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Interestingly, the insert orientation differed between the mutants.
Insert orientation was determined by restriction digest with HindIII.
Proper insert orientation was confirmed by restriction endonuclease analysis and sequencing.
The resultant plasmid, pCR4-Cdx4, wasequenceded and restriction digested to determine its insert orientation.
The insert orientation was tested by size analysis of KpnI/NdeI double digestion fragments.
The insert orientation was confirmed by PCR using M13 forward primer combined with MutLR primer, and complementation of PAO1ΔmutL phenotype shown using the rifampicin resistance method.
Similar(38)
However, the intensity of the bands in the ladder pattern changed subtly upon insertion of either DNA insert orientations.
Furthermore, we found that the proportions of sense- versus antisense- strand insertions are equivalent, both for the 63% insertions and for all insertions, indicating that transcribed sequences did not affect insert orientations.
For determination of insert orientations, proper controls should be used to ensure that the PCR products are derived only from recombinant molecules in the ligation mixture.
To our knowledge, this is the only method that can be used for determining insert orientations directly from ligation mixtures, as has been demonstrated in the results (Fig. 4).
The resulting clones were then screened for insert and orientation by PCR.
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