Skip to main content

Antisense Effects of PNAs in Bacteria

  • Protocol
  • First Online:
Peptide Nucleic Acids

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1050))

Abstract

Antisense peptide nucleic acid (PNA) can be used to control bacterial gene expression. PNAs are designed to target sequences within messenger RNA and knock-down gene expression. PNAs targeted to the translation initiation region of mRNA are particularly effective and result in mRNA degradation and reduced protein expression from the targeted gene. The antisense effects can be sufficient to alter phenotypes and even kill bacteria. PNAs provide useful tools for the study of bacterial gene function, and with improvements in cell uptake antisense PNAs may find applications as antimicrobial agents. This chapter details methods for designing antisense PNAs and testing their activities in bacteria, including suggestions for control experiments.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Thomason MK, Storz G (2010) Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet 44:167–188

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  2. Good L, Nielsen PE (1998) Antisense inhibition of gene expression in bacteria by PNA targeted to mRNA. Nat Biotechnol 16(4):355–358

    Article  PubMed  CAS  Google Scholar 

  3. Good L, Nielsen PE (1998) Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA. Proc Natl Acad Sci U S A 95(5):2073–2076

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  4. Harth G, Horwitz MA, Tabatadze D, Zamecnik PC (2002) Targeting the Mycobacterium tuberculosis 30/32-kDa mycolyl transferase complex as a therapeutic strategy against tuberculosis: proof of principle by using antisense technology. Proc Natl Acad Sci U S A 99(24):15614–15619

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  5. White DG, Maneewannakul K, von Hofe E, Zillman M, Eisenberg W, Field AK, Levy SB (1997) Inhibition of the multiple antibiotic resistance (mar) operon in Escherichia coli by antisense DNA analogs. Antimicrob Agents Chemother 41(12):2699–2704

    PubMed Central  PubMed  CAS  Google Scholar 

  6. Nikaido H (1994) Prevention of drug access to bacterial targets: permeability barriers and active efflux. Science 264(5157):382–388

    Article  PubMed  CAS  Google Scholar 

  7. Eriksson M, Nielsen PE, Good L (2002) Cell permeabilization and uptake of antisense peptide-peptide nucleic acid (PNA) into Escherichia coli. J Biol Chem 277(9):7144

    Article  PubMed  CAS  Google Scholar 

  8. Nekhotiaeva N, Awasthi SK, Nielsen PE, GOOD L (2004) Inhibition of Staphylococcus aureus gene expression and growth using antisense peptide nucleic acids. Mol Ther 10(4):652–659

    Article  PubMed  CAS  Google Scholar 

  9. Kulyté A, Nekhotiaeva N, Awasthi SK, GOOD L (2005) Inhibition of Mycobacterium smegmatis gene expression and growth using antisense peptide nucleic acids. J Mol Microbiol Biotechnol 9(2):101–109

    Article  PubMed  CAS  Google Scholar 

  10. Dryselius R, Aswasti SK, Rajarao GK, Nielsen PE, GOOD L (2003) The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli. Oligonucleotides 13(6):427–433

    Article  PubMed  CAS  Google Scholar 

  11. Good L (2003) Translation repression by antisense sequences. Cell Mol Life Sci 60(5):854–861

    PubMed  CAS  Google Scholar 

  12. Goh S, Boberek JM, Nakashima N, Stach J, Good L (2009) Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS One 4(6):e6061

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  13. Good L, Awasthi SK, Dryselius R, Larsson O, Nielsen PE (2001) Bactericidal antisense effects of peptide-PNA conjugates. Nat Biotechnol 19(4):360–364

    Article  PubMed  CAS  Google Scholar 

  14. Dryselius R, Nikravesh A, Kulyté A, Goh S, GOOD L (2006) Variable coordination of cotranscribed genes in Escherichia coli following antisense repression. BMC Microbiol 6(1):97

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  15. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):611–622

    Article  PubMed  CAS  Google Scholar 

  16. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8(2):R19

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  17. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25(4):402–408

    Article  PubMed  CAS  Google Scholar 

  18. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29(9):e45

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  19. Faridani OR, Nikravesh A, Pandey DP, Gerdes K, Good L (2006) Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli. Nucleic Acids Res 34(20):5915–5922

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  20. Hatamoto M, Nakai K, Ohashi A, Imachi H (2009) Sequence-specific bacterial growth inhibition by peptide nucleic acid targeted to the mRNA binding site of 16S rRNA. Appl Microbiol Biotechnol 84(6):1161–1168

    Article  PubMed  CAS  Google Scholar 

  21. Gruegelsiepe H, Brandt O, Hartmann RK (2006) Antisense inhibition of RNase P: mechanistic aspects and application to live bacteria. J Biol Chem 281(41):30613–30620

    Article  PubMed  CAS  Google Scholar 

  22. Bai H, Zhou Y, Hou Z, Xue X, Meng J, Luo X (2011) Targeting bacterial RNA polymerase: promises for future antisense antibiotics development. Infect Disord Drug Targets 11(2):175–187

    Article  PubMed  CAS  Google Scholar 

  23. Jeon B, Zhang Q (2009) Sensitization of Campylobacter jejuni to fluoroquinolone and macrolide antibiotics by antisense inhibition of the CmeABC multidrug efflux transporter. J Antimicrob Chemother 63(5):946–948

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  24. Kurupati P, Tan KSW, Kumarasinghe G, Poh CL (2007) Inhibition of gene expression and growth by antisense peptide nucleic acids in a multiresistant beta-lactamase-producing Klebsiella pneumoniae strain. Antimicrob Agents Chemother 51(3):805–811

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  25. Dryselius R, Nekhotiaeva N, Good L (2005) Antimicrobial synergy between mRNA-and protein-level inhibitors. Br Soc Antimicrob Chemother

    Google Scholar 

  26. Boberek JM, Stach J, Good L (2010) Genetic evidence for inhibition of bacterial division protein FtsZ by berberine. PLoS One 5(10):e13745

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  27. Prescott AM, Fricker CR (1999) Use of PNA oligonucleotides for the in situ detection of Escherichia coli in water. Mol Cell Probes 13(4):261–268

    Article  PubMed  CAS  Google Scholar 

  28. Gião MS, Wilks SA, Azevedo NF, Vieira MJ, Keevil CW (2009) Comparison between standard culture and peptide nucleic acid 16S rRNA hybridization quantification to study the influence of physico-chemical parameters on Legionella pneumophila survival in drinking water biofilms. Biofouling 25(4):343–351

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, New York

About this protocol

Cite this protocol

Goh, S., Stach, J., Good, L. (2014). Antisense Effects of PNAs in Bacteria. In: Nielsen, P., Appella, D. (eds) Peptide Nucleic Acids. Methods in Molecular Biology, vol 1050. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-553-8_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-553-8_18

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-552-1

  • Online ISBN: 978-1-62703-553-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics