DNA Synthesizer

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Biology Team's Pilot Project: A DNA Synthesizer for Space.

SSI Bio 2016 Pilot Project

SSI Bio is launching 2016 by sending a DNA synthesizer into space. For information on how to join the project, join the SSI Slack and go to the #biology channel, and read information on how to get Wet Lab Access on this wiki.

Components of the Synthesis Project

SSI Bio will be breaking up this DNA synthesizer project into several smaller subteams to tackle each critical component of the synthesizer.

Enzymatic Synthesis Chemistry

DNA synthesis is currently done using the phosphoramidite method. However, phosphoramidite chemistry produced large volumes of hazardous waste, requires precise chemical conditions, and is limited to producing short strands of DNA (oligonucleotides) on the order of ~100 basepairs. Most genes of interest are in the ~5,000 basepair range, so current synthesis methods cannot create a gene-length piece of DNA without further processing. TdT is one possible enzyme to consider, and has previously been the subject of some prior theoretical work.

Enzymatic DNA synthesis would be a great alternative way to synthesize DNA in space, for the following reasons:

Safety, Non-flammability, Non-toxicity

Most enzymatic reagents could in theory be aqueous solutions, unlike the acetonitrile organic solvents typically used in phosphoramidite chemistry.

Recyclability, On-Site Reagent Synthesis

If most of the reagents used are enzymes, then in theory these enzymes could be made by bacteria and then purified on site. This might mean that reagents could be produced, and modified, by the machine itself.

Improved Speed and Efficiency

It may be possible that an enzymatic method could improve the speed and efficiency of synthesizing DNA in space. This would be split into two effects. First, being able to make longer strands of DNA (oligonucleotides) would mean that the final product could be composed of fewer parts, which makes the creation of algorithms and strategies for reassembling this DNA to become much easier. Second, being able to make longer strands of DNA faster would cut down substantially on the complexity and time involved with synthesizing DNA.

Safe Phosphoramidite Chemistry

A more conventional alternative to aiming for enzymatic synthesis would be to try to adjust conventional phosphoramidite chemistry to be safer for use in space. This might involve creating a system that can synthesize DNA using safer organic solvents and less toxic reagents.

Microfluidic Synthesizer Design

To fit all of these fluidic parts into a small enough payload, we have to make everything quite small. Microfluidics is a good way to do this. Similar oligonucleotide synthesizers that don't quite fit our needs [have been made in the past, although our final design will most likely look different. Good things to know about when designing a device like this: diaphragm pumps, solenoid valves, and of course microfluidics in general.

Reassembly Chemistry and Algorithm

Our chemistry may look something like Polymerase Chain Assembly, also called Assembly PCR.

DNA Product Verification

Once a strand of DNA is made, we will need to check to make sure that it is the correct desired sequence. One possible strategy comes from this paper - essentially tagging oligo and looking for fluoresence as a sign that homology was sufficiently similar to produce a result.

Effects of Space on Synthesizer

Physical Stress of Launch

Similar to any other payload, our DNA synthesizer will have to be durable enough to withstand the stresses and forces associated with launch.

Payload Size and Power Constraints

We'd like to fit our synthesizer into a 10 centimeter cube, so that it could be launched on a CubeSat or another standardized research payload.

Shielding Requirements

We're not sure what kind of shielding we need! UV radiation can have damage DNA through a process called Direct DNA damage that can lead to thymine or pyrimidine dimers. This is what causes sunburn, and it's why your skin can tan to help block out UVB.

Communication from Device

Depending on our strategy for launching to space, communication from our device to some sort of receiver we can listen to involves a number of interesting questions. How do we return the message that synthesis has been carried out successfully? Will the message describe the sequence of the product created, or a simple boolean yes or no?

Inspiration and Research

History of DNA Synthesizer Idea in SSI

The idea of a DNA synthesizer for space has been floating around SSI for some time. One of the earliest recordings stretches back to 2013, in a talk given John Cumbers. John Cumbers was also consulted during the initial conception and planning of the project in the summer of 2015.