Editing DNA sequencing (section)

==== Nanopore DNA sequencing ====
{{Main|Nanopore sequencing}}
The DNA passing through the nanopore changes its ion current. This change is dependent on the shape, size and length of the DNA sequence. Each type of the nucleotide blocks the ion flow through the pore for a different period of time. The method does not require modified nucleotides and is performed in real time. Nanopore sequencing is referred to as "[[Third-generation sequencing|third-generation]]" or "long-read" sequencing, along with SMRT sequencing.

Early industrial research into this method was based on a technique called 'exonuclease sequencing', where the readout of electrical signals occurred as nucleotides passed by [[hemolysin|alpha(α)-hemolysin]] pores covalently bound with [[cyclodextrin]].<ref>{{cite journal | vauthors = Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H | title = Continuous base identification for single-molecule nanopore DNA sequencing | journal = Nature Nanotechnology | volume = 4 | issue = 4 | pages = 265–70 | date = April 2009 | pmid = 19350039 | doi = 10.1038/nnano.2009.12 | bibcode = 2009NatNa...4..265C }}</ref> However the subsequent commercial method, 'strand sequencing', sequenced DNA bases in an intact strand.

Two main areas of nanopore sequencing in development are solid state nanopore sequencing, and protein based nanopore sequencing. Protein nanopore sequencing utilizes membrane protein complexes such as α-hemolysin, MspA (''[[Mycobacterium smegmatis]]'' Porin A) or CssG, which show great promise given their ability to distinguish between individual and groups of nucleotides.<ref name="Torre 2012">{{cite journal|year=2012|title=Fabrication and characterization of solid-state nanopore arrays for high-throughput DNA sequencing|journal=Nanotechnology|volume=23|issue=38|page=385308|bibcode=2012Nanot..23L5308D|doi=10.1088/0957-4484/23/38/385308|pmc=3557807|pmid=22948520|vauthors=dela Torre R, Larkin J, Singer A, Meller A}}</ref> In contrast, solid-state nanopore sequencing utilizes synthetic materials such as silicon nitride and aluminum oxide and it is preferred for its superior mechanical ability and thermal and chemical stability.<ref name="Pathak 2012">{{cite journal|year=2012|title=Double-functionalized nanopore-embedded gold electrodes for rapid DNA sequencing|url=https://zenodo.org/record/890231|journal=Applied Physics Letters|volume=100|issue=2|page=023701|doi=10.1063/1.3673335|vauthors=Pathak B, Lofas H, Prasongkit J, Grigoriev A, Ahuja R, Scheicher RH|bibcode=2012ApPhL.100b3701P}}</ref> The fabrication method is essential for this type of sequencing given that the nanopore array can contain hundreds of pores with diameters smaller than eight nanometers.<ref name="Torre 2012" />

The concept originated from the idea that single stranded DNA or RNA molecules can be electrophoretically driven in a strict linear sequence through a biological pore that can be less than eight nanometers, and can be detected given that the molecules release an ionic current while moving through the pore.  The pore contains a detection region capable of recognizing different bases, with each base generating various time specific signals corresponding to the sequence of bases as they cross the pore which are then evaluated.<ref name="Pathak 2012" /> Precise control over the DNA transport through the pore is crucial for success. Various enzymes such as exonucleases and polymerases have been used to moderate this process by positioning them near the pore's entrance.<ref name="Korlach 2008">{{cite journal|year=2008|title=Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures|journal=Proceedings of the National Academy of Sciences|volume=105|issue=4|pages=1176–81|bibcode=2008PNAS..105.1176K|doi=10.1073/pnas.0710982105|pmc=2234111|pmid=18216253|vauthors=Korlach J, Marks PJ, Cicero RL, Gray JJ, Murphy DL, Roitman DB, Pham TT, Otto GA, Foquet M, Turner SW|doi-access=free}}</ref>