Problems with ligation after GeneCleaning

[Chris Houchens]

Anis Limami (limami at versailles.inra.fr) wrote:
: I suffered with the same probleme as you , it was impossible 
: to get ligation succesfull with fragments purified by 
: GeanClean after enzymic digestion, I dont no why.
: The only thing worked at the end in my hands is the "old" 
: purification by electroelution followed by phenol-chloroform 
: purification and alcohol precipitation.
: Cheers
: Anis

I experienced the very same problem as all of you, although the cause of 
my woes may have differed from others. Somehow, somebody contaminated our 
GeneClean beads with the same vector (supercoiled) plasmid that I was 
trying to clone into. So my ligation controls were fine (no insert, no 
contamination, no transformants), and the more insert I would ligate with 
(i.e. the more contamination that I was adding) - the greater number of 
transformants I would get back. But when I minipreped my transformants, 
all I got back was the vector w/o insert. I finally took some of the 
beads (no DNA), washed them a few times with New Wash, and eluted in water 
at 55 degrees (standard procedure for fragment purification) and 
transformed cells. Guess what? The more I added, the more greater number 
of transformants I got. So, although this may not be the reason for the 
problems that your are experiencing, it is always wise to suspect that 
the reagents that you are working with are not entirely clean - esp. if 
they are used by other members of your lab. 

Chris
(houchens at salus.med.uvm.edu)