Miniaturized Optical Components for Fluorescent DNA Detection System

In a world that no longer sleeps, advances in technology are driven to provide accessibility and speed alongside accurate reliable data. Procedures previously designated to a lab, run by specially certified personal, now find niches among all facets of society by way of portable, rugged instrumentation coupled with intuitive graphical user interfaces. The demand for instrumentation to swiftly analyze human blood and tissue samples, especially among the medical field and military personnel, has driven research to focus on minimizing both instrument footprint and length of assay time.

Traditionally, fluorescence microscopy, while highly sensitive and able to provide precise data, is bulky and requires a full lab and a great deal of time to analyze. The possibility of maintaining accurate data retrieval while also being able to identify fallen soldiers and enemies on the physical field of battle, or unidentified deceased in the hospital, near to real time has motivated a multitude of research in on-chip microfluidics using fluorescence detection schemes. The principle focus of research has centered on simplifying the polymerase chain reaction process, identifying fewer spots in the genome to approach ultra-rapid DNA screening times of thirty to forty-five minutes, maintaining multi-color color detection using instrumentation that is smaller and sturdier than photomultiplier tubes and solid state lasers, and using rotation-driven micro devices to integrate all microfluidics necessary onto one chip.

Given these goals, this thesis uses both computational simulations and experiments to explore alternatives to photomultiplier tubes as a primary detector and to characterize the laser diodes proposed over the traditional solid state lasers as excitation sources. Models of the optical components needed in detection as well as the in-house designed microscope objective are presented using Zemax OpticsStudio. In addition, three fully functional systems are presented and the changes made in designing each system are discussed. This body of work is considered the first step toward fully integrating and miniaturizing a rapid DNA screening device into the smallest footprint possible.