Positional mapping of specific DNA sequences relative to the nuclear substructure by direct polymerase chain reaction on nuclear matrix-bound templates.

Nuclear DNA of higher eukaryotes is organized in supercoiled loops anchored to a proteinaceous substructure commonly known as the nuclear matrix. Current evidence suggests that important processes of nuclear physiology, such as replication, transcription, and processing of primary transcripts, take place at macromolecular complexes located at discrete, well-defined sites upon the nuclear matrix. A number of authors have reported that actively transcribed genes are closely associated with the nuclear matrix. The topological relationship between the gene sequences located in the DNA loops and the nuclear matrix appears to be very important for appropriate nuclear physiology. Here, we describe a polymerase chain reaction-based method for directly mapping any DNA sequence position relative to the nuclear matrix that avoids the problem posed by DNA fragments nonspecifically bound to the nuclear matrix, without the need of purifying the specifically nuclear matrix-bound DNA.