17 December 2024 0 8K Report

I am attempting to incorporate two restriction enzyme sites into a plasmid vector (p15A origin PREGFP) using super primer PCR. My desired insert length is 80 bp, containing one restriction sites followed by a nonspecific sequence and followed by another restriction site. Despite several cloning attempts, sequencing of the extracted plasmid from the ligated colony showed no insertion.

Here's what I tried:

  • Ran PCR products on a 2.2% gel, extracted them, measured the concentration by running gel, and digested with SalI HF and AvrII . I then extracted the digested products from the gel and performed ligation with the digested vector. I used various ratios for ligation: 3:1, 4:1, 5:1, and 7:1.
  • Purified PCR products using a nucleotide removal kit instead of running them on a gel.
  • Another issue is the low concentration after super primer PCR, around 50 ng/µL. I tried changing cycle numbers and gradient PCR, but the concentration value did not improve.

    I would appreciate your suggestions to resolve these issues.

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