Editing DNA extraction (section)

== Method selection ==
Some of the most common DNA extraction methods include [[Phenol-chloroform extraction|organic extraction]], [[Chelex 100|Chelex extraction]], and [[solid phase extraction]].<ref>https://journals.sagepub.com/doi/abs/10.1177/10815589251327503</ref><ref name="Elkins2013">{{cite book |last1=Elkins |first1=Kelly M. |title=Forensic DNA Biology |year=2013 |isbn=9780123945853 |pages=39–52 |chapter=DNA Extraction |doi=10.1016/B978-0-12-394585-3.00004-3}}</ref> These methods consistently yield isolated DNA, but they differ in both the quality and the quantity of DNA yielded. When selecting a DNA extraction method, there are multiple factors to consider, including cost, time, safety, and risk of contamination.

[[Phenol-chloroform extraction|Organic extraction]] involves the addition of incubation in multiple different chemical solutions;<ref name=Elkins2013/> including a [[Cell lysis|lysis]] step, a phenol-chloroform extraction, an [[ethanol precipitation]], and washing steps. Organic extraction is often used in laboratories because it is cheap, and it yields large quantities of pure DNA. Though it is easy, there are many steps involved, and it takes longer than other methods. It also involves the unfavorable use of the toxic chemicals [[phenol]] and [[chloroform]], and there is an increased risk of contamination due to transferring the DNA between multiple tubes.<ref name=":1">{{Cite book |last=Butler |first=John M |title=Forensic DNA typing : biology, technology, and genetics of STR markers |date=2005 |publisher=Elsevier Academic Press |isbn=9780080470610 |edition=2nd |location=Amsterdam |oclc=123448124}}</ref> Several protocols based on organic extraction of DNA were effectively developed decades ago,<ref>{{cite journal |doi=10.1016/S0022-2836(61)80047-8 |title=A procedure for the isolation of deoxyribonucleic acid from micro-organisms |journal=Journal of Molecular Biology |volume=3 |issue=2 |pages=208–IN1 |year=1961 |last1=Marmur |first1=J. }}</ref> though improved and more practical versions of these protocols have also been developed and published in the last years.<ref>{{Cite journal |last=Salvà Serra |first=Francisco |last2=Salvà-Serra |first2=Francisco |last3=Svensson-Stadler |first3=Liselott |last4=Busquets |first4=Antonio |last5=Jaén-Luchoro |first5=Daniel |last6=Karlsson |first6=Roger |last7=R. B. Moore |first7=Edward |last8=Gomila |first8=Margarita |date=2018-08-09 |title=A protocol for extraction and purification of high-quality and quantity bacterial DNA applicable for genome sequencing: a modified version of the Marmur procedure. |url=https://www.nature.com/protocolexchange/protocols/6915 |journal=Protocol Exchange |doi=10.1038/protex.2018.084 |issn=2043-0116|doi-access=free }}</ref>

[[Chelex 100|The chelex extraction]] method involves adding the Chelex resin to the sample, boiling the solution, then vortexing and centrifuging it. The cellular materials bind to the Chelex beads, while the DNA is available in the [[Precipitation (chemistry)|supernatant]].<ref name=":1" /> The Chelex method is much faster and simpler than organic extraction, and it only requires one tube, which decreases the risk of DNA contamination. Unfortunately, Chelex extraction does not yield as much quantity and the DNA yielded is single-stranded, which means it can only be used for [[Polymerase chain reaction|PCR]]-based analyses and not for [[Restriction fragment length polymorphism|RFLP]].<ref name=":1" />

[[Solid phase extraction]] such as using a [[Spin column-based nucleic acid purification|spin-column-based extraction]] method takes advantage of the fact that DNA binds to [[Silica gel|silica]]. The sample containing DNA is added to a column containing a silica gel or silica beads and [[Chaotropic agent|chaotropic]] salts. The chaotropic salts disrupt the hydrogen bonding between strands and facilitate the binding of the DNA to silica by causing the nucleic acids to become hydrophobic. This exposes the phosphate residues so they are available for adsorption.<ref>{{Cite book |last=Li |first=Richard |title=Forensic biology |date=11 March 2015 |publisher=CRC Press |isbn=978-1439889725 |edition=2nd |location=Boca Raton |oclc=907517669}}</ref> The DNA binds to the silica, while the rest of the solution is washed out using ethanol to remove chaotropic salts and other unnecessary constituents.<ref name=Elkins2013/> The DNA can then be rehydrated with aqueous low-salt solutions allowing for [[elution]] of the DNA from the beads.

This method yields high-quality, largely double-stranded DNA which can be used for both [[Polymerase chain reaction|PCR]] and [[Restriction fragment length polymorphism|RFLP]] analysis. This procedure can be automated<ref name=":1" /> and has a high throughput, although lower than the [[Phenol-chloroform extraction|phenol-chloroform method]]. This is a one-step method i.e. the entire procedure is completed in one tube. This lowers the risk of contamination making it very useful for the forensic extraction of DNA. Multiple solid-phase extraction commercial kits are manufactured and marketed by different companies; the only problem is that they are more expensive than organic extraction or Chelex extraction.