Literature DB >> 17951788

Physical principles and visual-OMP software for optimal PCR design.

John SantaLucia1.   

Abstract

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.

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Year:  2007        PMID: 17951788     DOI: 10.1007/978-1-59745-528-2_1

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  43 in total

1.  Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex.

Authors:  Nilshad Salim; Rajan Lamichhane; Rui Zhao; Tuhina Banerjee; Jane Philip; David Rueda; Andrew L Feig
Journal:  Biophys J       Date:  2012-03-06       Impact factor: 4.033

2.  Development and characterization of a highly specific and sensitive SYBR green reverse transcriptase PCR assay for detection of the 2009 pandemic H1N1 influenza virus on the basis of sequence signatures.

Authors:  Rafael A Medina; Mark Rojas; Astrid Tuin; Stephen Huff; Marcela Ferres; Constanza Martinez-Valdebenito; Paula Godoy; Adolfo García-Sastre; Yuriy Fofanov; John SantaLucia
Journal:  J Clin Microbiol       Date:  2010-11-17       Impact factor: 5.948

3.  Multiplex Solid-Phase Melt Curve Analysis for the Point-of-Care Detection of HIV-1 Drug Resistance.

Authors:  Dana S Clutter; Gelareh Mazarei; Ruma Sinha; Justen Manasa; Janin Nouhin; Ellen LaPrade; Sara Bolouki; Philip L Tzou; Jessica Hannita-Hui; Malaya K Sahoo; Peter Kuimelis; Robert G Kuimelis; Benjamin A Pinsky; Gary K Schoolnik; Arjang Hassibi; Robert W Shafer
Journal:  J Mol Diagn       Date:  2019-04-23       Impact factor: 5.568

4.  Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection.

Authors:  Brian N Tse; Thomas M Snyder; Yinghua Shen; David R Liu
Journal:  J Am Chem Soc       Date:  2008-10-29       Impact factor: 15.419

5.  Dilute-'N'-Go dideoxy sequencing of all DNA strands generated in multiplex LATE-PCR assays.

Authors:  Yanwei Jia; Adam Osborne; John E Rice; Lawrence J Wangh
Journal:  Nucleic Acids Res       Date:  2010-02-26       Impact factor: 16.971

6.  Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm.

Authors:  Christina Ohrmalm; Magnus Jobs; Ronnie Eriksson; Sultan Golbob; Amal Elfaitouri; Farid Benachenhou; Maria Strømme; Jonas Blomberg
Journal:  Nucleic Acids Res       Date:  2010-09-22       Impact factor: 16.971

7.  Application of equilibrium models of solution hybridization to microarray design and analysis.

Authors:  Raad Z Gharaibeh; Joshua M Newton; Jennifer W Weller; Cynthia J Gibas
Journal:  PLoS One       Date:  2010-06-10       Impact factor: 3.240

8.  A thermodynamic approach to PCR primer design.

Authors:  Tobias Mann; Richard Humbert; Michael Dorschner; John Stamatoyannopoulos; William Stafford Noble
Journal:  Nucleic Acids Res       Date:  2009-06-15       Impact factor: 16.971

9.  Model-based probe set optimization for high-performance microarrays.

Authors:  Germán Gastón Leparc; Thomas Tüchler; Gerald Striedner; Karl Bayer; Peter Sykacek; Ivo L Hofacker; David P Kreil
Journal:  Nucleic Acids Res       Date:  2008-12-22       Impact factor: 16.971

10.  Hybridization thermodynamics of NimbleGen microarrays.

Authors:  Ulrike Mueckstein; Germán G Leparc; Alexandra Posekany; Ivo Hofacker; David P Kreil
Journal:  BMC Bioinformatics       Date:  2010-01-19       Impact factor: 3.169

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