TREATMENT OF CELLS WITH ALKALINE BORATE BUFFER EXTENDS THE CAPABILITYOF INTERPHASE FISH MAPPING

Interphase fluorescence in situ hybridization (FISH) has been shown to be a means to map DNA sequences relative to each other in the 100 kb to 1-2 Mb genomic-separation range. At distances below 0.1 Mb, probe s ites are infrequently resolved in interphase chromatin. In the 0.1- to 1-Mb range, interphase chromatin can be modeled as a freely flexible chain. The mean square interphase distance between two probes is propo rtional to the genomic separation between the probes on the linear DNA molecule. Above 1-2 Mb, the relationship between interphase distance and genomic separation changes abruptly and appears to level off. We h ave used alkaline-borate treatment to expand the capability of interph ase FISH mapping. We show here that alkaline-borate treatment increase s nuclear diameter, the interphase distance between probes on homologo us chromosomes, and the distance between probes on the same chromosome . We also show that the mean square distance between hybridization sit es in berate-treated nuclei is proportional to genomic separation up t o 4 Mb. Thus, alkaline-borate treatment enhances the capability of int erphase FISH mapping by increasing the absolute distance between probe s and extending the range of the simple relationship between interphas e distance and genomic separation. (C) 1995 Academic Press, Inc.