Difference between revisions of "Part:BBa K165007:Experience"

Revision as of 17:26, 26 October 2010

This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K165007

[http://2010.igem.org/Team:Slovenia/ Team Slovenia 2010] further characterized Gli-1 DNA-binding protein. Gli-1 belongs to zinc finger family of proteins. Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as DNA binding proteins. Zinc fingers coordinate zinc ions with a combination of cysteine and histidine residues and can be classified by the type and order of these zinc coordinating residues. Gli-1 is composed of five tandem fingers that bind to DNA sequence: GAC CAC CCA AGA CGA. For isolation, purification and other experiments we added HIS tag to N-terminal side of Gli1 sequence and N-terminal split CFP on C-terminal part of Gli1 after an extension linker. We deposited modified variant of Gli1 as Gli1_link_nCFP BBa_K323016 and additionally characterized it with several methods, including SDS-page, Western Blot and circular dichroism spectroscopy. In vitro binding of Gli-1 to target DNA sequence was determined with surface plasmon resonance (SPR) and in vivo with betagalactosidase assay as a reporter.

Production and isolation of Gli-1 confirmed with SDS-page and Western blot

Gli1_link_nCFP was cloned behind T7 promoter to ensure its strong production in E.coli BL21(De3)pLysS strain and further purified. [http://2010.igem.org/Team:Slovenia/ Team Slovenia 2010] also deposited this part. Left figure represents SDS-page and Western blot of Gli1_link_nCFP after purification. Arrows on both figures indicate Gli1_link_nCFP (42.303 kDa). Molecular weight was determined in silico, using sequence and ProtParam online tool. [http://2010.igem.org/Team:Slovenia/METHODS_and_PARTS Check out the protocol on Team Slovenia iGEM 2010 web site]

Circular dichroism spectroscopy:

Circular dichroism is a method that refers to the differential absorption of left and right circularly polarized light, a phenomenon exhibited in the absorption bands of optically active chiral molecules. Circular dichroism spectroscopy is usually used after protein purification to determine its secondary structure. Using CD spectroscopy we showed (figure right) that Gli1_link_nCFP refolds mostly in α-helical structure, what is known for zinc finger proteins.

[http://2010.igem.org/Team:Slovenia/METHODS_and_PARTS Check out the protocol on Team Slovenia iGEM 2010 web site]

In vitro study of Gli-1 binding characteristics with surface plasmon resonance:

Surface plasmon resonance is a method used for qualitative and quantitive analysis of molecular interactions, in our case binding of zinc fingers to target DNA. We used surface plasmon resonance to demonstrate if Gli1_link_nCFP binds specifically to its target DNA sequence. Figure left implays specific binding of Gli-1 to target DNA. [http://2010.igem.org/Team:Slovenia/METHODS_and_PARTS Check out the protocol on Team Slovenia iGEM 2010 web site]

In vivo study of Gli-1 binding characteristics

Since all above experiments were done in in vitro system, we further characterise if Gli-1 binds to its target binding site in vivo. For that purpose beta-galactosidase assay was used where instead of lac operator Gli-1 binding sequence was inserted. Figure on the right represents binding of Gli-1 to its binding site resulting in transcription inhibition, lower betagalactosidase production and as a result lower betagalactosidase activity.

Reference:

Kasper M., Regl G., Frischauf A., Aberger F. 2006. GLI transcription factors: Mediators of oncogenic Hedgehog signalling. EUROPEAN JOURNAL OF CANCER 42 (2006) 437–445

User Reviews

UNIQ5917e4d34ee2dc81-partinfo-00000000-QINU UNIQ5917e4d34ee2dc81-partinfo-00000001-QINU