Visual OMP

Visual OMP™ (Oligonucleotide Modeling Platform) is desktop software developed by DNA Software for simulating, visualizing, and optimizing PCR primers and probes. It is designed for researchers and assay developers who need to troubleshoot existing assays, design new oligonucleotide sets, or analyze secondary structures and hybridization behavior under defined experimental conditions.

The platform applies nearest-neighbor thermodynamic models combined with coupled multi-state equilibrium models to simulate thousands of possible oligonucleotide combinations, identifying the most selective and sensitive solutions. It accounts for solution conditions including temperature, primer concentrations, salt, buffers, and additives, and supports both Taqman probes and Taqman minor groove binding probes.

Core Capabilities

• Simulation and visualization of secondary structures and impediments to hybridization or primer extension.
• Thermodynamic parameter calculations for assay optimization and folding prediction using a dynamic programming algorithm and an experimentally validated thermodynamic database.
• Cross-hybridization analysis via a visual grid that displays all heterodimer interactions between oligos, with color-customizable filtering.
• Support for modified nucleotides, including modified backbones, sugars, and bases that affect target binding.
• Import of existing sequences from FASTA files for analysis and redesign.
• Experimentally validated fluorophore and quencher library for accurate Taqman simulation.

Supported Design Types

• PCR Primer Design: Accounts for the major factors affecting primer performance, including assay temperature, cation concentration (K+, Na+, Mg2+, NH4+), buffer additives (glycerol, DMSO, formamide, TMAC, betaine), annealing temperatures, amplicon size, secondary structure, and synthetic nucleotide modifications.
• Multiplex PCR Primer Design: Designs multiple primers and probes simultaneously using a dynamic algorithm that checks each oligo against every other oligo in the system for intended and unintended cross- and mishybridization. Supports typical use cases up to approximately 20-plex targets of around 500 nucleotides at standard endpoint PCR conditions.
• Existing PCR Assay Analysis: Uses the multi-state coupled equilibrium simulation engine to identify offending primers or probes in assays that did not perform as expected, then designs replacement oligos in the presence of existing oligos to optimize sensitivity and selectivity.
• Taqman Design: Supports design of both standard Taqman probes and Taqman Minor Groove Binder probes, with the ability to exclude or selectively target specific regions of the template. Thermodynamic contributions of fluorophore, quencher, and minor groove binder are incorporated into simulation.
• Molecular Beacon Design: Designs molecular beacons and allele-specific molecular beacon pairs, with control over loop and stem size, melting temperature, and free energy. Stems are designed to avoid mishybridization to adjacent target sequences, with an optional terminal G/C pair stem optimization.
• Microarray Probe Design and Analysis: Allows visual inspection of all heterodimer interactions between probes and targets to identify cross-hybridization or mishybridization issues.
• Polymorphism Design: Designs allele-specific primers and probes targeting single SNP sites using binary IUPAC ambiguity codes. Multiple SNP sites or ambiguity codes are not currently supported.
• RNA Target Selection: Generates a Target Accessibility plot showing regions of strong secondary structure in RNA sequences under defined experimental conditions, helping users identify optimal and suboptimal areas for primer and probe design.

Key Factors Modeled in PCR Primer Design

1. Assay temperature and its effect on the equilibrium constant of oligo binding.
2. Cation concentration and its effect on oligonucleotide stability.
3. Buffer additives and their thermodynamic effects on hybridization stability.
4. Desired annealing temperatures relative to oligo length and amplicon size.
5. Secondary structure and its impact on oligonucleotide binding, calculated using a dynamic programming algorithm.
6. Synthetic nucleotide modifications and their influence on target binding affinity.

Visual OMP is a desktop application. For multiplex designs larger than approximately 20-plex, DNA Software offers OMP-Developers Edition, a server-based command-line application for design and simulation at greater scale. The platform supports a range of modified nucleotides, with a full list available from DNA Software.