Part:BBa_K4361011

BlcR-binding oligo, 51 bp, IR1 + IR2 flip

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.
Part:BBa_K4361010 up to Part:BBa_K4361013 have been designed to test whether or not the exact orientation of IRs influences the binding strength of BlcR to DNA. This is achieved by 'flipping' the IRs, or replacing them by their reverse complements. To create this part, the nucleotides originally designated as belonging to IR2 have been replaced by the reverse complement of IR2, resulting in 'ATTAGagttcaaCTAAT' (IR2 flip). The BlcR-binding domain of this part thus consists of IR1-tca-IR2 flip, where tca is the original 3 nt linker sequence between IRs.

Based off of BBa_K4361011, but having the sequence of "Inverted repeat pair 2" be the reverse complement of the original.

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.