A modifiable microarray-based universal sensor: providing sample-to-results automation

Abstract

A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA “universal” probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined “reporter” probes that are complementary at their 3′ termini to one or more of the universal probes and complementary to the target amplicons at their 5′ termini. The system was able to detect single-plex and multiplex PCR amplicons from various infectious agents as well as wild type and mutant alleles of single nucleotide polymorphisms. The system's ease of use was further demonstrated by converting a published PCR assay for the detection of Mycobacterium genitalium in a fully automated manner. Excellent correlation between traditional manual methods and the automated analysis performed by the workstation suggests that the system can provide a means to easily design and implement a variety of customized PCR-based assays. The system will be useful to researchers or clinical investigators seeking to develop their own user defined assays. As the U.S. FDA continues to pursue regulatory oversight of LDTs, the system would also allow labs to continue to develop compliant assays.

Application of magnetic nanoparticles in nucleic acid detection

“…Automated nucleic acid extraction had a higher repeatability and performed better when compared to manual testing. In recent years, many researchers such as Verigene (Nanosphere, Northbrook, US), iCubate2.0 (iCubate, Huntsville, US) and Rheonix (Rheonix, Ithaca, US) have used gene chips as detection tools and integrated microarrays into automated diagnostic equipment [180][181][182][183]. With the help of MNPs, these devices can automatically amplify, hybridize and detect gene targets.…”

Development and Evaluation/Verification of a Fully Automated Test Platform for the Rapid Detection of Cyclospora cayetanensis in Produce Matrices

“…The original Mit1C qPCR assay format employed real-time PCR amplification, while the streamlined format uses an end-point PCR approach. In the end-point PCR approach, the primer sets are biotinylated at their 5 termini, and after automatic denaturation controlled by the workstation's software, the amplicons are captured on an integrated DNA array and detected via a colorimetric reaction mediated by streptavidinylated horse radish peroxidase [8,9]. The availability of a more streamlined assay and accessible format can help reduce the time, complexity, and labor associated with screening food and environmental samples for traceback and risk assessment by food producers and public health agencies.…”

A Novel Method That Allows SNP Discrimination with 160:1 Ratio for Biosensors Based on DNA-DNA Hybridization

“…Biosensors based on concurrent DNA-DNA hybridization for the simultaneous detection of various bacterial strains of the same species have unparallel importance in selecting accurate drug therapy [1,2]. DNA biosensors have become the leading diagnostic technology for detecting and discriminating genotypes of various bacterial and viral strains [3,4].…”