Visual OMP™ ( Oligonucleotide Modeling Platform )
Visual OMP™ can be used for Simulation, Visualization, troubleshooting, manual assay optimization of primers and probes. In addition, users can check their multiplex primers and probes to ensure they are optimized to work under different experimental conditions helping to take the “trial and error” out of your assay design workflow.
Advantages of Visual OMP™ :
- 1. “Best in class” simulation and visualization to examine secondary structure and impediments to hybridization or primer extension.
2. Powerful algorithms for designs which use the nearest-neighbor model along with coupled multi-state equilibrium models in order to simulate thousands of possible combinations to identify and find the most selective and sensitive oligo solution sets.
3. Correct thermodynamic parameters for assay optimization and folding prediction.
4. Visual OMP™ accommodates both Taqman probes & Taqman minor groove binding probes properly accounting for solution conditions (temperature, primer concentrations, salt, buffers, additives, etc.)
How to design a highly multiplexed PCR assay design?
DNA Software will walk you through the design process of your multiplex PCR assay designs to make sure that you get great designs that simply work!
We also provide:
– Online training and customer support.
– Money back guarantee.
– Free redesigns.
Specify a target, choose a design type, and define experiment conditions and Visual OMP’s design engine will automatically determine the most stable and specific PCR primer design for your single-plexed assay.
Visual OMP’s simulation engine allows for the input and thermodynamic analysis of existing primers in the presence of newly designed primers in a molecular simulation.
Visual OMP will optimize beacon probe and stem length design for a given set of experimental conditions to ensure that free beacons form hairpins to quench fluorescence, while selectively bound beacons fluoresce. Beacons can also be simulated using a variety of flurophore and quencher pairs to optimize your assay.
Sensitivity can be a huge factor when designing for SNPs due to cross-hybridization which may lead to false positives. Visual OMPs design engine can design allele-specific primers and probes to optimize polymorphism detection sensitivity.
Visual OMP provides a ranked set of highly specific PCR primer designs which do not cross-hybridize or form primer dimers.
Visual OMP can design highly selective Taqman probe sequences that can be simulated to exhibit the thermodynamic effects of fluorophores, quenchers and minor groove binders to DNA duplex stability.
False positives and negatives can be avoided by utilizing Visual OMP to increase the quality and performance of DNA probes while simultaneously avoiding cross-hybridization and mishybridization.
Fast and accurate simulated folding under a variety of salt and temperature profiles simplifies RNA target accessibility and complexity to optimize primer and probe design.