCCTACCGCTCGCCCCCCTATTATACCCA</font>
 |align="center"|13.4
 |align="center"|0.211
+|align="center"|63.4
 |-
 |align="center"|Col. 13
@@ Line 55: / Line 69: @@
 |align="center"|10.9
 |align="center"|0.096
+|align="center"|113.6
 |-
 |align="center"|Col. 15
@@ Line 60: / Line 75: @@
 |align="center"|15.5
 |align="center"|0.235
+|align="center"|65.8
 |-
 |align="center"|Col. 18
@@ Line 65: / Line 81: @@
 |align="center"|19.8
 |align="center"|0.524
+|align="center"|37.8
 |-
 |align="center"|Col. 19
@@ Line 70: / Line 87: @@
 |align="center"|18.0
 |align="center"|0.315
+|align="center"|57
 |-
 |align="center"|Col. 31
@@ Line 75: / Line 93: @@
 |align="center"|3.8
 |align="center"|0.161
+|align="center"|23.6
 |-
 |align="center"|Col. 29
@@ Line 80: / Line 99: @@
 |align="center"|14.8
 |align="center"|0.301
+|align="center"|49.2
 |-
 |align="center"|Col. 26
@@ Line 85: / Line 105: @@
 |align="center"|13.8
 |align="center"|0.292
+|align="center"|47.2
 |-
 |align="center"|Col. 22
@@ Line 90: / Line 111: @@
 |align="center"|16.8
 |align="center"|0.466
+|align="center"|36.1
 |-
 |align="center"|Col. 33
@@ Line 95: / Line 117: @@
 |align="center"|14.4
 |align="center"|1.01
+|align="center"|14.3
 |-
 |align="center"|Col. 34
@@ Line 100: / Line 123: @@
 |align="center"|12.4
 |align="center"|0.187
+|align="center"|65.9
 |-
 |align="center"|Col. 35
@@ Line 105: / Line 129: @@
 |align="center"|18.4
 |align="center"|0.89
+|align="center"|20.7
 |-
-|align="center"|<partinfo>J23118</partinfo>
-|<font face="Courier" size="+1">ttgac<font color="red">g</font>gctagctcagtcctaggtatt<font color="red">g</font>tgctagc</font>
-|align="center"|0.56
-|-
 |}
+<html>
+<script>
+function more_color(){
+    var amino_string_containers = $("table font");
+    for(var i=0; i < amino_string_containers.length; i++){
+        var amino_string_container = amino_string_containers[i];
+        var amino_string = amino_string_container.textContent;
+        amino_string_container.textContent = "";
+        for(var j=0; j < amino_string.length; j++){
+            var letter = amino_string[j];
+            var color = "black";
+            //if( letter == "C"){
+            //    color = "green";
+            //} else if( letter == "A"){
+            //    color = "blue";
+            //} else if( letter == "T"){
+            //    color = "orange";
+            //} else if( letter == "G"){
+            //    color = "red";
+            //}
+            //$(amino_string_container).append("<font color=" + color + ">" + letter + "</font>");
+            if( letter == "C"){
+                color = "rgb(26,204,26)";
+            } else if( letter == "A"){
+                color = "rgb(128,179,230)";
+            } else if( letter == "T"){
+                color = "rgb(230,153,77)";
+            } else if( letter == "G"){
+                color = "rgb(230,128,128)";
+            }
+            $(amino_string_container).append('<font style="background-color: ' + color + '">' + letter + '</font>');
+        }
+    }
+}
+more_color();
+</script>
+</html>
+<sup>a</sup> The sequence of each pBAD promoter characterized. To use this simply produce a primer with the promoter sequence you wish in a tail. Replace the old promoter in your system e.g. [[Part:BBa_K808000]] with the new and see the chance. For more information go to ([http://2013.igem.org/Team:DTU-Denmark/pBAD_SPL link]).
+<sup>b</sup> Inducibility = Induced Strength divided by leakiness.
+=Characterization=
+We did a characterization by running growth experiments in parallel on a BioLector ([http://2013.igem.org/Team:DTU-Denmark/pBAD_SPL see more]). Below diagram sums up our results:
+[[File:690px-Induced vs basal.png|600px|center|Diagram over the promoter strength]]
+=Conclusion=
+The pBAD SPL contain promoters to the arabinose inducible system that will enable low leakiness but still maintain a reasonable promoter strength when turned on. This verifies that the SPL standard ([http://dspace.mit.edu/handle/1721.1/60080 RFC 63]) also can be used to produce promoters for inducible systems.

Difference between revisions of "PBAD SPL"

Latest revision as of 22:06, 4 October 2013

Contents

Description

The library

Characterization

Conclusion