Editing DNA sequencing (section)

==== Microfluidic Systems ====
There are two main microfluidic systems that are used to sequence DNA; [[Droplet-based microfluidics|droplet based microfluidics]] and [[digital microfluidics]]. Microfluidic devices solve many of the current limitations of current sequencing arrays.

Abate et al. studied the use of droplet-based microfluidic devices for DNA sequencing.<ref name=":3">{{cite journal | vauthors = Abate AR, Hung T, Sperling RA, Mary P, Rotem A, Agresti JJ, Weiner MA, Weitz DA | display-authors = 6 | title = DNA sequence analysis with droplet-based microfluidics | journal = Lab on a Chip | volume = 13 | issue = 24 | pages = 4864–9 | date = December 2013 | pmid = 24185402 | pmc = 4090915 | doi = 10.1039/c3lc50905b }}</ref> These devices have the ability to form and process picoliter sized droplets at the rate of thousands per second. The devices were created from [[Polydimethylsiloxane|polydimethylsiloxane (PDMS)]] and used Forster resonance energy transfer, [[Förster resonance energy transfer|FRET assays]] to read the sequences of DNA encompassed in the droplets. Each position on the array tested for a specific 15 base sequence.<ref name=":3" />

Fair et al. used digital microfluidic devices to study DNA [[pyrosequencing]].<ref name=":4">{{Cite journal| vauthors = Fair RB, Khlystov A, Tailor TD, Ivanov V, Evans RD, Srinivasan V, Pamula VK, Pollack MG, Griffin PB, Zhou J |date= January 2007 |title=Chemical and Biological Applications of Digital-Microfluidic Devices |journal=IEEE Design & Test of Computers|volume=24|issue=1|pages=10–24|doi=10.1109/MDT.2007.8 |hdl= 10161/6987 |citeseerx=10.1.1.559.1440 |s2cid= 10122940 }}</ref> Significant advantages include the portability of the device, reagent volume, speed of analysis, mass manufacturing abilities, and high throughput. This study provided a proof of concept showing that digital devices can be used for pyrosequencing; the study included using synthesis, which involves the extension of the enzymes and addition of labeled nucleotides.<ref name=":4" />

Boles et al. also studied pyrosequencing on digital microfluidic devices.<ref name=":5">{{cite journal | vauthors = Boles DJ, Benton JL, Siew GJ, Levy MH, Thwar PK, Sandahl MA, Rouse JL, Perkins LC, Sudarsan AP, Jalili R, Pamula VK, Srinivasan V, Fair RB, Griffin PB, Eckhardt AE, Pollack MG | display-authors = 6 | title = Droplet-based pyrosequencing using digital microfluidics | journal = Analytical Chemistry | volume = 83 | issue = 22 | pages = 8439–47 | date = November 2011 | pmid = 21932784 | pmc = 3690483 | doi = 10.1021/ac201416j }}</ref> They used an electro-wetting device to create, mix, and split droplets. The sequencing uses a three-enzyme protocol and DNA templates anchored with magnetic beads. The device was tested using two protocols and resulted in 100% accuracy based on raw pyrogram levels. The advantages of these digital microfluidic devices include size, cost, and achievable levels of functional integration.<ref name=":5" />

DNA sequencing research, using microfluidics, also has the ability to be applied to the [[RNA-Seq|sequencing of RNA]], using similar droplet microfluidic techniques, such as the method, inDrops.<ref>{{cite journal | vauthors = Zilionis R, Nainys J, Veres A, Savova V, Zemmour D, Klein AM, Mazutis L | title = Single-cell barcoding and sequencing using droplet microfluidics | journal = Nature Protocols | volume = 12 | issue = 1 | pages = 44–73 | date = January 2017 | pmid = 27929523 | doi = 10.1038/nprot.2016.154 | s2cid = 767782 }}</ref> This shows that many of these DNA sequencing techniques will be able to be applied further and be used to understand more about genomes and transcriptomes.