Editing Recombinant DNA (section)

==Properties of organisms containing recombinant DNA==
In most cases, organisms containing recombinant DNA have apparently normal [[phenotype]]s. That is, their appearance, behavior and metabolism are usually unchanged, and the only way to demonstrate the presence of recombinant sequences is to examine the DNA itself, typically using a polymerase chain reaction (PCR) test.<ref name="isbn1-4051-1121-6">{{cite book |author=Brown, Terry |title=Gene Cloning and DNA Analysis: an Introduction |publisher=Blackwell Pub |location=Cambridge, MA |year=2006 |isbn=978-1-4051-1121-8 }}{{pn|date=December 2024}}</ref> Significant exceptions exist, and are discussed below.

If the rDNA sequences encode a gene that is expressed, then the presence of RNA and/or protein products of the recombinant gene can be detected, typically using [[RT-PCR]] or [[Western blot|western hybridization]] methods.<ref name="isbn1-4051-1121-6"/> Gross phenotypic changes are not the norm, unless the recombinant gene has been chosen and modified so as to generate biological activity in the host organism.<ref name="pmid|10634784">{{Cite journal
| last1 = Ye | first1 = X.
| last2 = Al-Babili | first2 = S.
| last3 = Klöti | first3 = A.
| last4 = Zhang | first4 = J.
| last5 = Lucca | first5 = P.
| last6 = Beyer | first6 = P.
| last7 = Potrykus | first7 = I.
| title = Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm
| journal = Science
| volume = 287
| issue = 5451
| pages = 303–305
| year = 2000
| pmid = 10634784 | doi=10.1126/science.287.5451.303
| bibcode = 2000Sci...287..303Y
}}</ref> Additional phenotypes that are encountered include toxicity to the host organism induced by the recombinant gene product, especially if it is [[Protein expression (biotechnology)|over-expressed]] or expressed within inappropriate cells or tissues.{{cn|date=October 2023}}

In some cases, recombinant DNA can have deleterious effects even if it is not expressed. One mechanism by which this happens is [[Insertion (genetics)|insertional inactivation]], in which the rDNA becomes inserted into a host cell's gene. In some cases, researchers use this phenomenon to "[[Gene knockout|knock out]]" genes to determine their biological function and importance.<ref name="pmid1591000">{{Cite journal
| last1 = Koller | first1 = B. H.
| last2 = Smithies | first2 = O.
| doi = 10.1146/annurev.iy.10.040192.003421
| title = Altering Genes in Animals by Gene Targeting
| journal = Annual Review of Immunology
| volume = 10
| pages = 705–730
| year = 1992
| pmid = 1591000
}}</ref> Another mechanism by which rDNA insertion into chromosomal DNA can affect gene expression is by inappropriate activation of previously unexpressed host cell genes. This can happen, for example, when a recombinant DNA fragment containing an active promoter becomes located next to a previously silent host cell gene, or when a host cell gene that functions to restrain gene expression undergoes insertional inactivation by recombinant DNA.{{cn|date=October 2023}}