Vector gets shorter when insert is added.

[Harry Witchel]

Greetings fellow molecular explorers!
	In explicably, when ligating a 3.5 kb insert (65% GC rich, with 
a veriety of hairpin structures) into pcDNA 1.1 AMP (InVitrogen, 4.8 
kb), I got colonies which produced plasmids with the insert, in which 
the vector was only 3.5 kb.  In the original gel where I purified the 
vector (EcoRI digested, heat inactivated, CIAP treated, heat 
inactivated, NuSieve 1% gel purified, agarase purified), the vector is 
the correct size.  In mapping the minipreps, the insert seems to be 
normal and full length.  I have found the insert in different colonies 
in different directions.  My bug is XL1 blue MRF'.
	Anyone else get anything like this?  Any explanantions?
Thanks,
	Harry