Team:CU-Boulder/Project/Kit/RestrictionEnzymes

The main focus of our project was to create the constructs and purification methods necessary to produce and isolate the restriction enzyme EcoRI. EcoRI is commonly used for research and is one of the primary restriction endonucleases used in the Biobrick standard. Synthesizing a plasmid containing the gene for EcoRI and producing a simple purification method would provide a cheaper option for obtaining the enzyme.

Bacteria lack an immune system so rely on restriction-modification (R-M) systems for defense against foreign viruses. The first enzyme involved in the system is the restriction endonuclease (REase). It is specific to a single DNA sequence that is typically four to eight nucleotides in length and is usually palindromic. When the REase recognizes this sequence, it will cleave both strands of the DNA at the backbone, resulting in “blunt” or “sticky” ends, depending on the exact function of the specific enzyme. When a bacterial cell is infected by a virus, the REase will bind to and cut its recognition sequence if present in the virus DNA; thereby, hindering or stopping the effects of the virus on the host. But this process is not specific to host or virus DNA.

To protect their own genetic information, bacterial cells also produce a methyltransferase (MTase). This enzyme is specific to the same site as its corresponding REase, but instead of cutting the DNA at this site, it tags the DNA with a methyl group, which sterically inhibits the binding of the REase. In type I R-M systems, the REase and MTase are apart of a single enzyme whereas in the simpler, type II system, they are found as two individual enzymes. When isolated, the REase from a type II system can be used independently of the methylase to digest DNA for analysis and synthesis making these enzymes a valuable tool in synthetic biology.

In order to produce restriction enzymes in vivo, it is necessary to protect the host DNA from auto-restriction and cell death. This is possible by expressing an excess of the MTase in relation to the REase that is being produced within the cell. Since REases form dimers (whereas MTases are monomeric) in their active form there is a natural lag phase before enzymatic activity is observed. This also implies a 2:1 excess of active MTase within the cell if both enzymes are expressed at the same rate. We intend to create a c onstruct that expresses both enzymes on the same promoter in order to test if MTase can effectively protect the cell's DNA through this mechanism alone. It is likely that this will not provide the MTase with the advantage needed to sufficiently protect the host DNA from auto-restriction. It may be possible for the MTase to out compete the REase by simply expressing the MTase on a strong constitutive promoter and the MTase on a weak constitutive promoter. Alternatively, it should be possible to express the MTase on a constitutive promoter and use an inducible promoter system to delay the expression of the REase until the host genome is protected.

In addition to successfully producing restriction enzymes, it is also necessary to separate the MTase from the REase in order for the REase to be functional for the purposes of synthetic biology.

We ordered 500bp segments of DNA that, when connected through a Gibson Assembly, contained the full sequence of our genes of interest (EcoRI and EcoRI methylase). After our first failed attempt, we used a PCR purification kit to clean the samples. Smearing in later gels disappeared while our expected bands became more prominent.

Using PCR with the flanking primers, we isolated and amplified the desired gene from the Gibson Assembly. These primers also included tails that added AgeI and XbaI cut-sites, thereby making our parts Freiburg compatible. Multiple bands appeared during gel electrophoresis, most likely due to the DNA blocks in the Gibson Assembly annealing incorrectly, especially in the EcoRI Methylase where three 500bp DNA blocks were required. To remedy this problem, we gel extracted the band of the correct size to isolate it from the other products. The resulting DNA was at such a low concentration that a second round of PCR was required and a subsequent purification.

In order to synthesize a plasmid containing the desired genes, we digested EcoRI, its methylase, and a previously made Freiburge pSB1C3 backbone with XbaI and AgeI. All three DNA sequences were extracted and purified with an extraction kit.

We then ligated EcoRI into the pSB1C3 backbone and EcoRI methylase into the pSB1C3 backbone at 16C for 12 hours. The ligation products were then transformed into DH10B cells and selected for on Chloramphenicol plates. We received over 200 colonies for EcoRI and about 150 colonies for EcoRI methylase.

The samples with the correct band size on the gel were sequenced. Both EcoRI and EcoRI methylase were sequence confirmed; however, we found a nonsense mutation in the methylase, which rendered it non-functional. At this point, we successfully produced and submitted a Freiburg 1C3 backbone with an EcoRI coding gene.