Question 2 of 9 Intermediate Practical
How would you verify that a plasmid contains the intended insert?
Short answer
Check plasmid identity using a diagnostic assay, then sequence the insert, its junctions and any essential features. A band of the expected size confirms length, not nucleotide accuracy.
Why
I would first confirm the expected plasmid map, antibiotic marker, insert orientation and the experiment-critical sequence regions. A diagnostic restriction digest or junction PCR checks gross construct architecture, but two unrelated sequences can produce the same band size. Use Sanger reads covering both junctions and the full insert, with internal primers for long sequences, or whole-plasmid sequencing when available.
Inspect traces or quality scores and align the consensus to the intended reference, explicitly checking reading frame, tags, promoters and mutations. For instance, a single-base indel before a fluorescent fusion tag may produce the expected digest pattern but destroy the open reading frame. Maintain a plasmid ID, lot, sequence file and aliquot provenance.
Functional expression is useful supporting evidence but is not a substitute for sequence verification. Confirm that the actual working stock, not just the original deposited construct, has the required identity.
Common mistakes
- Treating a correct digest band as proof of the correct sequence and reading frame
The interviewer might ask next
When would you choose whole-plasmid sequencing instead of two junction Sanger reads?