Difference between revisions of "Part:BBa K243000:Design"

Latest revision as of 02:46, 22 October 2009

Protein domain (active) of the restriction endonuclease FokI

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 487

Design Notes

Planning the design of two different FokI-heterodimers

For the catalytically active Fok component named Fok_a, the first 1158 nucleotides naturally forming the DNA recognition domain were deleted. The residue glutamate 490 was switched to lysine (GAA->AAA) and isoleucine 538 to lysine (ATC->AAA) to abolish the formation of homodimers.

Fig.2 The two cleavage domains derived from the FokI protein.
Red: Catalytically active FokI cleavage domain (Fok_a); Cyan: Catalytically inactive FokI cleavage domain (Fok_i); Green: aminoacids naturally involved in catalysis (in FokI); Pink: residues glutamate 490 and isoleucine 538; Blue: residues glutamine 486 and isoleucine 499.
Modifications of the genes were created according to [http://www.ncbi.nlm.nih.gov/pubmed/17603475 Miller J et al. Nature Biotechnology 2007] to abolish the formation of homodimers and to enable heterodimerization.
For exchanging the individual amino acids we used the E. coli codon usage table from [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm Hénaut and Danchin].

Designed with Biobrick pre-and suffix for the creation of fusion proteins according to the RFC 25
Commented GenBank file

Source

Source of the protein was the coding region of FokI from the restriction-modification genes of the chromosomal DNA of
[http://www.ncbi.nlm.nih.gov/nuccore/148723?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum Flavobacterium okeanokoites fokIR and fokIM genes]

Planed and designed by Team Freiburg Bioware and synthesized by Mr.Gene.

References

Mary C. Looneya, Laurie S. Morana, William E. Jacka, George R. Feeherya, Jack S. Bennera, Barton E. Slatkoa and Geoffrey G. Wilson;(1989)
Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase; Gene Vol.80 Issue:2 Pages:193-208

Jeffrey C Miller1, Michael C Holmes1, Jianbin Wang1, Dmitry Y Guschin1, Ya-Li Lee1, Igor Rupniewski1, Christian M Beausejour1,2, Adam J Waite1, Nathaniel S Wang1, Kenneth A Kim1, Philip D Gregory1, Carl O Pabo1,2 & Edward J Rebar (2007);
An improved zinc-finger nuclease architecture for highly specific genome editing; Nature Biotechnology 25, 778 - 785

@@ Line 8: / Line 8: @@
 '''Planning the design of two different FokI-heterodimers'''
 <br>
-For the catalytic active Fok partner, named Fok_a, the first 1158 nucleotides, i.e. the recognition domain, were deleted and glutamate 490 was switched to lysine (GAA->AAA) as well as isoleucine 538 to lysine (ATC->AAA) for the heterodimer formation<br>
+For the catalytically active Fok component named Fok_a, the first 1158 nucleotides naturally forming the DNA recognition domain were deleted. The residue glutamate 490 was switched to lysine (GAA->AAA) and isoleucine 538 to lysine (ATC->AAA) to abolish the formation of homodimers.<br>
 <br>
 [[Image:Freiburg09 fokmodel fig2.png]]
-<p class=MsoNormal><span class=itatext><b>Fig.2 two FokI cleavage domains aminoacid
+<p class=MsoNormal><span class=itatext><b>Fig.2 The two cleavage domains derived from the FokI protein.<br></b>
-to 579. </b>Red:<b> </b>Catalytically active FokI cleavage domain; Cyan:
+Red: Catalytically active FokI cleavage domain (Fok_a); Cyan:
-Catalytically inactive FokI cleavage domain; Green: catalytically active aminoacids;
+Catalytically inactive FokI cleavage domain (Fok_i); Green: aminoacids naturally involved in catalysis (in FokI);
-Pink: </span>glutamate 490 and isoleucin 538; Blue: glutamin 486 and isoleucin
+Pink: residues glutamate 490 and isoleucine 538; Blue: residues glutamine 486 and isoleucine
-.</p>
+.<br>
-<br>
-Modifications of the single vectors to introduce heterodimeric modifications according to [http://www.ncbi.nlm.nih.gov/pubmed/17603475 Miller J, Rebar E ''Nature biotech'' 2007] <br><br>
+Modifications of the genes were created according to [http://www.ncbi.nlm.nih.gov/pubmed/17603475 Miller J et al. ''Nature Biotechnology'' 2007] to abolish the formation of homodimers and to enable heterodimerization.<br>
+For exchanging the individual amino acids we used the E. coli codon usage table from [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm Hénaut and Danchin].<br><br>
-'''Annotations:'''
+Designed with Biobrick pre-and suffix for the creation of fusion proteins according to the [https://parts.igem.org/Assembly_standard_25 RFC 25]
-*The notation e.g. for Cystein 541/463-465 means the amino acid 541 in literature which correspond to the codons 463-465 in our vector. <br>
-*For exchanging the amino acids we used the Codon usage table in E.coli from Hénaut and Danchin. [http://www.faculty.ucr.edu/~mmaduro/codonusage/codontable.htm E.coli Codon Usage]<br><br>
-<br>
-Designed according the assembly standard 25 [https://parts.igem.org/Assembly_standard_25 RFC 25]
 <br>[https://static.igem.org/mediawiki/parts/5/5f/Freiburg09_fok_a.txt  Commented GenBank file]
@@ Line 30: / Line 27: @@
 Source of the protein was the coding region of FokI from the restriction-modification genes of the chromosomal DNA of<br>[http://www.ncbi.nlm.nih.gov/nuccore/148723?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum Flavobacterium okeanokoites fokIR and fokIM genes]<br>
-<br>Part synthesized by Mr.Gene
+<br>Planed and designed by Team Freiburg Bioware and synthesized by Mr.Gene.
 ===References===