Applied Microbiology and Biotechnology

, Volume 98, Issue 23, pp 9595–9608 | Cite as

Mathematical tools to optimize the design of oligonucleotide probes and primers

  • Daniel R. NogueraEmail author
  • Erik S. Wright
  • Pamela Camejo
  • L. Safak Yilmaz


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.


Oligonucleotides DNA probes FISH PCR Microarrays Mismatch stability Microbial diversity Primer design 



The authors would like to thank Alexander Steinbüchel for the invitation to write this review. This research was partially supported by a fellowship from Becas Chile (Conicyt) to Pamela Camejo.

Conflict of interest

The authors declare that they have no conflict of interest.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Daniel R. Noguera
    • 1
    • 2
    • 6
    Email author
  • Erik S. Wright
    • 3
    • 4
  • Pamela Camejo
    • 1
  • L. Safak Yilmaz
    • 5
  1. 1.Department of Civil and Environmental EngineeringUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Great Lakes Bioenergy Research CenterUniversity of Wisconsin-MadisonMadisonUSA
  3. 3.Systems Biology Theme, Wisconsin Institute for DiscoveryUniversity of Wisconsin-MadisonMadisonUSA
  4. 4.Department of BacteriologyUniversity of Wisconsin-MadisonMadisonUSA
  5. 5.Program in Systems BiologyUniversity of Massachusetts Medical SchoolWorcesterUSA
  6. 6.MadisonUSA

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