Assessing the Detection Capacity of Microarrays as Bio/Nanosensing Platforms

Abstract

Microarray is one of the most powerful detection systems with multiplexing and high throughput capability. It has significant potential as a versatile biosensing platform for environmental monitoring, pathogen detection, medical therapeutics, and drug screening to name a few. To date, however, microarray applications are still limited to preliminary screening of genome-scale transcription profiling or gene ontology analysis. Expanding the utility of microarrays as a detection tool for various biological and biomedical applications requires information about performance such as the limits of detection and quantification, which are considered as an essential information to decide the detection sensitivity of sensing devices. Here we present a calibration design that integrates detection limit theory and linear dynamic range to obtain a performance index of microarray detection platform using oligonucleotide arrays as a model system. Two different types of limits of detection and quantification are proposed by the prediction or tolerance interval for two common cyanine fluorescence dyes, Cy3 and Cy5. Besides oligonucleotide, the proposed method can be generalized to other microarray formats with various biomolecules such as complementary DNA, protein, peptide, carbohydrate, tissue, or other small biomolecules. Also, it can be easily applied to other fluorescence dyes for further dye chemistry improvement.

A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge

“…However, the microarray image analyses showed that the signal intensity of spots could not be compared and analyzed statistically, because of the low SNR values of features. To obtain a reliable signal intensity value, for example, to estimate a limit of detection (LOD) and a limit of quantification (LOQ), the SNR value should be higher than 3 [ 17 , 18 ]. However, even though they could be visually discriminated as described above, most of features showed SNR values lower than 3 (see Additional file 4 : Table S2).…”

“…The low SNR, i.e. , low signal intensity, of each spot could be related to the probe length and/or the low discrimination power of the microarray [ 17 ]. More uniformly digested and shorter DNA would allow increasing the efficiency of the probe-target hybridization on the microarray.…”

“…The 30 μL of the learned products, a negative control ( i.e., learned products without input DNA), and a blank ( i.e., 1× printing buffer only) were transferred into a 384-well plate. Each sample in the well plate was printed with 10 replications onto CodeLink™ activated microarray slide (Amersham Biosciences) using MicroGrid II microarray printing system with BioRobotics MicroSpot 2500 pins (Genomic Solutions, MI) at 40% relative humidity according to the previously established protocol [ 17 ]. After printing, the slides were stored in a customized hybridization chamber (GeneTix, CA), which was filled with saturated NaCl solution at bottom, for 15 hr at ~75% of relative humidity to couple the amine group at the 5′ end of the learned products to the activated N-hydroxysuccinimide-ester group on the microarray slide surface.…”

Scoping review of the applications of peptide microarrays on the fight against human infections

“…They provide rapid, reproducible ways to simultaneously screen and detect hundreds to thousands of different pathogen related peptides or epitopes on standard microscope slides from small quantities of serum, plasma and cerebrospinal fluid [9][10][11]. Peptide microarrays offer a wide range of applications in the fight against infectious diseases, such as, B-cell and Tcell epitope discovery for development of diagnostics and rationally designed vaccines, drug discovery (antimicrobial peptides discovery), immunosignature characterisation and pathogen immunodiagnostics [12][13][14][15][16]. Additionally, peptide microarrays are used for autoimmune disease research, cancer research and enzyme profiling [17].…”

Scoping review of the applications of peptide microarrays on the fight against human infections

“…They provide rapid, reproducible ways to simultaneously screen and detect hundreds to thousands of different pathogen related peptides or epitopes on standard microscope slides from small quantities of serum, plasma and cerebrospinal fluid (10)(11)(12). Peptide microarrays offer a wide range of applications in the fight against infectious diseases, such as, B-cell and T-cell epitope discovery for development of diagnostics and rationally designed vaccines, drug discovery (antimicrobial peptides discovery), immunosignature characterisation and pathogen immunodiagnostics (13)(14)(15)(16)(17). Additionally, peptide microarrays are used for autoimmune disease research, cancer research and enzyme profiling (18).…”