A semiconductor structure for use in single molecule real time DNA sequencing technology is provided. The structure includes a semiconductor substrate including a first region and an adjoining second region. A photodetector is present in the first region and a plurality of semiconductor devices is present in the second region. A contact wire is located on a surface of a dielectric material that surrounds the photodetector and contacts a topmost surface of the photodetector and a portion of one of the semiconductor devices. An interconnect structure is located above the first region and the second region, and a metal layer is located atop the interconnect structure. The metal layer has a zero waveguide module located above the first region of the semiconductor substrate. A DNA polymerase can be present at the bottom of the zero waveguide module.