methods for targetted deletion of genomic regions?

Question

I would like to know what are currently used methods for targeted deletion of genomic regions in mammalian organisms or cell lines. I have heard of Zinc-Finger nucleases as a recent genetic engineering method, but I don't know if there are other methods, more efficient or better tailored, for the deletion of specific regions.

Answer 1

I can only provide you with a few pointers from memory, as an ad hoc search for "review of dna cutting techniques" was not prolific.

Please consider the provided information with precaution and only for pointers to help you do literature research.

• cre/lox system and variants (best known), belong to SSRs (Site specific recombinases)
• various Restriction enzyme based systems (see Homing Endonucleases)
• meganuclease based tools
• aptamer based
• based on hybridizing n-mer probes which yields a reactive species nicking the DNA at the probe's-site when introduced to certain chemicals such as oxoacids
• light twizzers and lasers /purely proof of concept (perhaps already commercialized?)
• ZFNs and variants / protein based-probes . http://en.wikipedia.org/wiki/Zinc_finger_nuclease

There are definitely published reviews on this exhaustive topic, notwithstanding the dozens of books.
I would estimate that there are at least 10 commercial methods, and almost 100 methods in total when theoretical and proof-of concepts are included.

Naturally (literally!), the vast majority of methods will be based on the noncovalent interaction of an n-mer "homing construct"/probe a)attached to an nuclease or b)an attachment site for a nuclease or c)participate in the reaction for the formation of a reactive chemical species to break the sugar-phosphate backbone.

I would speculate that most other methods are likely not practical in terms of either efficiency and/or affordability.

To learn about the applicability of the respective methods relating to your field of research, and be provided with an overview of the pros and cons of the methods, you will still need to find a good review paper.