Truncated inserts

[Man-Ho Chu]

Hi everybody,
I'm trying to get a 2.7 kb insert (excised from a parent plasmid) into
a plasmid.  The insert was excised w/ Nco I and Sma I.  The vector was
prepared by cutting w/ Eco RI, filling in w/ Pfu, and cutting w/ Nco
I.  The vetor was CIPed and the insert was cut from gel and purified.
I've done the ligation a few times but the clones with insert that I
sequenced always have the insert truncated at the 3' end, the length
of the missing sequence ranging from 2 kb to 400 bp.  I'm not sure
whether I can get the full length insert by keep screening, and I
can't figure out why this is happening.  Does anyone have any idea
what might have happened, and does anyone have any idea how to trouble
shoot this problem?  Any input is greatly appreciated!  TIA!

Man-Ho Chu