Difference between revisions of "Part:BBa K4361004"
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<partinfo>BBa_K4361004 short</partinfo>
 
<partinfo>BBa_K4361004 short</partinfo>
  
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Based off of BBa_K4361001. That part's region annotated as "Inverted repeat 1" is not a perfect inverted repeat, so for this part that region was mutated into one of the two perfect repeats, using positions 10 through 17 as the base sequence.
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BlcR is a transcription factor originating from the bacterium <i>Agrobacterium tumefaciens</i> ([[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]]. <br>
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The original IR1 sequence is not a perfect reverse complement of itself. This part and [[Part:BBa_K4361005]] have been designed to test whether or not exchanging IR1 for one of two perfect reverse complement sequences would increase its binding strength to BlcR. To create this part, the nucleotides on the 3' half of IR1 have been replaced by the reverse complement of those of the 5' half, designated as RV 1. The BlcR-binding domain of this part thus consists of IR1 RV 1-tca-IR2, where tca is the original 3 nt linker sequence between IRs.
  
 
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Revision as of 07:30, 10 October 2022


BlcR-binding oligo, 51 bp, IR1 perfect RV 1 + 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.
The original IR1 sequence is not a perfect reverse complement of itself. This part and Part:BBa_K4361005 have been designed to test whether or not exchanging IR1 for one of two perfect reverse complement sequences would increase its binding strength to BlcR. To create this part, the nucleotides on the 3' half of IR1 have been replaced by the reverse complement of those of the 5' half, designated as RV 1. The BlcR-binding domain of this part thus consists of IR1 RV 1-tca-IR2, 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.