Analytical and Bioanalytical Chemistry

, Volume 411, Issue 25, pp 6583–6590 | Cite as

Arabidopsis thaliana ITS sequence-specific DNA extraction by ion-tagged oligonucleotides coupled with a magnetic ionic liquid

  • Arianna Marengo
  • Miranda N. Emaus
  • Cinzia M. Bertea
  • Carlo Bicchi
  • Patrizia Rubiolo
  • Cecilia CaglieroEmail author
  • Jared L. Anderson


This study reports a follow-up investigation on the capture of specific DNA sequences using ion-tagged oligonucleotides (ITOs) and magnetic ionic liquids (MIL). Five allylimidazolium salts bearing octyl substituents ([AOIM+]-ITOs) were used for the selective extraction of the internal transcribed spacer region (ITS) from Arabidopsis thaliana. In this work, the ability of the [AOIM+]-ITOs to enhance the extraction of longer target sequences (~ 700 bp) of plant origin was shown. Moreover, the independence of the probe binding position and the importance of complementarity to the target region for the extraction performance were demonstrated. To test the specificity of the ITOs, the same experiments were performed using the ITS region from another plant species, with a lower target capture for the probes which were specific for the A. thaliana sequence. Finally, extraction in the presence of interferences (heterogenous DNA, primary and secondary metabolites, proteins) provided interesting and insightful results. This work illustrates the feasibility and versatility of these probes when coupled to MILs for rapid, cost-effective, and environmentally sensitive sample preparation in the extraction of specific target sequences from different origins.

Graphical abstract


Sequence-specific DNA extraction Arabidopsis thaliana Ion-tagged oligonucleotide Magnetic ionic liquid Internal transcribed spacer 


Funding information

JLA received funding from the Chemical Measurement and Imaging Program at the National Science Foundation (grant number CHE-1709372).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

216_2019_2054_MOESM1_ESM.pdf (580 kb)
ESM 1 (PDF 580 kb)


