Assay Validation

For a detailed, graphical explanation of the MaGellin work flow, please download the MaGellin Workflow Specifications Sheet, which includes all of the steps in the MaGellin workflow.


Our Team’s Solution. In order to address the challenges associated with developing new site-specific methylase proteins, our team proposed several different strategies. First, we proposed a migration away from mammalian systems and into E. coli. E. coli does not have a native cytosine methyltransferase, and therefore offers a noise-free environment for methylation studies. Any methylation of CpG sites in E Coli would be a product of a candidate engineered protein rather than the native organism. Second, we envisioned a modular one-plasmid system that can be employed for quickly and cheaply screening the activity and specificity of any DNA binding domain – methyltransferase fusion protein. This plasmid-based methylation assay is called MaGellin.





Plasmid Features. To accommodate the MaGellin assay, our team designed a plasmid with several key features:

1. CpG Methyltransferase (M.SssI) with a generic linker sequence in the cloning site. For a working fusion protein and assay, only a DNA binding domain must be cloned into the plasmid. This inherently standardizes MaGellin and lessens the time a user of the assay must spend cloning.
2. Multiple cloning site downstream of T7 promoter for orthogonal expression of fusion protein in T7 Express competent E. coli.
3. Cloning site for a smaller DNA sequence, specific to the fusion protein being screened – named the “target site”, where the protein will bind. This can be the binding site for a CRISPR-Cas, TALE, Zinc Finger, or transcription factor
4. AvaI restriction site 4 bases downstream of the target site – the AvaI restriction enzyme is blocked by methylated CpG sites, thus screening for site specific methylation becomes equivalent to screening for AvaI digestion
5. AvaI restriction site sufficiently further downstream of the target site – named the off-target site. This site screens for non-specific DNA methylation as it is spatially removed from where the fusion protein binds to the plasmid.
6. XbaI site for linearization of the plasmid. Linearizing the plasmid simplifies analysis of the AvaI digestion by gel electrophoresis.
7. Validated bisulfite conversion primer binding sites, so users do not need to go through the time-consuming primer design process if they choose to fortify MaGellin’s results with bisulfite sequencing results
8. sgRNA cloning site for users who want to target a CRISPR-Cas binding domain. The sgRNA is constitutively expressed and can be swapped by restriction digest.
9. Validated bisulfite conversion primers for users who choose to advance to bisulfite sequencing, for even higher resolution in detecting methylation, after proving their enzyme’s efficacy with our MaGellin assay.
10. Kanamycin resistance as a selection marker

Noiseless Chassis. After cloning this plasmid, we faced the challenge of choosing the correct cell line for the assay. We chose to transform into T7 Express cells for several reasons:

1. T7 RNA Polymerase in the lac operon allows us to turn on expression of fusion protein after induction with IPTG
2. In the T7 Express cell line, genes for several restriction enzymes known to target methylated DNA are knocked out (McrA-, McrBC-, EcoBr-m-, Mrr-). This ensures that our assay plasmid is not cleaved in vivo. Results are difficult, if not impossible, to interpret in the commonly used BL21 cell line.