DNA is inserted, replaced, or removed from a genome using artificially engineered nucleases, or "molecular scissors". The nucleases make specific double-strand breaks (DSBs) at desired places in the genome. The cell’s own mechanisms repair the induced break(s) by natural processes.
To understand the function of a gene or a protein one interferes with it in a sequence-specific way, and watches its effects on the organism. However, in some organisms it is difficult or impossible to do site-specific mutation. Therefore more indirect methods have to be used. Examples are:
- Silencing the gene of interest by short RNA interference (siRNA). Yet gene disruption by siRNA can be variable and incomplete.
- Genome editing with nucleases such as ZFN. This is different from siRNA. The engineered nuclease (the enzyme which cuts the DNA) is able to modify DNA-binding. Therefore it can in principle cut any targeted position in the genome, and introduce change the sequences for genes which cannot be specifically targeted by conventional RNAi.
In 2017 this system was announced as one of the biggest scientific achievements of the year. Cas9 is an enzyme which with a guide RNA, can put a new sequence of DNA into a genome. Sir John Skehel said "That might allow you to knock out a particular gene in a cell, or introduce a particular gene, or correct a particular mutated gene that you want to work better".
- sometimes "genome editing with engineered nucleases" (GEEN)
- The four types are: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), the CRISPR/Cas system, and engineered meganuclease re-engineered homing endonucleases.
- Esvelt, KM.; Wang, HH. (2013). "Genome-scale engineering for systems and synthetic biology". Mol Syst Biol. 9 (1): 641. doi:10.1038/msb.2012.66. PMC 3564264. PMID 23340847.
- Tan W.S.; et al. (2012). "Precision editing of large animal genomes". Adv Genet. 80: 37–97. doi:10.1016/B978-0-12-404742-6.00002-8. PMC 3683964. PMID 23084873.
- Puchta, H.; Fauser, F. (2013). "Gene targeting in plants: 25 years later". Int. J. Dev. Biol. 57: 629–637. doi:10.1387/ijdb.130194hp.
- Fire A. et al 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (6669), 806-811 (1998).
- Method of the Year 2011. Nat Meth 9 (1), 1-1.
- Gallagher, James 2015. Dawn of gene-editing medicine? BBC News Health. 
- Gallagher, James 2016. Scientists get 'gene editing' go-ahead. BBC News Health. 
- The biggest scientific developments of 2017, according to two scientists at the Royal Society of London.