Overview of the Optical Mapping platform. Bulk microscope cover glass is cleaned with a strong acid, then treated with a silane mixture to make positively charged Optical Mapping surfaces (i). A silicon wafer is patterned with standard photolithography techniques, and then replicated into a flexible PDMS microfluidic device (ii) using soft lithography. Finally, pure, high molecular-weight DNA (iii) is isolated from cultured eukaryotic cells using a gentle detergent-based lysis protocol. The microfluidic device is adhered to the Optical Mapping surface, and the DNA solution is pumped through the microchannels, wherein the DNA is elongated and attached to the Optical Mapping surface via electrostatic interaction (iv). The DNA is incubated with a restriction endonuclease (v), which cleaves the DNA at its cognate sites. The cleaved DNA is stained and imaged on an epifluorescence microscope (vi) illuminated by an argon-ion laser (vii) and controlled by a computer workstation (viii).