A PCR-based method for high stringency screening of DNA libraries

Nucleic Acids Res. 1993 Jun 11;21(11):2627-31. doi: 10.1093/nar/21.11.2627.


A rapid method for cloning genomic DNA utilizing a PCR-based screening protocol is described. A murine genomic library in lambda phage was subdivided into 64 wells, each containing 1000 clones, and propagated in bacteria. Amplified phage from each of 8 wells across columns, and each of 8 wells down rows, were pooled. The pooled phage were screened for the presence of murine M-CSF DNA by PCR using specific oligonucleotide primers. A single well that contained an M-CSF genomic clone was identified by the synthesis of a PCR product of the correct size that hybridized to an internal M-CSF oligonucleotide probe. This well was subdivided into 64 wells, each containing approximately 30 individual phage, reamplified, and rescreened utilizing the same protocol. A positive well was then subdivided and amplified a third time starting with an average of 2 phage per well, and rescreened for M-CSF DNA by PCR. Phage from a PCR-positive well, now highly enriched for M-CSF DNA, were grown as individual plaques. PCR-screening of randomly picked plaques demonstrated that the majority contained an M-CSF genomic insert. This method obviates the more labor and time intensive method of plaque hybridization screening of DNA libraries, and is more stringent since three oligonucleotides (the two PCR primers, and the hybridization probe) are required to give a true positive signal. Similar methodology has also been used to clone a cDNA gene contained within a plasmid library.

MeSH terms

  • Animals
  • Base Sequence
  • Cloning, Molecular
  • DNA / genetics*
  • Escherichia coli / genetics
  • Genomic Library*
  • Macrophage Colony-Stimulating Factor / genetics*
  • Mice
  • Molecular Sequence Data
  • Oligodeoxyribonucleotides
  • Oligonucleotide Probes
  • Polymerase Chain Reaction / methods*


  • Oligodeoxyribonucleotides
  • Oligonucleotide Probes
  • Macrophage Colony-Stimulating Factor
  • DNA