Detection and evaluation of non-recombinants in cDNA libraries by multiple cloning region PCR

Bacteriophages that are routinely used in cDNA libraries do not require any biological selection for forming plaques. Thus parental non-recombinant phages are always found in variable proportions together with recombinant ones in all cDNA libraries. The presence of non-recombinants in significant proportions dilutes the abundance of rare cDNA species and makes library screening difficult. If the exact proportion of non-recombinants in a library were known, then one would screen proportionately more plaques to get a positive clone. In the absence of such information, screening is conventionally conducted on a number that is based on the titer of the library. We have devised a method using the flanking sequences from either side of the multiple cloning region (MCR) of all λ phage vector derivatives as primers for PCR amplification. A non-recombinant phage produces a fragment equal to the size of the MCR, whereas a recombinant phage produces a fragment larger than the MCR, which is an MCR+ fragment. All cDNA libraries that we have studied show the presence of the MCR fragment (indicating nonrecombinants) at variable proportions ranging between 6% and 36% of the total phages present. We also show that their presence negatively influences the retrieval of target cDNA sequences.