Editing Molecular biology (section)

===Macromolecule blotting and probing===
The terms ''northern'', ''western'' and ''eastern'' blotting are derived from what initially was a molecular biology joke that played on the term ''[[Southern blot]]ting'', after the technique described by [[Edwin Southern]] for the hybridisation of blotted DNA. Patricia Thomas, developer of the RNA blot which then became known as the ''northern blot'', actually did not use the term.<ref>{{cite journal | vauthors = Thomas PS | title = Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 77 | issue = 9 | pages = 5201–5 | date = September 1980 | pmid = 6159641 | pmc = 350025 | doi = 10.1073/pnas.77.9.5201 | bibcode = 1980PNAS...77.5201T | doi-access = free }}</ref>

====Southern blotting====
{{main|Southern blot}}

Named after its inventor, biologist [[Edwin Southern]], the Southern blot is a method for probing for the presence of a specific DNA sequence within a DNA sample. DNA samples before or after [[restriction enzyme]] (restriction endonuclease) digestion are separated by gel electrophoresis and then transferred to a membrane by blotting via [[capillary action]]. The membrane is then exposed to a labeled DNA probe that has a complement base sequence to the sequence on the DNA of interest.<ref>{{cite journal |doi=10.1002/0471142735.im1006as06 |title=Southern Blotting |date=1993 |last1=Brown |first1=Terry |journal=Current Protocols in Immunology |volume=6 |pages=Unit 10.6A |pmid=18432697 }}</ref> Southern blotting is less commonly used in laboratory science due to the capacity of other techniques, such as [[Polymerase chain reaction|PCR]], to detect specific DNA sequences from DNA samples. These blots are still used for some applications, however, such as measuring [[transgene]] copy number in [[Genetically modified organism|transgenic mice]] or in the engineering of [[gene knockout]] [[Stem cell line|embryonic stem cell lines]].<ref name="Tian_2013"/>

====Northern blotting====
{{main|Northern blot}}
[[File:Northern blot diagram.png|thumb|Northern blot diagram]]
The northern blot is used to study the presence of specific RNA molecules as relative comparison among a set of different samples of RNA. It is essentially a combination of [[denaturing gel|denaturing RNA gel electrophoresis]], and a [[blot (biology)|blot]]. In this process RNA is separated based on size and is then transferred to a membrane that is then probed with a labeled [[complementarity (molecular biology)|complement]] of a sequence of interest. The results may be visualized through a variety of ways depending on the label used; however, most result in the revelation of bands representing the sizes of the RNA detected in sample. The intensity of these bands is related to the amount of the target RNA in the samples analyzed. The procedure is commonly used to study when and how much gene expression is occurring by measuring how much of that RNA is present in different samples, assuming that no post-transcriptional regulation occurs and that the levels of mRNA reflect proportional levels of the corresponding protein being produced. It is one of the most basic tools for determining at what time, and under what conditions, certain genes are expressed in living tissues.<ref>{{cite book |doi=10.1007/978-1-59745-248-9_7 |chapter=Northern Blotting Analysis |title=RNA |series=Methods in Molecular Biology |date=2011 |last1=Josefsen |first1=Knud |last2=Nielsen |first2=Henrik |volume=703 |pages=87–105 |pmid=21125485 |isbn=978-1-58829-913-0 }}</ref><ref>{{cite book | vauthors = He SL, Green R | title = Laboratory Methods in Enzymology: RNA | chapter = Northern blotting | volume = 530 | pages = 75–87 | date = 1 January 2013 | pmid = 24034315 | pmc = 4287216 | doi = 10.1016/B978-0-12-420037-1.00003-8 | isbn = 978-0-12-420037-1 }}</ref>

====Western blotting====
{{main|Western blot}}
A western blot is a technique by which specific proteins can be detected from a mixture of proteins.<ref name="Mahmood-2012" /> Western blots can be used to determine the size of isolated proteins, as well as to quantify their expression.<ref>{{Cite web|title=Western blot {{!}} Learn Science at Scitable|url=https://www.nature.com/scitable/definition/western-blot-288/|access-date=2021-11-25|website=www.nature.com|language=en}}</ref> In [[western blot]]ting, proteins are first separated by size, in a thin gel sandwiched between two glass plates in a technique known as [[SDS-PAGE]]. The proteins in the gel are then transferred to a [[polyvinylidene fluoride]] (PVDF), nitrocellulose, nylon, or other support membrane. This membrane can then be probed with solutions of [[antibody|antibodies]]. Antibodies that specifically bind to the protein of interest can then be visualized by a variety of techniques, including colored products, [[chemiluminescence]], or [[autoradiography]]. Often, the antibodies are labeled with enzymes. When a [[chemiluminescent]] [[Substrate (biochemistry)|substrate]] is exposed to the [[enzyme]] it allows detection. Using western blotting techniques allows not only detection but also quantitative analysis. Analogous methods to western blotting can be used to directly stain specific proteins in live [[cell (biology)|cells]] or [[biological tissue|tissue]] sections.<ref name="Mahmood-2012">{{cite journal | vauthors = Mahmood T, Yang PC | title = Western blot: technique, theory, and trouble shooting | journal = North American Journal of Medical Sciences | volume = 4 | issue = 9 | pages = 429–34 | date = September 2012 | doi = 10.4103/1947-2714.100998 | doi-broken-date = 1 November 2024 | doi-access = free | pmid = 23050259 | pmc = 3456489 }}</ref><ref>{{cite journal | vauthors = Kurien BT, Scofield RH | title = Western blotting | journal = Methods | volume = 38 | issue = 4 | pages = 283–93 | date = April 2006 | pmid = 16483794 | doi = 10.1016/j.ymeth.2005.11.007 }}</ref>

====Eastern blotting====
{{main|Eastern blot}}

The eastern blotting technique is used to detect [[post-translational modification]] of proteins. Proteins blotted on to the PVDF or nitrocellulose membrane are probed for modifications using specific substrates.<ref>{{cite journal | vauthors = Thomas S, Thirumalapura N, Crossley EC, Ismail N, Walker DH | title = Antigenic protein modifications in Ehrlichia | journal = Parasite Immunology | volume = 31 | issue = 6 | pages = 296–303 | date = June 2009 | pmid = 19493209 | pmc = 2731653 | doi = 10.1111/j.1365-3024.2009.01099.x }}</ref>