Difference between revisions of "DNA Synthesizer"
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[[Category:Biology]] | [[Category:Biology]] | ||
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Biology Team's Pilot Project: A DNA Synthesizer for Space. | Biology Team's Pilot Project: A DNA Synthesizer for Space. | ||
| − | ==SSI | + | ==SSI Biology Pilot Project== |
| − | + | The DNA synthesizer project was started in 2016 as SSI Biology Team's first project. For information on how to join the project, join the SSI Slack and go to the #biology channel. Read information on how to get [[Wet Lab Access]] on this wiki. | |
==Components of the Synthesis Project== | ==Components of the Synthesis Project== | ||
| − | SSI Bio will be breaking up this DNA synthesizer project into several smaller | + | SSI Bio will be breaking up this DNA synthesizer project into several smaller and more defined subcomponents. |
===Enzymatic Synthesis Chemistry=== | ===Enzymatic Synthesis Chemistry=== | ||
| − | Enzymatic DNA synthesis would be a great way to synthesize DNA in space, for the following reasons: | + | |
| + | DNA synthesis is currently done using the [https://en.wikipedia.org/wiki/Oligonucleotide_synthesis#Synthetic_cycle phosphoramidite method], which involves hazardous chemicals and solvents like acetonitrile. Phosphoramidite chemistry is also restricted to centralized synthesis facilities that are hard for scientists in remote locations (like space) to access reliably. Using [[enzymatic synthesis methods]] rather than phosphoramidites would enable small-scale distributed synthesis of short single strands of DNA (oligonucleotides) on the order of 100 base pairs. We are currently working with the enzyme [[Terminal Deoxynucleotidyl Transferase]] (TdT), which has previously been the subject of some prior [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735642/pdf/11693_2009_Article_9023.pdf 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==== | ====Safety, Non-flammability, Non-toxicity==== | ||
Most enzymatic reagents could in theory be aqueous solutions, unlike the acetonitrile organic solvents typically used in phosphoramidite chemistry. | Most enzymatic reagents could in theory be aqueous solutions, unlike the acetonitrile organic solvents typically used in phosphoramidite chemistry. | ||
| − | ====Recyclability, | + | ====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 | + | 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 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. | |
===Microfluidic Synthesizer Design=== | ===Microfluidic Synthesizer Design=== | ||
| − | To | + | To run a DNA synthesis reaction in a small autonomous payload, we need to precisely move tiny nanoliter-scale amounts of liquid. 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]. 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]. |
| + | |||
| + | We are currently designing and prototyping an autonomous fluid handling system based on [[Electrowetting on Dielectric]] (EWOD) technology. | ||
===Reassembly Chemistry and Algorithm=== | ===Reassembly Chemistry and Algorithm=== | ||
| + | Our oligonucleotides will likely be used directly in downstream applications (as PCR primers, for example), but they could also be put together into biologically functional genes. 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 and assembly. Our assembly chemistry may look something like [https://en.wikipedia.org/wiki/Polymerase_cycling_assembly Polymerase Chain Assembly, also called Assembly PCR]. | ||
===DNA Product Verification=== | ===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. [ | + | Once a strand of DNA is made, we will need to purify it, check to make sure that it is the correct desired sequence, and purify it for use in downstream applications. This verification can be done a variety of different ways in the lab, including [[Polyacrylamide Gel Electrophoresis]] (PAGE), [[Pyrosequencing]], [[Ligation and Sequencing]], or [https://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization MALDI-TOF Mass Spectrometry]. |
==Effects of Space on Synthesizer== | ==Effects of Space on Synthesizer== | ||
===Physical Stress of Launch=== | ===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. | 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 | + | ===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 [https://en.wikipedia.org/wiki/CubeSat CubeSat] | + | We'd like to fit our synthesizer into a 10 centimeter cube, so that it could be launched on and powered by a [https://en.wikipedia.org/wiki/CubeSat CubeSat] as a standardized research payload. To do this, we'll need to design and optimize our fluid handling system, microprocessor, power supply, temperature regulator, and verification technology with size and other constraints in mind. |
| − | === | + | ===Shielding Requirements=== |
We're not sure what kind of shielding we need! UV radiation can have damage DNA through a process called [https://en.wikipedia.org/wiki/Direct_DNA_damage 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. | We're not sure what kind of shielding we need! UV radiation can have damage DNA through a process called [https://en.wikipedia.org/wiki/Direct_DNA_damage 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? | 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? | ||
| − | ==History of DNA | + | ==Inspiration and Research== |
| − | The idea of a DNA synthesizer for space has been floating around SSI for some time. | + | |
| + | |||
| + | ===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 records stretches back to 2013, in a [[John Cumbers - Synthetic Biology |talk given by John Cumbers.]] John Cumbers was also consulted during the initial conception and planning of the project in the summer of 2015. | ||
Latest revision as of 05:54, 25 September 2017
Biology Team's Pilot Project: A DNA Synthesizer for Space.
SSI Biology Pilot Project
The DNA synthesizer project was started in 2016 as SSI Biology Team's first project. For information on how to join the project, join the SSI Slack and go to the #biology channel. 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 and more defined subcomponents.
Enzymatic Synthesis Chemistry
DNA synthesis is currently done using the phosphoramidite method, which involves hazardous chemicals and solvents like acetonitrile. Phosphoramidite chemistry is also restricted to centralized synthesis facilities that are hard for scientists in remote locations (like space) to access reliably. Using enzymatic synthesis methods rather than phosphoramidites would enable small-scale distributed synthesis of short single strands of DNA (oligonucleotides) on the order of 100 base pairs. We are currently working with the enzyme Terminal Deoxynucleotidyl Transferase (TdT), which 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 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.
Microfluidic Synthesizer Design
To run a DNA synthesis reaction in a small autonomous payload, we need to precisely move tiny nanoliter-scale amounts of liquid. Microfluidics is a good way to do this. Similar oligonucleotide synthesizers that don't quite fit our needs have been made in the past. Good things to know about when designing a device like this: diaphragm pumps, solenoid valves, and of course microfluidics in general.
We are currently designing and prototyping an autonomous fluid handling system based on Electrowetting on Dielectric (EWOD) technology.
Reassembly Chemistry and Algorithm
Our oligonucleotides will likely be used directly in downstream applications (as PCR primers, for example), but they could also be put together into biologically functional genes. 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 and assembly. Our assembly 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 purify it, check to make sure that it is the correct desired sequence, and purify it for use in downstream applications. This verification can be done a variety of different ways in the lab, including Polyacrylamide Gel Electrophoresis (PAGE), Pyrosequencing, Ligation and Sequencing, or MALDI-TOF Mass Spectrometry.
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 and powered by a CubeSat as a standardized research payload. To do this, we'll need to design and optimize our fluid handling system, microprocessor, power supply, temperature regulator, and verification technology with size and other constraints in mind.
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 records stretches back to 2013, in a talk given by John Cumbers. John Cumbers was also consulted during the initial conception and planning of the project in the summer of 2015.