Part:BBa_K4361014
BlcR-binding oligo, 56 bp, IR1 + 5 bp linker + IR2
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.
As explained below under Usage and Biology, the length of the linker sequence between IRs (normally 3 nt) is crucial for BlcR's ability to correctly bind the DNA and tetramerize. This part has been designed to show whether or not a larger linker indeed inhibits this behaviour. To create this part, the final five nucleotides of the wildtype oligo (gcggg) have been added between the original linker and IR2. The BlcR-binding domain of this part thus consists of IR1 outer 5-tcagcggg-IR2. As a 3 nt linker is hypothesized to result in two BlcR dimers binding on the same side of a DNA strand, an 8 nt linker as found in this part should result in two dimers binding on opposite parts of the DNA, severely reducing the amount of BlcR bound to DNA strands.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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