Primer Prim'r: A web based server for automated primer design

  • John K. Everett
  • Thomas B. Acton
  • Gaetano T. Montelione


The Northeast Structural Genomics Consortium (NESG) is one of nine NIH-funded pilot projects created to develop technologies needed for structural studies of proteins on a genome-wide scale. One of the most challenging aspects of this emerging field is the production of protein samples amenable to structural determination. To do this efficiently, all steps in the protein production pipeline must be automated. Here we describe the Primer program (linked from,, a web-based primer design program freely available to the scientific community, which was created to automate this time consuming and laborious task. This program has the ability to simultaneously calculate plasmid specific primer sets for multiple open reading frame (ORF) targets, including 96-well and greater formats. Primer includes a library of commonly used plasmid systems and possesses the ability to upload user-defined plasmid systems. In addition to calculating gene-specific annealing regions for each target, the program also adds appropriate restriction endonuclease recognition or viral recombination sites while preserving a reading frame with plasmid based fusions. Primer has several useful features such as sorting calculated primer sets by target size, facilitating interpretation of PCR amplifications by agarose gel electrophoresis, as well as supplying the molecular biologist with many important characteristics of each target such as the expected size of the PCR amplified DNA fragment and internal restriction sites. The NESG has cloned over 1500 genes using oligonucleotide primers designed by Primer.

domain parsing Northeast Structural Genomics Consortium primer design program, structural genomics 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Walhout, A.J., Temple, G.F., Brasch, M.A., Hartley, J.L., Lorson, M.A., van den Heuvel, S. and Vidal, M. (2000) Methods Enzymol. 328, 575–592.PubMedGoogle Scholar
  2. 2.
    Acton, T.B., Xiao, R., Clement, T., Gunsalus, K, Everett, J.K., Shastry, R., Ma, L.C., Chiang, Y., Wu, M., Ho, C.K., Palacios, D., Montelione, G.T., to be published.Google Scholar
  3. 3.
    Qamar, S., Islam, M. and Tayyab, S. (1993) J. Biochem. (Tokyo) 114, 786–792.Google Scholar
  4. 4.
    Yokoyama, S. (2003) Curr. Opin. Chem. Biol., 7, 39–43.CrossRefPubMedGoogle Scholar
  5. 5.
    Scott, E.E., Spatzenegger, M. and Halpert, J.R. (2001) Arch. Biochem. Biophys. 395, 57–68.CrossRefPubMedGoogle Scholar
  6. 6.
    Rebrin, I., Geha, R.M., Chen, K. and Shih, J.C. (2001) J. Biol. Chem. 276, 29499–29506.CrossRefPubMedGoogle Scholar
  7. 7.
    Wallace, R.B., Shaffer, J., Murphy, R.F., Bonner, J., Hirose, T. and Itakura, K. (1979) Nucleic Acids Res. 6, 3543–3557.PubMedGoogle Scholar
  8. 8.
    Rychlik, W., Spencer, W.J. and Rhoads, R.E. (1990) Nucleic Acids Res. 18, 6409–6412.PubMedGoogle Scholar
  9. 9.
    SantaLucia, J. Jr, Allawi, H.T. and Seneviratne, P.A. (1996) Biochemistry 35, 3555–3562.CrossRefPubMedGoogle Scholar
  10. 10.
    Le Novere, N. (2001) Bioinformatics 17, 1226–1227.CrossRefPubMedGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2004

Authors and Affiliations

  • John K. Everett
    • 1
    • 2
  • Thomas B. Acton
    • 2
  • Gaetano T. Montelione
    • 1
    • 2
  1. 1.Department of BiochemistryRobert Wood Johnson Medical SchoolPiscatawayUSA
  2. 2.Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics ConsortiumRutgers UniversityPiscatawayUSA

Personalised recommendations