Difference between revisions of "Part:BBa K243036"
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<partinfo>BBa_K243036 short</partinfo> | <partinfo>BBa_K243036 short</partinfo> | ||
| − | This | + | This biobrick serves as one part of the universal endonuclease and possesses the catalytically active FokI domain Fok_a. When the expressed fusion protein comes into proximity of its counterpart, a fusion protein with the Fok_i domain, an active heterodimer can form. |
| + | A terminal His tag (Polyhistidin tag) allows easy purification. The lipocalin DigoxigeninA (DigA) targets the fusion protein to labeled molecules such as oligonucleotides. The Split Linker connects the parts and adds additional space between them to guarantee the independent function of DigA tag and the protein domain Fok_a. | ||
===Usage and Biology=== | ===Usage and Biology=== | ||
| − | This composite part is one part of our universal endonuclease and | + | This composite part is one part of our universal endonuclease and needs another composite part like BBa_K243010 to build a heterodimer functional as a restriction enzyme. The DigA guides the part to the DNA which is hybridized with a Digoxigenin labeled oligonucleotide. The Split Linker creates a distance of 17 aa between the DigA and the linked Fok_a protein domain. The His Tag serves as a purification tag for Ni-NTA columns. |
| − | + | ||
| − | + | ||
| − | + | ||
===Application=== | ===Application=== | ||
| − | + | We succeeded to create a working universal endonuclease with this part in combination with the part BBa_K243010 by cotransformation into ''E.coli''(XL1blue). The part BBa_K243010 (the Fok_i fusion protein) was cloned into our expression vector BBa_K243033 whereas this part was cloned into the vector pJS419 BBa_K243035. | |
| − | + | A cutting assay was conducted with crude E. coli cell lysate and DNA hybridized with oligonucleotides labeled with the fluophore Cy3. The two Fok fusion proteins can form a heterodimer which can bind to hybridized oligonucleotides and subsequently cut target DNA. We proved the cutting event by gel electrophoresis and excitation of fluorescence. | |
| + | <br><br> | ||
| − | [Image:Freiburg09_Fok_80mer.jpg] | + | [[Image:Freiburg09_Fok_80mer.jpg|250x400px]]<br> |
| + | Agarose gel lanes:1.Marker (1kb ladder mix) 2.Cell extract+sample1 3.Cell extract+sample2 4.control w/o cell extract.<br> | ||
| + | <br> | ||
| + | [https://static.igem.org/mediawiki/parts/a/ac/Fok_in_vitro_80mer_cutting_assay.pdf Method]<br> | ||
| + | The pictures show our agarose gels, on the left excited by wavelength of 535 nm and filtered with a 580 nm cutoff filter. On the left picture, the daylight image has been superimposed. The first lane shows the marker (DNA bands slightly visible on the left gel, dye on the right gel), the second and third lane show the products of the cutting event catalyzed by our universal endonuclease. In the fourth lane only the oligonucleotides were loaded. Comparison with the fourth lane shows that the original oligonucleotides have been cut to smaller products. | ||
| + | '''Detection of the Cy3<br>'''<br> | ||
| + | To excite the Cy3-tagged nucleotides, a laser with a wavelength of 535 nm was used. To block the excitation wavelength when recording the pictures, a cutoff filter of 580 nm was used. In an alternative approach a Zeiss SteREO Lumar.V12 was used to excite the Cy3-tagged oligonucleotides. | ||
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Latest revision as of 04:39, 22 October 2009
His-Dig-Split Linker-Fok_a
This biobrick serves as one part of the universal endonuclease and possesses the catalytically active FokI domain Fok_a. When the expressed fusion protein comes into proximity of its counterpart, a fusion protein with the Fok_i domain, an active heterodimer can form. A terminal His tag (Polyhistidin tag) allows easy purification. The lipocalin DigoxigeninA (DigA) targets the fusion protein to labeled molecules such as oligonucleotides. The Split Linker connects the parts and adds additional space between them to guarantee the independent function of DigA tag and the protein domain Fok_a.
Usage and Biology
This composite part is one part of our universal endonuclease and needs another composite part like BBa_K243010 to build a heterodimer functional as a restriction enzyme. The DigA guides the part to the DNA which is hybridized with a Digoxigenin labeled oligonucleotide. The Split Linker creates a distance of 17 aa between the DigA and the linked Fok_a protein domain. The His Tag serves as a purification tag for Ni-NTA columns.
Application
We succeeded to create a working universal endonuclease with this part in combination with the part BBa_K243010 by cotransformation into E.coli(XL1blue). The part BBa_K243010 (the Fok_i fusion protein) was cloned into our expression vector BBa_K243033 whereas this part was cloned into the vector pJS419 BBa_K243035.
A cutting assay was conducted with crude E. coli cell lysate and DNA hybridized with oligonucleotides labeled with the fluophore Cy3. The two Fok fusion proteins can form a heterodimer which can bind to hybridized oligonucleotides and subsequently cut target DNA. We proved the cutting event by gel electrophoresis and excitation of fluorescence.
Agarose gel lanes:1.Marker (1kb ladder mix) 2.Cell extract+sample1 3.Cell extract+sample2 4.control w/o cell extract.
Method
The pictures show our agarose gels, on the left excited by wavelength of 535 nm and filtered with a 580 nm cutoff filter. On the left picture, the daylight image has been superimposed. The first lane shows the marker (DNA bands slightly visible on the left gel, dye on the right gel), the second and third lane show the products of the cutting event catalyzed by our universal endonuclease. In the fourth lane only the oligonucleotides were loaded. Comparison with the fourth lane shows that the original oligonucleotides have been cut to smaller products.
Detection of the Cy3
To excite the Cy3-tagged nucleotides, a laser with a wavelength of 535 nm was used. To block the excitation wavelength when recording the pictures, a cutoff filter of 580 nm was used. In an alternative approach a Zeiss SteREO Lumar.V12 was used to excite the Cy3-tagged oligonucleotides.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 272
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI.rc site found at 1126