The modern optical mapping platform works as follows:
#Genomic DNA is obtained from lysed cells, and randomly sheared to produce a "library" of large genomic molecules for optical mapping.
#A single molecule of DNA is stretched (or elongated) and held in place on a slide under a fluorescent microscope due to charge interactions.
#The DNA molecule is digested by added restriction enzymes, which cleave at specific digestion sites. The resulting molecule fragments remain attached to the surface. The fragment ends at the cleavage sites are drawn back (due to elasticity of linearized DNA), leaving gaps which are identifiable under the microscope.
#DNA fragments stained with intercalating dye are visualized by fluorescence microscopy and are sized by measuring the integrated fluorescence intensity. This produces an optical map of single molecules.
#Individual optical maps are combined to produce a consensus, genomic optical map.