Difference between revisions of "Part:BBa K4361000"
Line 14: Line 14:
 
<h3>Usage and Biology</h3>
 
<h3>Usage and Biology</h3>
 
~~~
 
~~~
 +
</html>
  
 +
<html>
 
<h3>Results</h3>
 
<h3>Results</h3>
 
~~~
 
~~~
 +
</html>
  
 
<figure>
 
<figure>

Revision as of 15:10, 6 October 2022


BlcR-binding oligo, 51 bp, scrambled

BlcR is a transcription factor originating from the bacterium Agrobacterium tumefaciens (Part:BBa_K4361100). In a homodimer state it contains a single DNA-binding domain that specifically binds one of two DNA sequences. This is further described in the wildtype oligo, Part:BBa_K4361001. To test the binding strength of BlcR to its operator sequence and variations thereof, one needs a negative control. To create the negative control, the 51 nt sequence of the wildtype oligo was scrambled using the Genscript Sequence Scramble tool, set to species 'Human'. This tool randomizes the order of the nucleotides of the input sequence, resulting in this part. As a scrambled variant of the original sequence, it has the same amount of each nucleotide, but lacks the specific binding sequence which is otherwise recognized by BlcR. As such, BlcR should not be able to specifically bind this molecule, allowing for its use as a negative control during measurements.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal SpeI site found at 37
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal SpeI site found at 37
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal SpeI site found at 37
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal SpeI site found at 37
  • 1000
    COMPATIBLE WITH RFC[1000]

Usage and Biology

~~~

Results

~~~

<figure> <a href="add-blcr.png"><img src="add-blcr.png" style="width:300px;margin-left:275px"></a> <figcaption> Figure 1. Results of the first Tapestation experiment, to measure the fraction of BlcR bound to DNA either in the presence or absence of BlcR. Numbers below bars denote Part BBa_K43610XX, where XX is said numbers. </figcaption> </figure>

<figure> <a href="oligos.png"><img src="oligos.png" style="width:600px;margin-left:125px"></a> <figcaption> Figure 2. Results of the second Tapestation experiment, in which the fraction of bound BlcR was determined for different types of oligos. The bottom and top dashed line represent the fraction of bound BlcR for the scrambled oligo (this part, negative control) and wildtype oligo (Part:BBa_K4361001, positive control), respectively. Numbers below bars denote Part BBa_K43610XX, where XX is said numbers. </figcaption> </figure>

</html>