Part:BBa_K4361013

BlcR-binding oligo, 51 bp, IR2 flip + IR1 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 this part 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. Additionally, to test if the order of IRs also influences binding strength, the order of IRs has been reversed in this part as well. Thus, to create this part, the nucleotides originally designated as belonging to IR1 have been replaced by the reverse complement of IR2 ('ATTAGagttcaaCTAAT', IR2 flip) and those of IR2 by the reverse complement of IR1 ('ACTTGAATcATTAGAGT', IR1 flip). The BlcR-binding domain of this part thus consists of IR2 flip-tca-IR1 flip, where tca is the original 3 nt linker sequence between IRs.

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.