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Related Experiment Videos

Primer Prim'er: a web based server for automated primer design.

John K Everett1, Thomas B Acton, Gaetano T Montelione

  • 1Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854-5638, USA.

Journal of Structural and Functional Genomics
|July 21, 2004
PubMed
Summary

The Primer program automates protein production for structural biology by designing gene-specific primers. This tool aids in efficiently cloning thousands of genes for large-scale structural genomics projects.

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Area of Science:

  • Structural Biology
  • Genomics
  • Bioinformatics

Background:

  • Structural studies of proteins are crucial for understanding biological functions.
  • Automating protein production is essential for large-scale structural genomics.
  • The Northeast Structural Genomics Consortium (NESG) aims to develop technologies for genome-wide protein structural studies.

Purpose of the Study:

  • To introduce the Primer program, a web-based tool for automating primer design.
  • To streamline the protein production pipeline for structural determination.
  • To facilitate efficient cloning of multiple genes for structural genomics.

Main Methods:

  • Development of a web-based primer design program called Primer.
  • Simultaneous calculation of plasmid-specific primer sets for multiple open reading frame (ORF) targets.

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  • Inclusion of a library of common plasmid systems and user-defined plasmid uploads.
  • Addition of restriction endonuclease recognition or viral recombination sites while preserving reading frames for plasmid-based fusions.

    • Main Results:

    • The Primer program automates the design of gene-specific primers for protein production.
    • It supports multiple ORF targets and various well formats (e.g., 96-well).
    • The program provides features like sorting primer sets by target size and calculating expected PCR fragment sizes.
    • The NESG has successfully cloned over 1500 genes using primers designed by this program.

    Conclusions:

    • The Primer program significantly automates and accelerates the time-consuming task of primer design for structural genomics.
    • It enhances the efficiency of the protein production pipeline, enabling large-scale gene cloning.
    • This bioinformatics tool is a valuable resource for molecular biologists engaged in structural studies.