title: Mathematical tools to optimize the design of oligonucleotide probes and primers.
abstract: The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose.
authors.affiliation: Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA, noguera@engr.wisc.edu.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Noguera
authors.forename: Erik S
authors.initials: ES
authors.lastname: Wright
authors.forename: Pamela
authors.initials: P
authors.lastname: Camejo
authors.forename: L Safak
authors.initials: LS
authors.lastname: Yilmaz
mesh_terms: D058448:Biota; D017076:Computer-Aided Design; D017931:DNA Primers / Q000737:chemistry* / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D056186:Metagenomics / Q000379:methods*; D046228:Microarray Analysis / Q000379:methods; D008962:Models, Theoretical; D015345:Oligonucleotide Probes / Q000737:chemistry* / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D012984:Software
chemical_list: D017931:DNA Primers; D015345:Oligonucleotide Probes