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restriction enzymes/sites to avoid - (Apr/11/2014 )

Dear all,


I can (vaguely) remember reading something about restriction enzymes that you should avoid when doing cloning.

Too bad, I forgot what exactly it was and I also cant remember the enzymes..


Anyone an idea what restriction enzymes/sites one should avoid for cloning?




If you are using a manufacturer provided plasmid, chances are each RE present in the multiple cloning site has been thoroughly tested and will give decent results. I tend to avoid RE sites that produce weird overhangs or require any (N) nucleotide to cut. Always avoid compatible end producing enzymes (isoschizomers)


SalI has a bad reputation when used as a site created by placing it on the 5' end of a PCR primer.

I always choose enzymes which can be heat killed, which often avoids a purification step.

Choose cheap enzymes.


SalII thats it!


I remember this. But why would it cause problems ?


I often dont even do a purification step.. Even heat inactivation is something I often dont do when transforming cells. So far I had no problems with this.





what do you mean by "weird overhangs" ?


And require any nucleotide to cut? You mean the standard "rule" they often mention that you need some extra bps to have it cut your restriction site?


Isoschizomers, I can see this also as an advantage , but I guess this depends on the reason why you use it.


Weird overhangs such as AleI that produce weird cut sites with "any" nucleotide. I just try to avoid using these all together.




Edit - I guess they are not necessarily weird, I just prefer not to tinker with them. I like my common REs.