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Virtually every cellular process is regulated by protein-protein interactions. Identifying and ultimately understanding these protein-protein interactions is a critical step in functional genomic analysis (1). Toward this end, the yeast two-hybrid system has been widely used for the identification of protein-protein interactions (2). A pivotal step to the success of the two-hybrid assay is the design of suitable primers. Several primer prediction and analysis programs, e.g., Primer3, Web Primer and ExonPrimer, have been developed for diverse applications. However, none of these existing programs can be directly used for the design of primers in protein interaction experiments, since proteins may have transmembrane domains (TMDs) and/or a signal peptide that must be excluded from experiments. Furthermore, it is frequently the case that a short restriction sequence must be added to each primer in order to clone PCR products into destination vectors for expression.

DePIE, a web-based primer design tool, was developed to address these deficiencies. The program takes as input NCBI protein accession numbers and returns primer information including nucleotide sequences, thermodynamic melting temperature of the nucleotide sequences and the target positions. DePIE is implemented in JAVA, PERL and PHP and available via web browser from http://biocore.unl.edu/primer/primerPI.html.

References

1. Eisenberg, D., Marcotte, E. M., Xenarios, I. and Yeates, T. O. (2000) Protein function in the post-genomic era. Nature, 405: 823-826.

2. Toby, G. G. and Golemis E. A. (2001) Using the Yeast Interaction Trap and Other Two-Hybrid-Based Approaches to Study Protein-Protein Interactions. Methods 24: 201-217.

Last update: March 2, 2003

DePIE
Design Primers for Protein Interaction Experiments
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HOME Virtually every cellular process is regulated by protein-protein interactions. Identifying and ultimately understanding these protein-protein interactions is a critical step in functional genomic analysis (1). Toward this end, the yeast two-hybrid system has been widely used for the identification of protein-protein interactions (2). A pivotal step to the success of the two-hybrid assay is the design of suitable primers. Several primer prediction and analysis programs, e.g., Primer3, Web Primer and ExonPrimer, have been developed for diverse applications. However, none of these existing programs can be directly used for the design of primers in protein interaction experiments, since proteins may have transmembrane domains (TMDs) and/or a signal peptide that must be excluded from experiments. Furthermore, it is frequently the case that a short restriction sequence must be added to each primer in order to clone PCR products into destination vectors for expression. DePIE, a web-based primer design tool, was developed to address these deficiencies. The program takes as input NCBI protein accession numbers and returns primer information including nucleotide sequences, thermodynamic melting temperature of the nucleotide sequences and the target positions. DePIE is implemented in JAVA, PERL and PHP and available via web browser from http://biocore.unl.edu/primer/primerPI.html. References 1. Eisenberg, D., Marcotte, E. M., Xenarios, I. and Yeates, T. O. (2000) Protein function in the post-genomic era. Nature, 405: 823-826. 2. Toby, G. G. and Golemis E. A. (2001) Using the Yeast Interaction Trap and Other Two-Hybrid-Based Approaches to Study Protein-Protein Interactions. Methods 24: 201-217. Last update: March 2, 2003

DePIE

Design Primers for Protein Interaction Experiments