Team:EPF Lausanne/Notebook/Ecoli

EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits

E. Coli Laboratory Notebook

Construction of pdCas9-w

pdCas9-w was constructed using PCR and Gibson assembly from the following plasmids:

  • pdCas9 (pdCas9-bacteria, plasmid #44249, Addgene): dCas9 under a Tetracyclin inducible promoter and a Chlorampheicol resistance gene
  • pWJ66 (pWJ66, plasmid #46570, Addgene): tracrRNA, w-dCas9 (dCas9 fused at its C-terminal to rpoZ, which encodes for the w subunit of RNA polymerase) and CRISPR array

pdCas9 was opened by PCR and the w subunit was extracted from pWJ66 by pCR. The w subunit was then fused to the C-terminal of dCas9 by Gibson assembly, the final product is pdCas9-w.
A site-directed mutagenesis was done on this plasmid to eliminate an EcoRI restriction site. This will allow us to submit pdCas9-w as a BioBrick.

Construction of pdCas9-w
Open pdCas9 by PCR

We received plasmid pdCas9 in bacteria and did a Miniprep (cf. Protocols) on overnight cultures to isolate it. This step consists of linearizing pdCas9 by PCR.

Materials and method

  • 20 µL Phusion PCR (cf. Protocols) of pdCas9 with primers f_Gbs_pdCas9 and r_Gbs_pdCas9
  • PCR product purification (cf. Protocols)
  • Agarose gel electrophoresis of 2 µL purified PCR products

Results

Linearized pdCas9-w is expected to be 6705 bp.
The first try of this PCR was unsuccessful (gel is not shown here). For our second try, we tested many parameters: HF vs. GC buffer, different annealing temperatures and different extension times. This time, many, but not all, of our samples were successfully amplified (cf. Fig.1). The difficulty of this PCR is probably due to the fact that the size of the ampicon is very long, almost 7 kb.
For next steps, sample from lane 1 (cf. Fig.1) was used.

Figure 1
Fig.1 - Gel of linearized pdCas9

Construction of pdCas9-w
Extract w subunit from pWJ66 by PCR

We received plasmid pWJ66 in bacteria and did a Miniprep (cf. Protocols) on overnight cultures to isolate it. This step consists of extracting rpoZ, the w subunit, from pW66 by PCR.

Materials and method

  • 20 µL Phusion PCR (cf. Protocols) of pWJ66 using primers f_Gbs_w and r_Gbs_w.
  • PCR product purification (cf. Protocols)
  • Agarose gel electrophoresis of 2 µL purified PCR products

Results

Successful PCR reactions are expected to yield 340 bp fragments.
PCR was succesful for sample visible gel. (cf. Fig.2)

Figure 2
Fig.2 - Gel of extracted w subunit

Construction of pdCas9-w
Gibson assembly of pdCas9-w

This step consists of fusing the w subunit to dCas9 by Gibson assembly, using the PCR products from previous steps. We transformed cells with the Gibson assembly product and tested for colonies that contain the construct by colony PCR, restriction digest and sequencing.

Materials and method

  • Gibson assembly (cf. Protocols) with purified PCR products:
    • Open pdCas9: 0.02 pmol = 95 ng
    • w subunit extracted from pWJ66: 0.06 pmol = 12.5 ng
  • Transformation (cf. Protocols) of ultra-competent DH5a cells (NEB) with Gibson assembly product, spreading on Chloramphenicol plates
  • Colony PCR (cf. Protocols) of colonies from plate used for culture of transformed cells with primers f_Gbs_w and r_Scq_pdCas9_w_sgRNA primers + agarose gel electrophoresis of 2 µL PCR prodcuts
  • Miniprep (cf. Protocols) of overnight liquid cultures in 5 mL LB with Chloramphenicol of colonies from plate used for culture of transformed cells to isolate pdCas9-w plasmids
  • Restriction digest (Cf. Protocols) of pdCas9-w plasmids with BamHI and KpnI seperately + agarose gel electrophoresis of 2 µL digested products
  • Sequencing (Microsynth) of one colony for which Gibson assembly worked according to colony PCR and restriction analysis

Results

Colony PCR

Primers were placed such as amplicons are 666 bp if Gibson assembly worked and 396 bp if the plasmid self-ligated.
Lane "C" is a negative control: PCR was run with all components except template DNA, ie. cells. It is empty which means there is no contamination.
Gibson assembly seems to have worked for some of our samples. (cf. Fig.3)
To avoid working with too many samples, we kept the ones from lanes 16, 22, 25, 31, 37 and 43 for the Minipreps and restriction digest. We did overnight liquid cultures of these colonies.

