Physical Principles and Visual-OMP Software for Optimal PCR Design

  • John SantaLuciaJr
Part of the Methods in Molecular Biology™ book series (MIMB, volume 402)


The physical principles of DNA hybridization and folding are described within the context of how they are important for designing optimal PCRs. The multi-state equilibrium model for computing the concentrations of competing unimolecular and bimolecular species is described. Seven PCR design “myths” are stated explicitly, and alternative proper physical models for PCR design are described. This chapter provides both a theoretical framework for understanding PCR design and practical guidelines for users. The Visual-OMP (oligonucleotide modeling platform) package from DNA Software, Inc. is also described.

Key Words

Thermodynamics nearest-neighbor model multi-state model Visual-OMP secondary structure oligonucleotide design software 


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Copyright information

© Humana Press 2007

Authors and Affiliations

  • John SantaLuciaJr
    • 1
    • 2
  1. 1.Department of ChemistryWayne State UniversityDetroitUSA
  2. 2.DNA Software, Inc.Ann ArborUSA

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