Difference between revisions of "Part:BBa K3889084"

 
 
(One intermediate revision by the same user not shown)
Line 3: Line 3:
 
<partinfo>BBa_K3889084 short</partinfo>
 
<partinfo>BBa_K3889084 short</partinfo>
  
−
Site-directed mutated P22 phage repressor protein DNA binding site.
+
P22 c2 repressor DNA binding site.
 +
 
 +
{| class=wikitable
 +
|-
 +
!Part Name
 +
!Part number
 +
!Sequence
 +
!Rel K<sub>D</sub>
 +
!K<sub>D</sub> (in M)
 +
|-
 +
|P22 binding site A
 +
|<partinfo>BBa_K3889080</partinfo>
 +
|ATTTAAGATATCTTAAAT
 +
|1
 +
|1.6 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site B
 +
|<partinfo>BBa_K3889081</partinfo>
 +
|AATTAAGATATCTTAATT
 +
|1.8
 +
|2.88 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site C
 +
|<partinfo>BBa_K3889082</partinfo>
 +
|ATTTAAGAATTCTTAAAT
 +
|2
 +
|3.2 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site D
 +
|<partinfo>BBa_K3889083</partinfo>
 +
|AGTTAAGATATCTTAACT
 +
|2.6
 +
|4.16 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site E
 +
|<partinfo>BBa_K3889084</partinfo>
 +
|ATTAAAGATATCTTTAAT
 +
|3.8
 +
|6.08 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site F
 +
|<partinfo>BBa_K3889085</partinfo>
 +
|ACTTAAGATATCTTAAGT
 +
|4.3
 +
|6.88 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site G
 +
|<partinfo>BBa_K3889086</partinfo>
 +
|ATTCAAGATATCTTGAAT
 +
|5
 +
|8.0 × 10<sup>-8</sup>
 +
|-
 +
|P22 binding site H
 +
|<partinfo>BBa_K3889087</partinfo>
 +
|ATTGAAGATATCTTCAAT
 +
|7.6
 +
|1.216 × 10<sup>-7</sup>
 +
|-
 +
|P22 binding site I
 +
|<partinfo>BBa_K3889088</partinfo>
 +
|ATTTAAGAGCTCTTAAAT
 +
|10
 +
|1.6 × 10<sup>-7</sup>
 +
|-
 +
|P22 binding site J
 +
|<partinfo>BBa_K3889089</partinfo>
 +
|ATTTAAGACGTCTTAAAT
 +
|10
 +
|1.6 × 10<sup>-7</sup>
 +
|-
 +
|P22 binding site K
 +
|<partinfo>BBa_K3889090</partinfo>
 +
|ATTTACGATATCGTAAAT
 +
|30
 +
|4.8 × 10<sup>-7</sup>
 +
|-
 +
|P22 binding site L
 +
|<partinfo>BBa_K3889091</partinfo>
 +
|ATTTAAAATATTTTAAAT
 +
|55
 +
|8.8 × 10<sup>-7</sup>
 +
|}
 +
 
 +
 
 +
[[File:T--IISER-Tirupati_India--Kd_values_of_P22_binding_site.png|thumb|center|400px|Fig.1:Kd values of P22 binding site]]<br>
 +
 
 +
Alignment of these sequences are as follows:
 +
 
 +
[[File:T--IISER-Tirupati India--P22 binding sites allignment.jpg]]<br>
 +
 
 +
Fig source: Geneious version 2021.2 created by Biomatters. Available from https://www.geneious.com
  
  
−
<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===Usage and Biology===
 +
Different binding affinities of a repressor provides a variable system that can be used for different types of systems. As K<sub>D</sub> increases the dissociation of repressor from the DNA sequence also increases providing with lower repression. P22 repressor (<partinfo>BBa_K3889020</partinfo>) binds to this sequence as a dimer. This inhibits the enzymes from transcription the genes on whose promoter this operator site is present. Hence this could be fused with any promoter in order to form a repressible system as done in <partinfo>BBa_K3889102</partinfo>.
 +
 +
 +
===Graph===
 +
<html>
 +
<head>
 +
<style>
 +
div.scroll {overflow-x: aut0; overflow-y: hidden;}
 +
</style>
 +
</head>
 +
<body>
 +
<div class="scroll">
 +
<img src="https://static.igem.org/mediawiki/parts/2/21/T--IISER-Tirupati_India--P22_binding_site_E.jpeg">
 +
</div>
 +
</body>
 +
</html>
 +
  
−
<!-- -->
 
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K3889084 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3889084 SequenceAndFeatures</partinfo>
Line 18: Line 123:
 
<partinfo>BBa_K3889084 parameters</partinfo>
 
<partinfo>BBa_K3889084 parameters</partinfo>
 
<!-- -->
 
<!-- -->
 +
 +
===References===
 +
 +
1. Watkins, D., Hsiao, C., Woods, K. K., Koudelka, G. B., & Williams, L. D. (2008). P22 c2 Repressor−Operator Complex:  Mechanisms of Direct and Indirect Readout. Biochemistry, 47(8), 2325–2338. https://doi.org/10.1021/bi701826f

Latest revision as of 06:33, 18 October 2021


P22 binding site E

P22 c2 repressor DNA binding site.

Part Name Part number Sequence Rel KD KD (in M)
P22 binding site A BBa_K3889080 ATTTAAGATATCTTAAAT 1 1.6 × 10-8
P22 binding site B BBa_K3889081 AATTAAGATATCTTAATT 1.8 2.88 × 10-8
P22 binding site C BBa_K3889082 ATTTAAGAATTCTTAAAT 2 3.2 × 10-8
P22 binding site D BBa_K3889083 AGTTAAGATATCTTAACT 2.6 4.16 × 10-8
P22 binding site E BBa_K3889084 ATTAAAGATATCTTTAAT 3.8 6.08 × 10-8
P22 binding site F BBa_K3889085 ACTTAAGATATCTTAAGT 4.3 6.88 × 10-8
P22 binding site G BBa_K3889086 ATTCAAGATATCTTGAAT 5 8.0 × 10-8
P22 binding site H BBa_K3889087 ATTGAAGATATCTTCAAT 7.6 1.216 × 10-7
P22 binding site I BBa_K3889088 ATTTAAGAGCTCTTAAAT 10 1.6 × 10-7
P22 binding site J BBa_K3889089 ATTTAAGACGTCTTAAAT 10 1.6 × 10-7
P22 binding site K BBa_K3889090 ATTTACGATATCGTAAAT 30 4.8 × 10-7
P22 binding site L BBa_K3889091 ATTTAAAATATTTTAAAT 55 8.8 × 10-7


Fig.1:Kd values of P22 binding site

Alignment of these sequences are as follows:

T--IISER-Tirupati India--P22 binding sites allignment.jpg

Fig source: Geneious version 2021.2 created by Biomatters. Available from https://www.geneious.com


Usage and Biology

Different binding affinities of a repressor provides a variable system that can be used for different types of systems. As KD increases the dissociation of repressor from the DNA sequence also increases providing with lower repression. P22 repressor (BBa_K3889020) binds to this sequence as a dimer. This inhibits the enzymes from transcription the genes on whose promoter this operator site is present. Hence this could be fused with any promoter in order to form a repressible system as done in BBa_K3889102.


Graph


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


References

1. Watkins, D., Hsiao, C., Woods, K. K., Koudelka, G. B., & Williams, L. D. (2008). P22 c2 Repressor−Operator Complex:  Mechanisms of Direct and Indirect Readout. Biochemistry, 47(8), 2325–2338. https://doi.org/10.1021/bi701826f