Base editing
Published
Some of the most useful differences between plants come down to a single letter of DNA. Base editing was built to change exactly one.
What is base editing?
Base editing is a gene-editing method that converts one DNA base into another at a chosen site, without cutting both strands of the DNA and without a donor template. It is steered to its target by a guide RNA.
What it is
Base editing was reported in 2016 as a way to convert one target DNA base into another in a programmable manner, without double-strand cleavage or a donor template [4]. The first base editors joined a CRISPR/Cas9 protein to a cytidine deaminase enzyme, turning a C into a T [4]. Adenine base editors, reported in 2017, convert an A-T pair into a G-C pair [10].
How it works
The editor keeps the guide RNA's ability to find a target but does not break the double helix [4]. It works within a window of about five DNA letters [4]. In later versions, a modified Cas9 nicks only the unedited strand, which steers the cell's own repair towards the intended change [4].
Use in crops
In 2017, researchers converted C to T at target sites in rice, wheat and maize plants, at frequencies of up to 43.48% [6]. In England, guidance for plant breeders notes that base editing makes the same type of genetic change that occurs naturally [9].
Limits
A 2019 whole-genome study in rice found that two cytosine base editors, but not an adenine base editor, caused substantial off-target single-letter changes across the genome [8]. A 2021 whole-genome study of base-edited tomato found no evidence of true off-target mutations from the editor it tested [7]. Results depend on the editor.
How it compares with the other four
Base editing is one of the five methods covered here. Prime editing also avoids cutting both strands, and can make a wider range of changes [5]. CRISPR/Cas9, TALENs and zinc finger nucleases cut both strands and rely on the cell's repair [1][2][3].
| Method | How it finds its target | What it does to the DNA | First described |
|---|---|---|---|
| CRISPR/Cas9 | A guide RNA pairs with the target sequence [1] | Cuts both DNA strands at the chosen site [1] | 2012 [1] |
| TALENs | A custom TAL effector protein that binds the target sequence [2] | A FokI cutting domain breaks both strands at the site [2] | 2010 [2] |
| Zinc finger nucleases | Zinc finger proteins built to match the target [3] | A FokI cutting domain cuts near the site [3] | 1996 [3] |
| Base editing | A guide RNA, as with CRISPR [4] | Converts one DNA base into another without cutting both strands [4] | 2016 [4] |
| Prime editing | A prime editing guide RNA that also carries the edit [5] | Writes a short new sequence into the site without cutting both strands [5] | 2019 [5] |
Frequently asked questions
What is the difference between base editing and CRISPR/Cas9?
CRISPR/Cas9 cuts both strands of DNA and relies on the cell's repair. A base editor uses a guide RNA to reach the site, then converts one letter into another without breaking the double helix.
What changes can base editors make?
Cytosine base editors turn a C into a T. Adenine base editors turn an A-T pair into a G-C pair. Each works within a small window of the target.
Is base editing used in plants?
Yes. Studies have used base editors in rice, wheat, maize and tomato, among other crops.
References
- Science (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity (Jinek and others)
- Genetics, via PubMed (2010). Targeting DNA double-strand breaks with TAL effector nucleases (Christian and others)
- Proceedings of the National Academy of Sciences (1996). Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain (Kim, Cha and Chandrasegaran)
- Nature (2016). Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage (Komor and others)
- Nature (2019). Search-and-replace genome editing without double-strand breaks or donor DNA (Anzalone and others)
- Nature Biotechnology (2017). Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion (Zong and others)
- Plant Physiology (2021). Genome- and transcriptome-wide off-target analyses of an improved cytosine base editor (Randall and others)
- Science (2019). Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice (Jin and others)
- Advisory Committee on Releases to the Environment, GOV.UK (2025). ACRE guidance on producing precision bred plants
- Nature (2017). Programmable base editing of A-T to G-C in genomic DNA without DNA cleavage (Gaudelli and others)
Last reviewed 2026-09-26. Edited by Mark Turner.