PCR Design


The Problem:

High sensitivity and specificity are difficult to achieve for PCR due to such obstacles as primer dimers, false hybridization and competing secondary structure. These issues only magnify as the multiplex size increases.

 

The Solution:

Perform your experiments in-silco before purchasing and optimizing your primers and probes experimentally with the industry's most accurate and comprehensive software tool.  Design, simulate and analyze Multiplex PCR, Taqman, Molecular Beacons, Microarrays, Allele specific and FRET assays and RNAi and Antisense probes, to name a few of the possible nucleic acid applications. 

Click here to get the 7 myths of PCR Design article  

 

Why "Free" Can Be Expensive

"Free" online software is free because it neglects to assess and identify many of the effects that may cause primer and probe designs to fail in an assay, thereby costing the user in the long run.  This can be a false positive to your budget, so to speak.  Elements of "Free" include:

  • Target concentration, secondary structure and false positives ignored
  • Primer and Probe concentration, secondary structure and "dimers" ignored
  • Salt concentration effects ignored
  • Sequence dependence of base stacking ignored
  • Modified backbones and bases ignored
  • Duplex basepair mismatches, bulges and loops ignored
  • Simple two-state models ignore mishybridization and crosshybridization which may also lead to false positives
  • "Free" multiplex applications are nearly impossible to design
  • Lost productivity and material costs in validating and optimizing re-designed assays

Visual OMP = Oligonucleotide Modeling Platform + Multistate Equilibrium

  • Rich GUI's to visualize assay performance and to diagnose problems in existing assays
  • Predict hybridization thermodynamics, secondary structure folding, and simulate melting curves
  • Integrated ThermoBLAST, CLUSTAL, BLAST, and Entrez search engine
  • Automated oligonucleotide assay design for many assay formats
  • DNA, RNA, DNA / RNA and modified backbones and bases
  • OMP was built for multiplexing applications
  • Reduce design, validation and optimization costs 

Schedule a Live Web Demo

The best way to learn how Visual OMP™ can assist your work is to schedule a live web demo specifically tailored to your research needs and interests. Click Here to Contact Us and Get Started with Visual OMP

World Class Science

Visual OMP is based on the Oligonucleotide Modeling Platform, the only software platform that uses the latest, validated, nearest-neighbor thermodynamic parameters to produce the most accurate results on the market. 

  • Complete nearest-neighbors for DNA-DNA, RNA-RNA and DNA-RNA duplex and monomer folding
  • Original nearest-neighbors for PNA, Morpholino, Phosphorothioate and 2'O-methyl backbones
  • Original nearest-neighbors for LNA, Inosine, Deoxy-U, Iso-C and Iso-G, 5-methylC, 7-deaza-G, rT and diaminopurine
  • Thermodynamic corrections for commonly used PCR additives and denaturing solvents
  • Thermodynamic corrections for commonly used salt mixtures and fluorophores

For more information about how Visual OMP works, please click on the following link.

How Visual OMP Works.

 

World Class Customers

“In my experience, DNA Software saved me 75% of my oligo costs...” ~Helen Minnis, Wave 80 

“I am a long-term user of Visual OMP. I like this program very much because it provides a solid scientific basis for oligo design and cuts the development time by more than half...” ~Olga Budker, longtime Visual OMP user

"I have designed over 10,000 PCR assays in my experience with DNA Software's Visual OMP and found greater than 95% success rate when using it to design my assays compared to less than 20% success without it." ~Dr. Eric Bruening, Molecular MD

 

 

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Our Latest

Thursday, 24 October 2013 00:00

DNA Software announces the release of version 1.15 of qPCR CopyCount with features that improve both relative and absolute quantification.

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“We find it [Visual OMP™] makes very accurate and sometimes surprising (but true) predictions about binding efficiency in multiplexes...” David Whitcombe, Chief Scientific Officer, DxS Ltd, UK.
“It [Visual OMP™] is very powerful software when used for multiplexing design...” Chris Novak, Ambion
“I have designed over 10,000 PCR assays in my experience with DNA Software’s Visual OMP™ and found greater than 95% success rate when using it to design my assays compared to less than 20% success without it.” Dr. Eric Bruening, MolecularMD
“I have been using DNA [Software™] for a long time, at least 8 years. I want to have the best tools available and that is why we use it.” Dr. Nancy Schoenbrunner, Roche Molecular Systems
“I am a long-term user of Visual OMP™. I like this program very much because it provides a solid scientific basis for oligo design and cuts the development time by more than half.” Olga Budker, longtime Visual OMP user
“In my experience, DNA Software™ saved me 75% of my oligo costs.” Helen Minnis, Wave 80
“DNA [Software™] has passed my tests. I’ve recommended it [Visual OMP™]. It performs extremely well.” Dr. Ned Sekinger, Luminex Corporation
“Learning to use the program [Visual OMP™] is time well spent, and the support staff at DNA Software is always ready and able to help” Dr. Sue J. Kohlhepp, Providence Portland Medical Center.