Difference between revisions of "Part:BBa K4361016"

Revision as of 08:44, 10 October 2022

BlcR-binding oligo, 91 bp, IR1 + IR2 + IR1 + 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.
To our understanding, one BlcR dimer contains two domains that allow for tetramerization, only one of which is used during tetramerization in vivo. Part:BBa_K4361015, this part, and Part:BBa_K4361018 have been designed to show whether or not BlcR dimers are able to form multimers larger than tetramers when bound to DNA. To create this part, the original 3 nt linker sequence (tca), a copy of IR1, tca, and a copy of IR2 have been added to the 3' end of the original IR2. The BlcR-binding domain of this part thus consists of IR1-tca-IR2-tca-IR1-tca-IR2. 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 four sequential BlcR dimers to bind to each other, resulting in a BlcR octamer.

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

-

Results

~~~

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4361016 short</partinfo>
-Similar to BBa_K4361015, but inserting an additional "tca + IR2" after the second IR1.
+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>. [[Part:BBa_K4361015]], this part, and [[Part:BBa_K4361018]] have been designed to show whether or not BlcR dimers are able to form multimers larger than tetramers when bound to DNA. To create this part, the original 3 nt linker sequence (tca), a copy of IR1, tca, and a copy of IR2 have been added to the 3' end of the original IR2. The BlcR-binding domain of this part thus consists of IR1-tca-IR2-tca-IR1-tca-IR2. 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 four sequential BlcR dimers to bind to each other, resulting in a BlcR octamer.
 <!-- -->