The study of low-copy viral or genomic DNA sequences by in situ hybridization is often limited by sensitivity. The ability to detect a single copy of a specific gene in situ has many advantages and multiple applications in molecular biology, pathology, and cell biology. One of the limitations of in situ hybridization, however, is detection and quantitation of very low levels of nucleic acid targets where the signal is insufficient to distinguish it clearly from background noise. The advent of polymerase chain reaction technology to amplify target nucleic acids provides an opportunity to develop new technologies to examine this end of the spectrum of gene expression or infection.