In article <489lds$m9s at highway.LeidenUniv.nl>,
nandy at ruly46.medfac.leidenuniv.nl says:
>For two months now I have been trying to clone a 2 kb blunt fragment
(NruI/HindIII, filled in with klenow) into a PvuII site of a 6.5 kb
>I am aware of the fact that blunt ligation are not as efficient as
sticky end ligations, but still it should work.
>There are some specific questions I would like to put forward:
>1. Self ligation of the PvuII cut vector does not work. Is anyone aware
of problems specific for a blunt PvuII site?
If this is so, you must suspect your PvuII or the phosphatase (I assume
that you have used ciap?), or the ligase. I have had no problems with
PvuII cloning (PvuI, yes, not PvuII). If the vector won't religate, one
or more enzymes are destroying the ends of your vector, or the ligase
isn't working. Suggest you check the ligase, and/or try different batches
of PvuII/ciap, if you haven't already. You should get 1000's of colonies
from 20ng vector on religation.
>2. From the catalog a learned that blunt NruI sites are difficult to
ligate. Does anybody know why, and if there is a way to imporve this?
>Have you considered the isoschizomer Bsp68I? Maybe NruI is simply one of
those not very reliable enzymes, hard to get very pure, or something.
SmaI used to have a bad reputation like this (Waaay back when).