Applied Microbiology and Biotechnology

, Volume 100, Issue 13, pp 5897–5906 | Cite as

Application of locked nucleic acid-based probes in fluorescence in situ hybridization

  • Sílvia Fontenete
  • Daniel Carvalho
  • Nuno Guimarães
  • Pedro Madureira
  • Céu Figueiredo
  • Jesper Wengel
  • Nuno Filipe AzevedoEmail author
Applied genetics and molecular biotechnology


Fluorescence in situ hybridization (FISH) employing nucleic acid mimics as probes is becoming an emerging molecular tool in the microbiology area for the detection and visualization of microorganisms. However, the impact that locked nucleic acid (LNA) and 2′-O-methyl (2′-OMe) RNA modifications have on the probe that is targeting microorganisms is unknown. In this study, the melting and hybridization efficiency properties of 18 different probes in regards to their use in FISH for the detection of the 16S rRNA of Helicobacter pylori were compared. For the same sequence and target, probe length and the type of nucleic acid mimics used as mixmers in LNA-based probes strongly influence the efficiency of detection. LNA probes with 10 to 15 mers showed the highest efficiency. Additionally, the combination of 2′-OMe RNA with LNA allowed an increase on the fluorescence intensities of the probes. Overall, these results have significant implications for the design and applications of LNA probes for the detection of microorganisms.


FISH Locked nucleic acids Urea Bacteria 


Compliance with Ethical Standards


This study was funded by Project UID/EQU/00,511/2013-LEPABE, by the FCT/MEC with national funds and when applicable co-funded by FEDER in the scope of the P2020 Partnership Agreement Project NORTE-07-0124-FEDER-000,025-RL2_Environment&Health; by FEDER funds through Programa Operacional Factores de Competitividade–COMPETE; by the Programa Operacional do Norte (ON2) program and by national funds through FCT-Fundação para a Ciência e a Tecnologia (DNA mimics Research Project PIC/IC/82,815/2007), PhD grant (SFRH/BD/72,999/2010 to SF), and Post-Doctoral fellowship (SFRH/BPD/78,846/2011 to NG); and by Nucleic Acid Center, University of Southern Denmark.

Conflict of interest

Jesper Wengel is cofounder of RiboTask ApS, which offers LNA/2′-OMe-RNA probes for RNA targeting. Nuno Filipe Azevedo is cofounder of Biomode SA, which develops molecular methods for the rapid detection of microorganisms. This does not alter the authors’ adherence to all the Applied Microbiology and Biotechnology policies on sharing data and materials.

Human and animals studies

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

253_2016_7429_MOESM1_ESM.pdf (362 kb)
ESM 1 (PDF 361 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Sílvia Fontenete
    • 1
    • 2
    • 3
    • 4
    • 5
    • 8
  • Daniel Carvalho
    • 1
  • Nuno Guimarães
    • 1
    • 2
    • 3
    • 4
  • Pedro Madureira
    • 2
    • 5
    • 6
  • Céu Figueiredo
    • 2
    • 3
    • 7
  • Jesper Wengel
    • 4
  • Nuno Filipe Azevedo
    • 1
    Email author
  1. 1.LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of EngineeringUniversity of PortoPortoPortugal
  2. 2.i3S, Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
  3. 3.IPATIMUP, Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
  4. 4.Nucleic Acid Center, Department of Physics, Chemistry and PharmacyUniversity of Southern DenmarkOdense MDenmark
  5. 5.ICBAS, Institute of Biomedical Sciences Abel SalazarUniversity of PortoPortoPortugal
  6. 6.IBMC, Institute for Molecular Biology and Cell BiologyPortoPortugal
  7. 7.FMUP, Faculty of Medicine of the University of Porto UniversityPortoPortugal
  8. 8.Epithelial Cell Biology Group; Cancer Cell Biology ProgramSpanish National Cancer Research CentreMadridSpain

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