title: PrimerSelect: a transcriptome-wide oligonucleotide primer pair design program for kinetic RT-PCR-based transcript profiling.
abstract: We describe PrimerSelect, a program capable of transcriptome-wide design of primer pairs for optimal performance in kinetic reverse-transcriptase polymerase chain reaction (RT-PCR). For the yeast Saccharomyces cerevisiae, PrimerSelect designs primer pairs for 86% of genomic open reading frames (ORFs) using design criteria we previously established to be optimal for kinetic RT-PCR (kRT-PCR)-based transcript quantitation. Primer pairs designed by PrimerSelect for 230 yeast ORFs were evaluated for primer dimer potential, PCR cyclewise yield, and cross-priming. Performance of 95% of these primer pairs is optimal with respect to primer dimer potential and PCR cyclewise yield for quantitating even the rarest yeast transcript. All of the primer pairs produced a single amplicon of the expected size from yeast genomic DNA template. The utility of PrimerSelect for designing primer pairs complementary to ORF sequences defined for multiple isolates of the human bacterial pathogens Helicobacter pylori and Staphylococcus aureus is also demonstrated.
authors.affiliation: Department of Biochemistry and Molecular Medicine, University of California, School of Medicine, Davis, California 95616, USA.
authors.forename: Kenneth J
authors.initials: KJ
authors.lastname: Graham
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Holland
mesh_terms: D017076:Computer-Aided Design; D017931:DNA Primers; D015195:Drug Design; D020869:Gene Expression Profiling; D016480:Helicobacter pylori / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007700:Kinetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics / Q000302:isolation & purification; D014158:Transcription, Genetic
chemical_list: D017931:DNA Primers