Since two decades we came across many tools to edit the desired gene and genome viz., clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), (2) transcription activator-like effector nucleases (TALENs), (3) zinc-finger nucleases (ZFNs), and (4) homing endonucleases (HENs).
Among them which is the best tool for editing the gene of interest?
There is no absolute best unless the criteria for the best is specified. Every method has its pros and cons. However, if one has to place the methods mentioned in a list of preferences, CRISPER-Cas9 can be the first candidate.
I agree that there is no such thing as "best" - it all depends on the purpose, the samples, the equipment, and... the experience of the specific researcher. For that reason, for most people, CRISPR-Cas9 is the "best" option - it is most commonly used, and thus any technical problems can easily find solutions from lots of other researchers. It is also the most user-friendly, quick, and, most of the time, cheaper than other gene-editing tools (again, depending on the specific purpose).
Kariyanna B.
HENs < ZFNs < TALENs < CRISPR/Cas9. CRISPR is the simplest tool to design and most versatile.
Yuan-Yeu Yau some of the literatures which I studied displayed HENs is equals to or best than CRISPR. But, you have given least ranking. Could you tell me the reason?
Kariyanna B.
Can HENs edit virtually any gene you wish to be modified, like CRISPR? No. Homing endonucleases only cut *specific DNA sequence* they recognize. You can transfer those *specific DNA sequence* into a genome (at a specific location or random locus), then do a so-called 'site-specific' genome modification.
" (HENs) Their catalytic activity is usually tightly coupled to recognition of their cognate DNA target sites, which allows them to be used for site-specific genome modification. " (https://www.pnas.org/content/pnas/108/32/13077.full.pdf)
Abhijeet Singh and Marta Jaskulak I was expected HENs based on the attached file.
Kariyanna B. *Site-specific recombination (SSR)* systems which derived from microbial organisms are also widely used in plants for genome modification. It is also based on "site-specific" modification, like HENs. Similarly, site-specific recombinases recognize specific DNA sequences for cutting. These 'specific DNA sequences' can be engineered into your gene transformation cassette and transfer into plants/animals. Then these inserted 'specific DNA sequences' can be used to delete a gene (ex. to remove a selection gene) or to insert a gene later, depending which SSR system is used and how the cassette is designed. But, it cannot be used the way CRISPR is offering, that you can use to modify any gene you wish.
Kariyanna B. You did not mention this tool in your question. The ODM-mediated gene editing. Paper: "Oligonucleotide‐directed mutagenesis for precision gene editing." (Article Oligonucleotide-directed mutagenesis for precision gene editing
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