Difference between revisions of "Part:BBa K4785005"

Latest revision as of 08:32, 11 October 2023

high-mobility group box 1 (hmgb1)

There is a special structure in the biofilm of bacteria: DNABII family DNA-binding proteins twist the extracellular DNA into a Z-type, many Z-types of DNA are connected together to form a three-dimensional grid structure, and polysaccharides act as a "glue" to make the network more stable. Bacteria live in the crevices of these grids, protected from antibiotics and shear forces in the fluid environment.

HMGB1 is a common eukaryotic protein that is a natural component of chromatin and can bind to Z-type DNA. In contact with the reticular structure in the biofilm described above, the protein can compete with DNABII family proteins for DNA binding sites. Due to the different binding ways with DNA, HMGB1 cannot distort DNA as effectively as DNABII family proteins, so the DNA in the biofilm will gradually recover from type Z to type B after binding with HMGB1, resulting in the collapse of the grid structure.

At the same time, since the HMGB1 protein is composed of two structurally similar domains: A box and B box, we will also explore the disintegration ability of HMGB1_FL, HMGB1_AB box, HMGB1_A box and HMGB1_B box to biofilm.

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
INCOMPATIBLE WITH RFC[1000]
Illegal SapI.rc site found at 73

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 <partinfo>BBa_K4785005 short</partinfo>
-This DNA sequence was used to express the HMGB1_A box. HMGB1_A box is a part of HMGB1 protein. The DNABII protein monomer responsible for stabilizing the eDNA structure in biofilm has a similar structure to HMGB1_A box. Therefore, we hypothesized that HMGB1_A box could inhibit the growth of biofilm and disrupt the mature biofilm. Therefore, we truncated the sequence of hmgb1 to obtain the present sequence, and recorded it on this page for the convenience of our team and other teams.
+There is a special structure in the biofilm of bacteria: DNABII family DNA-binding proteins twist the extracellular DNA into a Z-type, many Z-types of DNA are connected together to form a three-dimensional grid structure, and polysaccharides act as a "glue" to make the network more stable. Bacteria live in the crevices of these grids, protected from antibiotics and shear forces in the fluid environment.
+HMGB1 is a common eukaryotic protein that is a natural component of chromatin and can bind to Z-type DNA. In contact with the reticular structure in the biofilm described above, the protein can compete with DNABII family proteins for DNA binding sites. Due to the different binding ways with DNA, HMGB1 cannot distort DNA as effectively as DNABII family proteins, so the DNA in the biofilm will gradually recover from type Z to type B after binding with HMGB1, resulting in the collapse of the grid structure.
+At the same time, since the HMGB1 protein is composed of two structurally similar domains: A box and B box, we will also explore the disintegration ability of HMGB1_FL, HMGB1_AB box, HMGB1_A box and HMGB1_B box to biofilm.
 <!-- Add more about the biology of this part here