Miniaturization and integration of biosensor platforms is appealing due to smaller reaction volumes, larger numbers of detection sites and integration of various functionalities. Proper design of integrated biosensors is crucial in such systems due to limitation in resources such as power, chip area and cost. The optimal design involves determining the required sensor metrics and achieving these metrics with minimum use of the available resources. The system-level requirements of various biosensor arrays are discussed in this paper. We will show here, that while in certain applications, the best sensor performance in terms of signal-to-noise ratio (SNR) or dynamic range (DR) is desirable, in others, these metrics can be traded off with power, area and ease of design and implementation. As a practical example, the design of a high DR sensor array for bioluminescence detection is considered. Various high DR schemes are qualitatively compared in order to determine the advantages and disadvantages of each scheme in terms of SNR and power consumption. Two schemes are shown to be most suitable for such applications: synchronous self-reset with residue readout and read-self reset. The SNR and suitable applications of these techniques are compared in greater detail through behavioral simulations.
A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40μlit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.
Proc. SPIE. 4966, Microarrays and Combinatorial Technologies for Biomedical Applications: Design, Fabrication, and Analysis
KEYWORDS: Signal to noise ratio, Photodetectors, Digital signal processing, Imaging systems, Sensors, Luminescence, Photons, Signal processing, Charge-coupled devices, Acquisition tracking and pointing
We developed a simulation model of an integrated CMOS-based imaging platform for use with bioluminescent DNA microarrays. We formulate the complete kinetic model of ATP based assays and luciferase label-based assays. The model first calculates the number of photons generated per unit time, i.e., photon flux, based upon the kinetics of the light generation process of luminescence probes. The photon flux coupled with the system geometry is then used to calculate the number of photons incident on the photodetector plane. Subsequently the characteristics of the imaging array including the photodetector spectral response, its dark current density, and the sensor conversion gain are incorporated. The model also takes into account different noise sources including shot noise, reset noise, readout noise and fixed pattern noise. Finally, signal processing algorithms are applied to the image to enhance detection reliability and hence increase the overall system throughput. We will present simulations and preliminary experimental results.