Difference between revisions of "Part:BBa K4361020"

Revision as of 10:52, 10 October 2022

BlcR-binding oligo, 51 bp, Cro repressor variant

BlcR is a transcription factor originating from the bacterium Agrobacterium tumefaciens (Part:BBa_K4361100). Cro is a DNA-binding protein found in bacteriophage λ. Both proteins

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.
This part and Part:BBa_K4361017 have been designed to test whether or not multiple separate BlcR tetramers can form on a single DNA molecule. To create this part, a second and third IR1-tca-IR2 set have been added after the 3' end of the original IR2 in the wildtype sequence, each spaced by a 15 nt linker (gcgggtcagcgggtc). The BlcR-binding domain of this part thus consists of IR1-tca-IR2-gcgggtcagcgggtc-IR1-tca-IR2-gcgggtcagcgggtc-IR1-tca-IR2. The distance between the IR sets is assumed to be sufficient to prevent three potential BlcR tetramers from sterically hindering each other, as well as placing them on alternating sides of the DNA molecule due to being spaced 15 nt apart.

Based off of BBa_K4361001. This oligo was designed for a mutant of the BlcR transcription factor which contained the binding site found in the Cro repressor protein.

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]

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 __NOTOC__
 <partinfo>BBa_K4361020 short</partinfo>
+BlcR is a transcription factor originating from the bacterium <i>Agrobacterium tumefaciens</i> ([[Part:BBa_K4361100]]). Cro is a DNA-binding protein found in bacteriophage &lambda;. Both proteins
+ 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>
+This part and [[Part:BBa_K4361017]] have been designed to test whether or not multiple separate BlcR tetramers can form on a single DNA molecule. To create this part, a second and third IR1-tca-IR2 set have been added after the 3' end of the original IR2 in the wildtype sequence, each spaced by a 15 nt linker (gcgggtcagcgggtc). The BlcR-binding domain of this part thus consists of IR1-tca-IR2-gcgggtcagcgggtc-IR1-tca-IR2-gcgggtcagcgggtc-IR1-tca-IR2. The distance between the IR sets is assumed to be sufficient to prevent three potential BlcR tetramers from sterically hindering each other, as well as placing them on alternating sides of the DNA molecule due to being spaced 15 nt apart.
 Based off of BBa_K4361001. This oligo was designed for a mutant of the BlcR transcription factor which contained the binding site found in the Cro repressor protein.