Figure 3a Figure 3c
Fig.3 - Gels of colony PCR of Gibson assembly products
Figure 3b Figure 3d

Restriction digest

pdCas9-w samples from different colonies are present on gels in triplicates in the following order:

  • Undigested - expected to yield 7 kb circular plasmid (migrates faster than linear fragments of the same size)
  • Digested by BamHI - expected to yield two fragments of 6147 bp and 834 bp if insert is present or one 6705 bp fragment if it is not
  • Digested by KpnI - expected to yield two fragments of 45334 bp and 2447 bp if insert is present or one 6705 bp fragment if it is not

BamHI and KpnI are both unique cutters in pdCas9 (without the insert) and double cutters in pdCas9-w (with the insert).
Too much ladder was loaded so it is difficult to estimate the size of the fragments. The smaller fragments are also very difficult to see.
By looking at the relative heights, we can say that all colonies seem to have the w subunit insert. There is only the undigested sample for colony 16 that is not visible, probably due to an error while loading the gel.
Colony 22 was kept for next steps, it was stored in a glycerol stock (c.f. Protocols).

Figure 4a Figure 4b Figure 4c
Fig.4 - Gels of restriction digest of Gibson assembly products

Sequencing

As dCas9-w is very long, only part of it was sequenced (the w subunit and its surrounding base pairs). No mutations were detected.

Construction of pdCas9-w
Site-directed mutagenesis of dCas9-w

It was noticed after assembly of pdCas9-w that dCas9 contains an EcoRI restriction site, which makes it "un-BioBrick-able". Since it is an important part for our project, we decided to remove the restriction site by site-directed mutagenesis to be able to submit it as a functional BioBrick.

Materials and method

  • Site-directed mutagenesis (cf. Protocols) of pdCas9-w with primers f_Mt_A2080C_pdCas9-w and r_Mt_A2080C_pdCas9-w
  • Miniprep (cf. Protocols) of overnight liquid cultures in 7 mL LB with Chloramphenicol of colonies from site-directed mutagenesis plate to isolate mutated pdCas9-w plasmids
  • Restriction digest (cf. Protocols) of mutated pdCas9-w plasmids with EcoRI to identify colonies for which the mutagenesis was successful
  • Sequencing (Microsynth) of one pdCas9-w for which the mutageneis worked according to the restriction digest

    • Results

    Coming soon

Construction of pdCas9-w
BioBrick mutated dCas9-w

To submit dCas9-w as a BioBrick, we extracted dCas9-w from the mutated pdCas9-w and inserted it into pSB1C3, a BioBrick assembly plasmid.

Materials and method

Coming soon

Results

Coming soon

Construction of pdCas9-w-sgRNAs

These experiments consist of inserting one, two or three sgRNA producing cassettes into pdCas9-w.
pdCas9-w was linearized by restriction digest. The sgRNA cassettes were synthesized (IDT) and necessary overlaps were added by PCR. The sgRNAs were inserted into pdCas9-w by Gibson assembly.

The sgRNA cassettes were synthesized with sequences "A" and "B" at its ends (cf. Fig.8a). These are the same sequences as those found at the ends of the linearized pdCas9-w.
When one cassette is inserted, no overlaps need to be added.
When two or three cassettes are added, sequences "C" and/or "D" need to be added at the ends of the cassettes (cf. Fig.8b), thus obtaining unique overlaps for the Gibson assembly.

Figure ¨8a
Fig.8a - Structure of a sgRNA cassette
Figure ¨8b
Fig.8b - Assembly of three sgRNA cassettes

Construction of pdCas9-w-sgRNAs
Open pdCas9-w by restriction digest

Materials and method

  • Miniprep (cf. Protocols) of overnight liquid cultures in 5 mL LB with Chloramphenicol of pdCas9-w containing bacteria
  • Restriction digest (Cf. Protocols) of pdCas9-w with BsrBI (blunt ends)
  • Agarose gel electrophoresis of 2 µL of digested and undigested product

Results

The digested and undigested plasmids should have the same size. Circular fragments migrates faster than linear fragments of the same size. This means that the undigested plasmid should migrate faster than the digested plasmid.
Even though the ladder is not clear, by looking at the relative heights we can see that the digested sample migrated more slowly than the undigested sample (cf. Fig.9). The restriction digest was successful.

Note that this was repeated several times since we needed a lot of linearized pdCas9-w.

Figure 9
Fig.9 - Gel of digested pdCas9-w (lane 1) and undigested pdCas9-w (lane 2)

Construction of pdCas9-w-sgRNAs
Amplify sgRNA cassettes by PCR

Materials and method

  • 20 µL Phusion or Q5 PCR (cf. Protocols) of sgRNA cassette with primers as indicated in table below
  • Agarose gel electrophoresis of 2 µL purified PCR products
  • PCR product purification (cf. Protocols)
Construct sgRNA cassette(s) Forward primer(s) / Reverse primer(s)
pdCas9-w-Z0 Z0 f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-Z4 Z4 /br>f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-Z35 Z35 f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-Z0-Z4 Z0
Z4		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-Z0-Z35 Z0
Z35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-Z4-Z35 Z4
Z35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-Z0-Z4-Z35 Z0
Z4
Z35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-BtoD
f_Gbs_sgRNA-DtoA / r_Gbs_sgRNA-B
pdCas9-w-X0 X0 f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-X4 X4 f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-X35 X35 f_Gbs_sgRNA-A / r_Gbs_sgRNA-B
pdCas9-w-X0-X4 X0
X4		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-X0-X35 X0
X35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-X4-X35 X4
X35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-B
pdCas9-w-X0-X4-X35 X0
X4
X35		 f_Gbs_sgRNA-A / r_Gbs_sgRNA-BtoC
f_Gbs_sgRNA-CtoA / r_Gbs_sgRNA-BtoD
f_Gbs_sgRNA-DtoA / r_Gbs_sgRNA-B

Results

All amplified sgRNA cassettes are expected to be about 370 bp.

sgRNA cassette Z0 was amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-BtoD and primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Q5 PCR. Both samples were successfully amplified (cf. Fig.10a).

sgRNA cassette Z4 was amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Phusion PCR. Samples 3 and 4 were successfuly amplified (cf. Fig.10b).

sgRNA cassette Z35 was successfuly amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Phusion PCR. However, it is not easily visible on the gel. (cf. Fig.10c)

sgRNA cassette X0 was successfuly amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Phusion PCR. (cf. Fig.10d)

sgRNA cassette X4 was successfuly amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Phusion PCR. (cf. Fig.10e)

sgRNA cassette X35 was successfuly amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B with Phusion PCR. (cf. Fig.10f)

Figure 10a
Fig.10a - Gel of sgRNA cassette Z0 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-BtoD (lane 1) and primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B (lane 2)
Figure 10c
Fig.10c - Gel of sgRNA cassette Z35 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B
Figure 10e
Fig.10e - Gel of sgRNA cassette X4 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B
Figure 10b
Fig.10b - Gel of sgRNA cassette Z4 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B
Figure 10d
Fig.10d - Gel of sgRNA cassette X0 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B
Figure 10f
Fig.10f - Gel of sgRNA cassette X35 amplified with primers f_Gbs_sgRNA-A + r_Gbs_sgRNA-B

Construction of pdCas9-w-sgRNAs
Assemble pdCas9-w-sgRNA constructs by Gibson assembly

Materials and method

Coming soon

Results

Coming soon

EPFL 2015 iGEM bioLogic Logic Orthogonal gRNA Implemented Circuits

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