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Nucleic Acids Research, 2003, Vol. 31, No. 13 3763-3766
© 2003 Oxford University Press

CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design

Timothy M. Rose*, Jorja G. Henikoff1 and Steven Henikoff1

Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA 1 Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA

*To whom correspondence should be addressed. Tel: +1 206 616 2084; Fax: +1 206 543 3873; Email: trose{at}u.washington.edu

We have developed a new primer design strategy for PCR amplification of distantly related gene sequences based on consensus-degenerate hybrid oligonucleotide primers (CODEHOPs). An interactive program has been written to design CODEHOP PCR primers from conserved blocks of amino acids within multiply-aligned protein sequences. Each CODEHOP consists of a pool of related primers containing all possible nucleotide sequences encoding 3–4 highly conserved amino acids within a 3' degenerate core. A longer 5' non-degenerate clamp region contains the most probable nucleotide predicted for each flanking codon. CODEHOPs are used in PCR amplification to isolate distantly related sequences encoding the conserved amino acid sequence. The primer design software and the CODEHOP PCR strategy have been utilized for the identification and characterization of new gene orthologs and paralogs in different plant, animal and bacterial species. In addition, this approach has been successful in identifying new pathogen species. The CODEHOP designer (http://blocks.fhcrc.org/codehop.html) is linked to BlockMaker and the Multiple Alignment Processor within the Blocks Database World Wide Web (http://blocks.fhcrc.org).


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