xMAP® Technology- Pioneering Platform for Nucleic Acid Detection

xMAP® is commonly called as “Bead Array Technology”. It is a novel concept developed to eliminate the limitations of planar microarrays during array preparation. Planar microarrays employs glass slides as solid substrate which makes it technically challenging and laborious. With the advent of this new high throughput platform, there is a gradual shift from the microarray format of glass slides to the efficacious bead format. Being more flexible in array preparation the bead format is easy to use, cost effective and offers faster hybridization solution kinetics along with statistical superiority as compared to the conventional technique. In other assay chemistries utilizing a solid phase, the reaction kinetics can be adversely affected by immobilization of a reactant on a solid surface. The effects are less severe for a microsphere in suspension than for a flat array as the diffusion rate of the immobilized capture probe can be slower and the effective concentration is reduced as compared to free DNA in solution.

In broader terms the integration of three prominent technologies: PCR, microarray and fluorimeter into a small bead makes xMAP® both sensitive and specific.nnxMAP® or the suspension array technology involves the use of polystyrene microspheres or beads. These beads contains a unique mixture of internal fluorescent dyes or spectral addresses. In direct hybridization assays, DNA probes are attached to these beads. The probes bind to the target DNA molecule that are in turn labeled with distinct fluorescent dyes (reporter dye). To carry on the analysis of different probes simultaneously, bead sets coupled to the probes are thoroughly mixed in a microtiter plate of 100 wells.

In solution based microsphere capture assay format, microspheres are attached to a short stretch of unique sequence called as FlexMAP antitag which captures the complementary tags attached to the custom oligos. In allele specific primer extension assay, tags are attached to allele specific primers which are extended in the presence of biotinylated dNTPs. Tagged ASPE products are then detected by hybridization to antitag sequences attached to microspheres.

A two laser flow cytometer is employed for quantification and separation of the beads from the hybridized targets. In direct hybridization assays, the presence of the probe on the bead is detected by one laser which reads the unique internal color of the bead whereas the fluorescent signal emitted by the reporter dye on the labeled target DNA is detected by the second laser. For ASPE assays, the bead having antitag is detected by one laser and fluorescence emitted by tagged ASPE product is detected by the second laser.

Thus different microsphere sets can be combined within an assay enabling multiplexing of up to 100 samples in a single reaction. This greatly reduces the amount of the test sample utilized.nnxMAP® is highly desirable for bio-pharmaceutical studies which involves drug discovery researches and diagnostic applications. It is capable of providing high content data that enables high throughput nucleic acid detection. Its a promising technology that will suffice the present as well as the future requirements of the molecular research laboratory in the areas of SNP genotyping, gene expression profiling, HLA DNA typing and microbial detection.

This novel technology is now supported in-silico. PREMIER Biosoft has included support for designing oligos for multiplex analysis on suspension array systems in one of their tools called PrimerPlex. The tool is supported on both Windows and Mac. It designs specific capture probes for direct hybridization assays and primer pairs for Allele Specific PCR Extension (ASPE) assays. These assays are widely used for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping.