SmaI site gone!?

Hernan Espinoza espinoza at
Mon Sep 22 12:57:50 EST 1997

BMBTJY at (T.J. Young) writes:

>A strange thing has happened.  I subcloned a cDNA sequence into a eukaryote 
>expression vector using flanking SmaI restriction sites. I've used this 
>construct for expression and everything seems to be working fine.  However, 
>I've done some SDM on the gene in this vector and I now want to subclone it 
>into a different plasmid.  Well, seeing as I ligated it in at SmaI sites I 
>thought I would excise it at the SmaI sites but they appear to have gone!?  
>Now the only thing I can think of is that I had some exonuclease activty 
>arround when I did the ligation which has chewed back the SmaI recognition 
>site.  Is this something other people have seen? Or could there be another 
>explanation?  Thanks in advance.

	SmaI does that.  I don't know why, exactly (contaminating exonuclease?
SmaI is an exonuclease?), but SmaI will drop base pairs.  It has happened
to me twice (one unexpectedly led to a neat new allele 8-) ), so I never
use SmaI to clone with if I can avoid it (XmaI will substitute effectively
most of the time)

	-Hernan, SmaI is the devil's enzyme, never turn your back on it. 8-)

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