Team:SJTU-BioX-Shanghai/Parts

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We have four types of connector.</p>
We have four types of connector.</p>
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Revision as of 15:21, 17 October 2014

Overview

We have characterized and submitted 42 BioBricks which could either be used directly or serve as a universal tool readily for potential scientific or engineering use.
Those BioBricks could be divided into four groups.
1.BioBricks in Basic Parts are all basic components of the whole project. They can be assembled to carry out different tasks.
2.BioBricks in USB is our designed sequence. They can help us easily and quickly insert our target sequence and make a whole part.
3.BioBricks in application is our complete part.
4.BioBricks in New TAL is our new design TAL parts which are robust and perform better in Golden Gate method.

Basic Parts

Review previous parts

ssDsbA: SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of E.coli.
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand ( (BBa_K771002, SJTU-BioX-Shanghai)

Lgt: Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) is an inner membrane protein act as an membrane anchor of E.coli with seven transmembrane segments and has been successfully overexpressed in E. coli without causing harm to cells.
From: ssDsbA-PDZ Ligand-LGT-SH3 Ligand (BBa_K771002, SJTU-BioX-Shanghai)

mRFP: Red Fluorescent Protein. To visualize the localization of fusion protein with fluorescence test , we added mRFP in the Connectee1 and placed it just after the ssDsbA.
From: Highly engineered mutant of red fluorescent protein from Discosoma striata (BBa_E1010, Antiquity )

FL3-TALE(BBa_K1453300)

This is a TALE protein with a flexible linker 3 before it.
Since we cannot connect TALE by Golden Gate method designed by 2012 Freiburg, so the sequence was synthesized by Genwize company. This TALE can recognize the DNA sequence TTGGTCATGAGA(12bp). Moreover, we use this part with our part BBa_K14530000 to make our composite part BBa_K1453305.

Connector

We have four types of connector.


pBluescript II KS(+) ScaI deletion (BBa_K1453301)
pBluescript II KS(+) EcoRV deletion (BBa_K1453302)
pBluescript II KS(+)_3_copy (BBa_K1453303)
pBluescript II KS(+)_5_copy (BBa_K1453304)
Each type of connector has its own function. If you want to know the details, please click it. We have introduction on our part's main page.

USB

We make two kinds of USB. One is TAL USB, the other is Enzyme USB. They can help us easily and quickly insert our target TALE or Enzyme, respectively.

TAL USB(BBa_K1453000)

We design a sequence which can be used together with 2012 Freiburg's part. The TAL USB can make two specific sticky ends. The two ends are the same as the first part and the last part of Freiburg design. So when we digest and ligate them together, we can get a whole TALE. But unluckily, since the sticky ends designed by Freiburg are too similar, we can just have some mismatch sequence by using these TAL USB.

Enzyme USB

In order to easily and quickly insert the target function enzyme into our system, we design two enzyme-USBs. The enzyme USB have three fundamental components, flexible linker- enzyme adaptor-flexible linker.

The first flexible linker has deleted the PstI recognition site. And at the beginning of the sequence there is a Bsu36I recognition site. The second flexible linker we replace the original PstI site with a isocaudamer SduI, since our part can not have a PstI recognition site.

On the other hand, the enzyme adaptor has two same restriction enzyme recognition sites. In one of our enzyme-USB, it is the AarI recognition site; The other enzyme-USB is the BsmAI recognition site. The AarI and BsmAI are similar to BsmBI which all can make a 4bp sticky end designed by ourselves.

When we want to insert a functional enzyme into our fusion protein, first we need to have a PCR experiment to add a head and a tail around our enzyme. After that, the enzyme product also has the restriction enzyme recognition site. When digested by the specific restriction enzyme, it can generate the same sticky ends, so our enzyme can be inserted into our part.


(BBa_K1453400)
(BBa_K1453401)

New TAL

We design seven new sticky ends which get the least score when judging the similarity.
If you want to know how we design these ends, please go to see our project-Part3 TAL improve.


(BBa_K1453500) (BBa_K1453501) (BBa_K1453502)
(BBa_K1453503) (BBa_K1453504) (BBa_K1453505)
(BBa_K1453506)