Difference between revisions of "Part:BBa K4361000"
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BlcR is a transcription factor originating from the bacterium <i>Agrobacterium tumefaciens</i> ([[Part:BBa_K4361100]]). As a homodimer, 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]].  
 
BlcR is a transcription factor originating from the bacterium <i>Agrobacterium tumefaciens</i> ([[Part:BBa_K4361100]]). As a homodimer, 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]].  
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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 [https://www.genscript.com/tools/create-scrambled-sequence 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.
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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 <a href="https://www.genscript.com/tools/create-scrambled-sequence">Genscript Sequence Scramble tool</a>, 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.
  
  

Revision as of 14:02, 6 October 2022


BlcR-binding oligo, 51 bp, scrambled

BlcR is a transcription factor originating from the bacterium Agrobacterium tumefaciens (Part:BBa_K4361100). As a homodimer, 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 <a href="https://www.genscript.com/tools/create-scrambled-sequence">Genscript Sequence Scramble tool</a>, 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.


Shares nucleotides of BBa_K4361001, but in a scrambled order as to no longer allow specific binding.

Usage and Biology

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]