  1. 1.
    Clark KD, Zhu C, Anderson JL. Maximizing ion-tagged oligonucleotide loading on magnetic ionic liquid supports for the sequence-specific extraction of nucleic acids. Anal Chem. 2019;91:5945–52.CrossRefGoogle Scholar
  2. 2.
    Marengo A, Maxia A, Sanna C, Bertea CM, Bicchi C, Ballero M, et al. Characterization of four wild edible Carduus species from the Mediterranean region via phytochemical and biomolecular analyses. Food Res Int. 2017;100:822–31.CrossRefGoogle Scholar
  3. 3.
    Hebert PDN, Cywinska A, Ball SL, Jeremy R. Biological identifications through DNA barcodes. Proc R Soc Lond. 2003;270:313–21.CrossRefGoogle Scholar
  4. 4.
    Lee M-H, Leu C-C, Lin C-C, Tseng Y-F, Lin H-Y, Yang C-N. Gold-decorated magnetic nanoparticles modified with hairpin-shaped DNA for fluorometric discrimination of single-base mismatch DNA. Microchim Acta. 2019;186:80.CrossRefGoogle Scholar
  5. 5.
    Liu Y, Duan C, Zhang C, Yang X, Zhao Y, Dong R, et al. Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses. PLoS One. 2015;10:e0117626.CrossRefGoogle Scholar
  6. 6.
    Peng X, Clark KD, Ding X, Zhu C, Varona M, Emaus MN, et al. Coupling oligonucleotides possessing a poly-cytosine tag with magnetic ionic liquids for sequence-specific DNA analysis. Chem Commun. 2018;54:10284–7.CrossRefGoogle Scholar
  7. 7.
    Khater M, de la Escosura-Muñiz A, Quesada-González D, Merkoçi A. Electrochemical detection of plant virus using gold nanoparticle-modified electrodes. Anal Chim Acta. 2019;1046:123–31.CrossRefGoogle Scholar
  8. 8.
    Zeng Y, Zhang D, Qi P. Combination of a flow cytometric bead system with 16S rRNA-targeted oligonucleotide probes for bacteria detection. Anal Bioanal Chem. 2019;411:2161–8.CrossRefGoogle Scholar
  9. 9.
    Yamaguchi A, Matsuda K, Uehara M, Honda T, Saito Y. A novel automated device for rapid nucleic acid extraction utilizing a zigzag motion of magnetic silica beads. Anal Chim Acta. 2016;906:1–6.CrossRefGoogle Scholar
  10. 10.
    Clark KD, Varona M, Anderson JL. Ion-tagged oligonucleotides coupled with a magnetic liquid support for the sequence-specific capture of DNA. Angew Chemie Int Ed. 2017;56:7630–3.CrossRefGoogle Scholar
  11. 11.
    Omelchenko D, Speranskaya A, Ayginin A, Khafizov K, Krinitsina A, Fedotova A, et al. Improved protocols of ITS1-based metabarcoding and their application in the analysis of plant-containing products. Genes (Basel). 2019;10:122–38.CrossRefGoogle Scholar
  12. 12.
    Martinelli F, Scalenghe R, Davino S, Panno S, Scuderi G, Ruisi P, et al. Advanced methods of plant disease detection. A review. Agron Sustain Dev. 2015;35:1–25.CrossRefGoogle Scholar
  13. 13.
    Gonzalez García E, Ressmann AK, Gaertner P, Zirbs R, Mach RL, Krska R, et al. Direct extraction of genomic DNA from maize with aqueous ionic liquid buffer systems for applications in genetically modified organisms analysis. Anal Bioanal Chem. 2014;406:7773–84.CrossRefGoogle Scholar
  14. 14.
    Meinke DW. Arabidopsis thaliana: a model plant for genome analysis. Science (80- ). 1998;282:662–82.CrossRefGoogle Scholar
  15. 15.
    Kress WJ. Plant DNA barcodes: applications today and in the future. J Syst Evol. 2017;55:291–307.CrossRefGoogle Scholar
  16. 16.
    White TJ, Bruns T, Lee S, Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protoc Guid Methods Appl. 1990;3:315–22.Google Scholar
  17. 17.
    Pierson SA, Nacham O, Clark KD, Nan H, Mudryk Y, Anderson JL. Synthesis and characterization of low viscosity hexafluoroacetylacetonate-based hydrophobic magnetic ionic liquids. New J Chem. 2017;41:5498–505.CrossRefGoogle Scholar
  18. 18.
    Marengo A, Cagliero C, Sgorbini B, Anderson JL, Emaus MN, Bicchi C, et al. Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids. Plant Methods. 2019;15:23–34.CrossRefGoogle Scholar
  19. 19.
    Marengo A, Maxia A, Sanna C, Mandrone M, Bertea CM, Bicchi C, et al. Intra-specific variation in the little-known Mediterranean plant Ptilostemon casabonae (L.) Greuter analysed through phytochemical and biomolecular markers. Phytochemistry. 2019;161:21–7.CrossRefGoogle Scholar
  20. 20.
    Chester N, Marshak DR. Dimethyl sulfoxide-mediated primer Tm reduction: a method for analyzing the role of renaturation temperature in the polymerase chain reaction. Anal Biochem. 1993;209:284–90.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Arianna Marengo
    • 1
  • Miranda N. Emaus
    • 2
  • Cinzia M. Bertea
    • 3
  • Carlo Bicchi
    • 1
  • Patrizia Rubiolo
    • 1
  • Cecilia Cagliero
    • 1
    Email author
  • Jared L. Anderson
    • 2
  1. 1.Dipartimento di Scienza e Tecnologia del FarmacoUniversità di TorinoTurinItaly
  2. 2.Department of ChemistryIowa State UniversityAmesUSA
  3. 3.Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia VegetaleUniversità di TorinoTurinItaly

Personalised recommendations