A host of observations demonstrating the relationship between nuclear 
architecture and processes such as gene expression have led to a number of new 
technologies for interrogating chromosome positioning. Whereas some of these 
technologies reconstruct intermolecular interactions, others have enhanced our 
ability to visualize chromosomes in situ. Here, we describe an oligonucleotide- 
and PCR-based strategy for fluorescence in situ hybridization (FISH) and a 
bioinformatic platform that enables this technology to be extended to any 
organism whose genome has been sequenced. The oligonucleotide probes are 
renewable, highly efficient, and able to robustly label chromosomes in cell 
culture, fixed tissues, and metaphase spreads. Our method gives researchers 
precise control over the sequences they target and allows for single and 
multicolor imaging of regions ranging from tens of kilobases to megabases with 
the same basic protocol. We anticipate this technology will lead to an enhanced 
ability to visualize interphase and metaphase chromosomes.