Project Results

miRNA2911 (BBa_K1860700)

Aim

Our goal was to use synthetic biology to produce miRNA2911, which is endogenously expressed in Lonicera japonica.

Results

We were able to constructed a Biobrick (BBa_K1860700) that contains the anti-viral miRNA2911. The Biobrick was validated by sequencing.

Design of Oligos

We started our project by designing oligos of the miRNA2911. It was really important to consider that the desired sequence had to be in line with the iGEM standard. Meaning that the resulted Biobrick can be used for 3A-Assemblies later on. Hence the miRNA2911 is flanked by the appropriate restriction sites (EcoRI, XbaI, SpeI, PstI). Depicted in Figure 1 are the designed sequences.

Annealing of Oligos

In the next step the oligos needed to be annealed. We used the standard ‘Annealing Protocol’ and Figure 2 depicts the results of this annealing. The appropriate bands of the resulted miRNA2911 insert are at xx bp.

Ligation

After confirmation of successful annealing we proceeded with the ligation of the insert (miRNA2911) into the standard backbone pSB1C3. For this purpose the linearized backbone (pSB1C3) was cut with EcoRI and PstI and the insert was ligated into the vektor. The insert must not be cut as it was designed to form overhangs after annealing.

Shown in the following Figure is the verification of ligation. The ligation was verified positive as the ligated vector runs at 2050 bp and the control sample, only containing pSB1C3 runs at around 2000 bp, as seen in the agarose gel.

Following, the ligated product was transformed into the E.coli strain DH5α. Single colonies were picked, liquid culture were grown overnight and plasmids were prepped.

Verification

Colony PCR

To be able to verify if our E.coli actually carry our desired plasmid a colony PCR was performed. Therefore an aliquot of the liquid culture was again plated out and grown overnight. Sixteen different colonies were tested using the standard sequencing primers. The results of six of these PCRs are shown in the following Figure. The gel verifies that the E.coli are carrying our desired vector containing the miRNA2911.

Sequencing

Finally we verified our new Biobrick by sequencing. As our insert is really small (20 bp), we had to design new sequencing primers that are farther away from the insert because the standard sequencing primers of the registry directly flank the insert. The direct flankation of the primers would result in inconclusive sequencing data that can not be interpreted because Sanger XXX.

constitutive promoter and miRNA (BBa_K1860702)

We combined the generated Biobrick (BBa_K1860700), containing the miRNA2911, with a constitutive promoter (BBa_J23102) that was provided with the Standard Distribution by 3A-Assembly. This is necessary to further on be able to test if miRNA2911 is:

actually expressed

stable in E.coli and

how it is actually folded

Therefore we used the standard 3A-Assembly protocol. The constitutive promoter (BBa_J23102) was provided in pSB1A3, our constructed Biobrick (BBa_K1860700) is carried in pSB1C3, hence the assembly was performed on pSB1K3.

Verification by sequencing

XXX

GroEL - heat-inducible promoter (BBa_K1860701)

Design of Oligos

GroEl is a heat-inducible promoter and we started by designing oligos of GroEL. The sequence was kindly provided by Prof. Ignatova. Just like for the design of the miRNA2911 here we also needed to reconsider the that the desired sequence containing GroEL had to be in line with the iGEM standard. Hence also the GroEL promoter is flanked by the appropriate restriction sites (EcoRI, XbaI, SpeI, PstI). Depicted in Figure x are the designed sequences.

Annealing of Oligos

In the next step the oligos needed to be annealed. We used the standard ‘Annealing Protocol’ and Figure XXX depicts the results of this annealing. The appropriate bands of the resulted GroEL insert are at XXX bp.

Ligation

After confirmation of successful annealing we proceeded with the ligation of the insert (GroEL) into the standard backbone pSB1C3. For this purpose the linearized backbone (pSB1C3) was cut with EcoRI and PstI and the insert was ligated into the vektor. The insert must not be cut as it was designed to form overhangs after annealing.

to be continued

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Inspiration

See how other teams presented their results.

• 2014 TU Darmstadt
• 2014 Imperial
• 2014 Paris Bettencourt