Difference between revisions of "DNA Synthesizer"
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===Enzymatic Synthesis Chemistry=== | ===Enzymatic Synthesis Chemistry=== | ||
| − | DNA synthesis is currently done using the [https://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Synthetic_cycle 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. | + | DNA synthesis is currently done using the [https://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Synthetic_cycle 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. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846215/ TdT is one possible enzyme to consider,] and has previously been [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735642/pdf/11693_2009_Article_9023.pdf 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: | Enzymatic DNA synthesis would be a great alternative way to synthesize DNA in space, for the following reasons: | ||
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===Microfluidic Synthesizer Design=== | ===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. Good things to know about when designing a device like this: [https://en.wikipedia.org/wiki/Diaphragm_pump diaphragm pumps], [https://en.wikipedia.org/wiki/Solenoid_valve solenoid valves], and of course [https://en.wikipedia.org/wiki/Microfluidics microfluidics in general]. | + | 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 [[http://scholarbank.nus.edu.sg/bitstream/handle/10635/20904/WangC.pdf?sequence=1 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: [https://en.wikipedia.org/wiki/Diaphragm_pump diaphragm pumps], [https://en.wikipedia.org/wiki/Solenoid_valve solenoid valves], and of course [https://en.wikipedia.org/wiki/Microfluidics microfluidics in general]. |
===Reassembly Chemistry and Algorithm=== | ===Reassembly Chemistry and Algorithm=== | ||
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==Inspiration and Research== | ==Inspiration and Research== | ||
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===History of DNA Synthesizer Idea in SSI=== | ===History of DNA Synthesizer Idea in SSI=== | ||
The idea of a DNA synthesizer for space has been floating around SSI for some time. [[John Cumbers - Synthetic Biology | 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. | The idea of a DNA synthesizer for space has been floating around SSI for some time. [[John Cumbers - Synthetic Biology | 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. | ||
Revision as of 22:55, 18 October 2016
This biology-related article is a stub. You can help SSI by expanding it.
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.