Part:BBa_K4361015

BlcR-binding oligo, 71 bp, IR1 + IR2 + IR1

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. Both sequences are so-called inverted repeat pairs (IRs), short DNA sequences whose ends are reverse complements of each other. For the Blc operator, these sequences are 'ACTCTAATgATTCAAGT' (IR1) and 'ATTAGttgaactCTAAT' (IR2), as further explained in Part:BBa_K4361001.
To our understanding, one BlcR dimer contains two domains that allow for tetramerization, only one of which is used during tetramerization in vivo. This part, Part:BBa_K4361016, and Part:BBa_K4361018 have been designed to show whether or not BlcR dimers are able to form multimers larger than tetramers when bound to DNA. To create this part, the original 3 nt linker sequence (tca) and a copy of IR1 have been added to the 3' end of IR2. The BlcR-binding domain of this part thus consists of IR1-tca-IR2-tca-IR1. As the distance between the centers of all IRs is still 20 nt, see also Usage and Biology below, this oligo theoretically allows for the correct orientation of three sequential BlcR dimers to bind to each other, resulting in a BlcR hexamer.

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]

Usage and biology

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Results

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Figure 2. Results of the second Tapestation experiment, in which the fraction of DNA bound to BlcR was determined for different types of oligos. The first bar and bottom dashed line represent the results with Part:BBa_K4361000 (scrambled oligo, negative control), the second bar and top dashed line correspond to those with Part:BBa_K4361001 (wildtype oligo, positive control). The third bar depicts the measured fraction of bound DNA for this part.