'Specific' oligonucleotides often recognize more than one gene: the limitsof in situ hybridization applied to GABA receptors

As exquisite probes for gene sequences, oligonucleotides are one of the mos t powerful tools of recombinant molecular biology. In studying the GABA rec eptor subunits in the neonatal hippocampus we have used oligonucleotide pro bes in in situ hybridization and cloning techniques. The oligonucleotides u sed and assumed to be specific for the target gene, actually recognized mor e than one gene, leading to surprising and contradictory results. In partic ular, we found that a GABA(A)-rho specific oligonucleotide recognized an ab undant, previously unknown, transcription factor in both in situ and librar y screening, while oligos 'specific' for GABA(A) subunits were able to reco gnize 30 additional unrelated genes in library screening. This suggests tha t positive results obtained with oligonucleotides should be interpreted wit h caution unless confirmed by identical results with oligonucleotides from different parts of the same gene, or cDNA library screening excludes the pr esence of other hybridizing species. (C) 2000 Elsevier Science B.V. All rig hts reserved.