Team:Heidelberg/Project/miRNA Kit


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Synthetic miRNA Kit

miTuner - a kit for microRNA based gene expression tuning in mammalian cells

With the synthetic miRNA kit, we provide a comprehensive mean

to plan, conduct and evaluate experiments dealing with miBricks

(i. e. microRNA related Biobricks) as key regulators in mammalian cells.


… key regulators, one way, how specificity of gene therapy can be approached (beside target cell tropism of aavs)


MicroRNAs (miRNAs) are short endogenous, non-coding RNAs that mediate gene expression in a diversity of organisms (Bartel, 2004). Although the understanding of their biological functions is progressing remarkably, the exact mechanisms of regulation are still not unambiguously defined. However, it is commonly believed that miRNAs trigger target mRNA regulation by binding to 3’ untranslated region (UTR) of its target (Chekulaeva and Filipowicz, 2009). Exact principles of expression knockdown mediated by miRNA are still in debate (Eulalio et al., 2008).
However, sequence depending binding site properties have an essential impact on miRNA-mRNA interaction. Depending on pairing specificity translational repression is mediated through the imperfect miRNA-mRNA hybrids. The potential for stringent regulation of transgene expression makes the miRNA world a promising area of gene therapy (Brown et al.,2009). There is a need for tight control of gene expression, since cellular processes are sensitive to expression profiles. Non-mediated gene expression can lead to fatal dysfunction of molecular networks. It is widely known, that miRNAs can adjust such fluctuations (Brenecke et al., 2005). A combination of random and rational design of binding sites could become a powerful tool to achieve a narrow range of resulting gene expression knockdown. To ease in silico construction of miRNA binding sites with appropriate characteristics for its target, we wrote a program - the miBS designer. Using all of our theoretical models gives the user the opportunity to calculate knockdown percentages caused by the designed miRNA in the target cell. Our synthetic miRNA Kit guarantees at least for individually modifiable but still ready-to-use constructs to interfere genetic circuits with synthetic or endogenous miRNAs. We preciously show, that gene expression can thereby by adjusted - tuned - to an arbitrary level. The miTuner (see sidebar) allows on the simultaneous expression of a synthetic miRNA and a gene of interest that is fused with a designed binding site for this specific miRNA. Our modular kit comes with different parts that can be combined by choice, e. g. different mammalian promoters and characterized binding sites of specific properties. By choosing a certain binding site to tag the GOI, one can tune the expression of this gene. Depending on the GOI, different means for read out of gene expression come into play. At first, we applied dual-luciferase assay, since we used Luciferase as a reporter for a proof-of-principle approach. Later on, semi-quantitative immunoblots were prepared for testing of therapeutic genes. However, all the received information fed our models, thereby creating an integrative feedback loop between experiments and simulation.


Regulation of gene expression can be achieved by fusing miRNA binding sites right behind a GOI. In case a referring shRNA miR is expressed, the GOI is knocked down. Strength of regulation thereby depends on binding site properties. We are able to tune gene expression linearly over a broad range. This is a first proof of principle for various miRNA-mRNA interaction in vitro. Therefore, we transfected HeLa cells in principle with our pSMB_miTuner Plasmid HD3. It turned out, that there was no obvious effect of different binding sites on reporter gene expression (data not shown). We assume that the RSV driving the shRNA miR is too weak for tight regulation of the referring binding site behind the GOI. Only if a sufficient amount of shRNA miR binds to its target, translation is significantly repressed. Thus, we expressed the shRNA miR from a separate plasmid which was always co-transfected with the original tuning construct. The reporter genes - i. e. Luc2 and hRluc - were also expressed from separate plasmids to get a reference as well as a transfection control. Then, we conducted a Dual Luciferase Assay for quantification of gene expression. The data preciously shows a tuned expression from almost 0% to 100% (Fig. 1, Fig. 2). Lowest expression refers to complete knockdown through fusion of perfect binding sites (always green bar on the left hand side of the figures) to the reporter gene. 100% means ordinary expression from a construct without binding sites (always orange column on the right hand side of the figures). In presence of the specific shRNA miR, gene expression was mediated to various levels through interactions with the different imperfect binding sites. Whereas, when an unspecific shRNA miR was expressed, gene expression remained unaffected (see raw data below). The latter aspect reveals, that the binding sites were correctly designed, since they seem to interact specifically with a referring shRNA miR. The constructs were tested in two different backbones: pBS_U6 and pBS_H1. Both are in viral context, meaning that they contain inverted terminal repeats (ITRs). The constructs can be packed into the capsid of an adeno-associated virus (AAV). Those constructs we also chose for virus production to infect cells even more efficiently as compared to transfections. Because of the significant data, we decided to inject the viruses into mice to see the tuning effect also in vivo. The pBS_H1 construct should be preferred for mice injections since the expressed shRNA miR against human alpha-1-antitrypsine (hAAT) is cytotoxic in higher concentrations. The pBS_H1 backbone leads to moderate expression ranges, still obviously showing the tuning effect.

Figure 1: Tuning of gene expression through different imperfect shRNA miR binding sites in pBS_H1. Gene expression quantified via dual luciferase assay for M constructs containing different imperfect binding sites.
Figure 2: Tuning of gene expression through different imperfect shRNA miR binding sites in pBS_U6. Gene expression quantified via dual luciferase assay for M constructs containing different imperfect binding sites.

Strikingly, the order of constructs in terms of knockdown for the imperfect binding sites is similar. M4, M5 and M6 always show strong knockdown, whereas M9, M10 and M11 show only loose down-regulation. Consulting the binding site sequences, the weak knockdown can be addressed to bulges in the supplementary region or complete lack of the 3' region of the binding site. Still high strength could be maintained due to only single nucleotide exchanges in the central region of the binding site.

raw data

Media:Plate1 process H1.xls Media:Plate2 process H1.xls Media:Plate3 process H1.xls Media:Haat 20101022 M1-M4 ctrl H1.xls Media:Haat 20101026 M5-M8 ctrl H1.xls Media:Haat 20101026 M9M22 ctrl H1.xls Media:HAAT H1 final.xls Media:Plate1 process U6 haat.xls Media:Plate2 process U6 haat.xls Media:Plate3 process U6 haat.xls Media:Haat 20101026 plate2 U6.xls Media:Haat 20101026 plate1 U6.xls Media:Haat 20101026 plate3 U6.xls Media:HAAT U6 final.xls



The miTuner was assembled out of different parts. Cloning was done following standard protocols.

Since the miTuner was constructed initially for Dual Luciferase Assay assay, this was the method of choice for tuning quantification.


Eulalio, A., Huntzinger, E., and Izaurralde, E. (2008). Getting to the root of miRNA-mediated gene silencing. Cell 132, 9-14. Bartel, D.P. (2004). MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297.

working modes

The synthetic miR Kit can be applied in three different ways:

I) Tuning: adjusting the expression
of the GOI by expressing a synthetic microRNA in the target cell/tissue

II) Off-Targeting: switching OFF the expression
of the GOI in case a certain endogenous microRNA is present in the target cell/tissue

III) On-Targeting: switching ON the expression
of the GOI in case a certain endogenous microRNA is present in the target cell/tissue

miTuner plasmid

simple tuning procedure


  • digestion of miR Kit construct with BamHI
  • cloning into viral backbone (e. g. pBS_U6)
  • virus production
  • infection of cells
  • achievement of specific target cell tropism

→ further improvement of gene expression tuning