Part:BBa_K4361000

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

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Results

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Figure 1. Results of the first Tapestation experiment, to measure the fraction of DNA bound to BlcR either in the presence or absence of BlcR. First set of bars represent results with this part, second set of bars correspond to those of Part:BBa_K4361001.

Figure 2. Results of the second Tapestation experiment, in which the fraction of DNA bound to BlcR was determined for different types of oligos. First bar represents results with this part, second bar corresponds to those of Part:BBa_K4361001.

Figure 3. Results of the third Tapestation experiment, in which the fraction of DNA bound to BlcR was determined for different types of oligos in the presence or absence of 25 μM SSA. First set of bars represent results with this part, second set of bars correspond to those of Part:BBa_K4361001.