The objective of the proposed research is to design and characterize single photon counting systems (SPCSs) for detecting ultra-weak fluorescent signals in various biomedical applications, our application being DNA-sequencing. This thesis investigates the feasibility of designing cost-effective, SPCSs to perform fast, high performance DNA-sequencing at low cost.

This thesis presents design, development and characterization of unique single-channel and multi-channel (16 and 32 channel) SPCSs based on a large-area single photon avalanche diode (SPAD) having 0.5mm diameter (model C30902S-DTC from Perkin Elmer Optoelectronics. A novel logic circuit for generating precise quench and reset delays in the quenching circuit is presented. Further, the developed SPCSs are integrated into DNA-sequencing instruments. Excellent DNA sequencing results, demonstrating single fluorescent molecule sensitivity is presented. Thus, for the first time, experimental evidence of the application of large-area SPAD for highly sensitive detection of DNA-sequences is demonstrated.

Recently solid-state alternative to the traditional photomultiplier tube (PMT) called silicon photomultiplier (SiPM) became commercially available. SiPMs are analog detectors (output signal proportional to number of input photons) that are primarily used in applications in fields such as nuclear physics, nuclear medicine etc., where the incoming photons usually arrive simultaneously in few numbers. SiPM is designed using standard CMOS technology and offer exciting advantages, but it is not used in photon counting applications as digital detectors, mainly due to their high dark count rate (DCR). This thesis investigates the photon counting properties of SiPM and demonstrates, for the first time, their use for detecting very weak fluorescence signals. SiPMs have high level of noise such as cross-talk and after-pulsing. This thesis investigates the noise of SiPM when used as a photon counter. Furthermore, this work demonstrates, for the first time, DNA-sequencing with SiPM, opening up a new application area, and potentially more, for this device. Multi-channel photon counting systems based on large-area SPAD (>200μm diameter) are needed in some applications, for e.g. multi-lane DNA-sequencing, but are unavailable. SiPM arrays are relatively easy to design and fabricate (CMOS), facilitating design of multi-channel photon counting systems and hence high-throughput and highly sensitive DNA-sequencing at low-cost.