PrimerPlex is an efficient and sophisticated tool for designing oligos for multiplex analysis on suspension array systems such as Luminex 100, Luminex 200 and Bio-Plex 200. Based on Luminex xMAP technology, these systems offer a versatile platform for multiplex nucleic acid detection in the 96-well format.
PrimerPlex designs specific capture probes for direct hybridization assays and primers for Allele Specific PCR Extension (ASPE) assays. The assays are used for high throughput SNP applications such as genotyping, pathogen detection, strain typing, and haplotyping. To ensure specificity, the oligos are designed after avoiding the regions of homologies identified by a BLAST search.
PrimerPlex then checks the oligos for cross reactivity and minimizes Tm mismatches to give you the best possible multiplex set. In the process, it analyzes millions of possible multiplex sets in a few seconds and presents a list of alternate sets to you as well.
Direct Hybridization Assays: PrimerPlex designs optimal allele specific capture probes for direct hybridization assays. The probes are designed such that the mutations are at their centers to maximize differentiation. Our innovative and proprietary algorithm analyzes each one of these probes for their suitability in a multiplex reaction. The probes are screened for cross and self dimers, assuring strong signal strength.
This functionality makes PrimerPlex the only software product capable of designing probes for 100 individual targets in a multiplex reaction. Also included is the ability to design compatible primer pairs for amplifying the template.
A series of probes can also be designed for detecting all the variable sites of a medium to large genomic sequence. For such cases, PrimerPlex designs allele specific capture probes after BLAST searching the sequences and avoiding the regions of homology.
ASPE Assays: Another approach to detect mutations is to use a solution-based sequence specific enzymatic reaction such as Allele Specific Primer Extension (ASPE) to determine the target genotype. PrimerPlex designs highly specific primers for multiplexed ASPE assays. The ASPE primers are designed such that the mutations lies at their 3 end. PrimerPlex also designs primers to amplify the target sequence for ASPE assays.