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From 2012.igem.org

Contents 1 4. Safety suggestions 1.1 Short term: Standard Kill-switch 1.2 Long run: Unnatural DNA 1.3 References 1.3.1 Safety

4. Safety suggestions

Synthetic biology is a field of science that is subject to intrinsic hazards to both the researcher, the public and the environment. Many of these dangers are well documented and prevented in different ways, like working in containment labs or using strains of E. coli that are unable to grow outside of laboratory conditions. However, as our supply of organisms, genes and functions that can be used grows, so does the probability of accidents. All over the world, researchers add functions to organisms that were previously not existent. With large areas of metabolic pathways and cross-talk interactions still unknown, it is not hard to imagine the accidental creation of pollutants, super-fit micro-organisms or even pathogens. Combined with the risk of horizontal gene transfer, this may turn out to be a serious problem.

Short term: Standard Kill-switch

To overcome the risk of GMO living freely in the environment, so-called ‘kill-switches’ have been developed. These are devices that actively kill the host, unless blocked by a specific, rare chemical. Assuming this chemical will not be present in sufficient quantities unless actively provided, such a system ensures containment of the GMO. However, such systems are only rarely actually applied. Take our project as an example: We modify bacteria to make certain proteins for us, but as we don’t ever want to remove these bacteria from the lab or release them in any way, we don’t deem it necessary to go through the effort of implementing a kill-switch. All over the world, the majority of GMO-related science projects is like this. But somewhere, someday, something can go wrong and someone will wish the kill-switch had been there after all.

For our iGEM project, inserting a kill-switch to go through the standard lab procedures we used had indeed been (literally) an overkill. However, had there been standard E. coli strains available in our lab that had a kill-switch built in already, we certainly would have used them! Most regularly used laboratory strains of E. coli have lost their ability to live outside of our well-defined growth media due to genetic defects. This is a very convenient, passive containment mechanism. Inserting a kill-switch next to this mechanism adds an active containment mechanism and makes E. coli double contained in our media. This adds an extra evolutionary barrier between GMO and the environment and therefore, we believe that all laboratories should work with standard lab stains that have this mechanism. Since E. coli kill-switches have already been developed and are freely available via the Parts Registry, this should not be too difficult to implement. Yet by increasing the safety of all those projects that by themselves don’t seem to need extra safety measures, the general safety of researchers, public and environment worldwide should be dramatically increased.

Long run: Unnatural DNA

In the long run, we can come up with even better systems to isolate our synthetic constructs from the natural environment. Eventually, we think that all synthetic biology should be disconnected from the natural world. This would require a new biological language that is unreadable for ‘normal’ organisms. Schmidt and de Lorenzo[1] describe a variety of systems that are being developed to approach this end goal. Ribosomes and tRNA’s have been developed that recognize nucleic acid quadruplets instead of triplets, DNA-like polymers have been made that bear an unnatural modification on either the bases or the backbone itself and many more very interesting endeavors are described in this paper.

We were struck by a certain example, where DNA was developed that instead of the four natural bases ATGC consisted of six bases ATGCPZ. Polymerases were developed that could amplify this extended genetic code[2]. We think that if two unnatural bases can be incorporated, then maybe so can four bases or even more. More importantly: If a polymerase can be developed that can handle these unnatural polymers like it would normal DNA, then maybe so can other enzymes!

We can envision a future in which synthetic biology is based on unnatural genetic material, encoded using four (or why not more?) nucleotide bases that are unknown to natural biology. This would create an almost impassable barrier between genetic constructs and natural organisms, creating for the first time a Certainty of Containment and changing the definition of Synthetic Biology for all times.

References

1. Schmidt, M. and V. de Lorenzo, Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology. FEBS Letters, 2012. 586(15): p. 2199-2206.

2. Yang, Z., et al., Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System. Journal of the American Chemical Society, 2011. 133(38): p. 15105-15112.

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Safety

Introduction

1. General safety

2. Virus-related safety

3. Regulations

4. Suggestions

5. Safety of application