Difference between revisions of "Part:BBa K4361015"

Revision as of 08:34, 10 October 2022

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 has been designed to show whether or not a BlcR dimer is able to bind two other dimers, thus resulting in a BlcR hexamer. 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.

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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 <partinfo>BBa_K4361015 short</partinfo>
-Based off of BBa_K4361001, but inserting an additional "tca + IR1" after inverted repeat pair 2.
+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>
+To our understanding, one BlcR dimer contains two domains that allow for tetramerization, only one of which is used during tetramerization <i>in vivo</i>. This part has been designed to show whether or not a BlcR dimer is able to bind two other dimers, thus resulting in a BlcR hexamer. 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 <b>Usage and Biology</b> below, this oligo theoretically allows for the correct orientation of three sequential BlcR dimers to bind to each other.
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