Difference between revisions of "Part:BBa K801100"

Revision as of 22:27, 26 October 2012

RFP Coding Device - RFC10 and RFC25 compatible

This is an improved version of the RFP generating device BBa_J04450 designed by [http://openwetware.org/wiki/Davidson:Davidson_2005 Team Davidson 2005] that is now RFC10 and RFC25 compatible.

In 2012 the Registry of Standard Biological Parts defined BBa_J04450 as the standard shipping part that is required for submission of backbones, creating the need for a RFC25 compatible standard shipping part.

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]

Composite part of the following BioBricks:

LacI R0010	B0034	mRFP1 E1010	B0015

BBa_R0010: Promoter (lacI regulated)
BBa_B0034: RBS (Elowitz 1999)
BBa_E1010: Red Fluorescent Protein from Discosoma striata
BBa_B0015: Double Terminator

Functional parameters

The colonies are clearly red in color under natural light after about 18 hours. Smaller colonies are visibly red under UV. The RFP part does not contain a degradation tag and the RBS is strong.

LacI sensitive
CAP sensitive

This part is commonly used, but can fail if the system contains LacI or CAP protein.
(--Meagan 15:39, 23 July 2009 (UTC))

Petri dish with BBa_J04450 visualized under non-UV lightbox
Petri dish with BBa_J04450 visualized under 254 nm wavelength UV lightbox
Colonies with and without BBa_J04450 on petri dish.

Usage as a cloning tool

[http://2010.igem.org/Team:Groningen Team Groningen 2010] reports the usage of this part as a cloning tool. When ligating any part, or part assembly, into any standard backbone that contains this part, the non-restricted and single-restricted backbones that self-circularize will produce red colonies on rich media plates (we use TY). These undesired transformants can than be avoided in the screening for the correct construct. With this method, the backbone desired for a new construct does not need to be purified from agarose gel to decrease the amount of undesired tranformants caused by ligation of the original part present in the backbone. The amount of incorrect transformants depends, of course, on the ratio of backbone (mixed with BBa_J04450) vs. BioBrick insert, the size of the BioBrick insert, and whether the insert is an assembly of two BioBricks. The images below show two ligations with different efficiencies.

An inefficient assembly ligation of two BioBricks into the pSB1C3 backbone producing many red colonies.
A more efficient, single BioBrick ligation into the pSB1C3 backbone.

Extension of the standard compability to RFC10 and RFC25

[http://2012.igem.org/Team:TU_Munich Team TU_Munich 2012] extended the standard compability of the RFP coding device (BBa_J04450) to RFC10 and [http://hdl.handle.net/1721.1/45140 RFC25] by adding the NgoMIV and AgeI restriction sites into the prefix and suffix of this part. Additionally two AgeI restriction sites that were present in the generator itself were deleted.

This part may be used as a standard insert for RFC10 as well as [http://hdl.handle.net/1721.1/45140 RFC25] backbones. This improvement became necessary because insertion of BBa_J04450 into a RFC25 compatible backbone leads to the deletion of the desired [http://hdl.handle.net/1721.1/45140 RFC25] restriction sites that are needed for protein fusions.

Absorption spectrum from RFP1 produced by BBa_K801100

The BioBrick BBa_K801100 was characterized by expression of RFP1 (BBa_E1010) in E. coli XL1 blue. Cells were cultivated on a LB petri dish to guarantee sufficient oxygen supply. Afterward the cells were harvested and desintegrated using ultrasonic sound and cell debris was removed using centrifugation. The absorption of the cell extract was measured in a photometer. The spectrum recorded is shown in the figure on the right in witch the RFP absorption peakt arroung 584 nm is present as described in literature.

Absorption spectrum of cell lysate expressing BBa_K801100

Cell lysate of BBa_K801100-expressing E. coli under UV illumination

(by [http://2012.igem.org/Team:TU_Munich Team TU_Munich 2012])

@@ Line 54: / Line 54: @@
 ==Absorption spectrum from RFP1 produced by BBa_K801100==
-The BioBrick BBa_K801100 was characterized by expression of RFP1 (<partinfo>BBa_E1010</partinfo>) in ''E. coli'' XL1 blue. Cells were cultivated on a LB petri dish to guarantee sufficient oxygien supply. Afterward the cells were harvested and desintegrated using ultrasonic sound and cell debris was pelleted using centrifugation. The absorption of the cell extract was measured in a photometer. The spectrum recorded is shown in the figure on the right in witch the RFP absorption peakt arroung 584 nm is present as described in literature.
+The BioBrick BBa_K801100 was characterized by expression of RFP1 (<partinfo>BBa_E1010</partinfo>) in ''E. coli'' XL1 blue. Cells were cultivated on a LB petri dish to guarantee sufficient oxygen supply. Afterward the cells were harvested and desintegrated using ultrasonic sound and cell debris was removed using centrifugation. The absorption of the cell extract was measured in a photometer. The spectrum recorded is shown in the figure on the right in witch the RFP absorption peakt arroung 584 nm is present as described in literature.
 [[Image:TUM12_K801100spectrum.png |thumb|left|400x300px|Absorption spectrum of cell lysate expressing <partinfo>BBa_K801100</partinfo>]]
 [[Image:TUM12_K801100fluorescence picture.jpg |thumb|left|160x300px|Cell lysate of <partinfo>BBa_K801100</partinfo>-expressing ''E. coli'' under UV illumination]]