title: Microarray synthesis through multiple-use PCR primer design.
abstract: A substantial percentage of the expense in constructing full-genome spotted microarrays comes from the cost of synthesizing the PCR primers to amplify the desired DNA. We propose a computationally-based method to substantially reduce this cost. Historically, PCR primers are designed so that each primer occurs uniquely in the genome. This condition is unnecessarily strong for selective amplification, since only the primer pair associated with each amplification need be unique. We demonstrate that careful design in a genome-level amplification project permits us to save the cost of several thousand primers over conventional approaches.
authors.affiliation: Applied Algorithm Laboratory, Department of Computer Science, State University of New York Stony Brook, NY, 11794-4400, USA.
authors.forename: Rohan J
authors.initials: RJ
authors.lastname: Fernandes
authors.forename: Steven S
authors.initials: SS
authors.lastname: Skiena
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D017076:Computer-Aided Design; D017931:DNA Primers / Q000235:genetics*; D004867:Equipment Design / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers