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

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Abstract

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.

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Funding

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

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Authors and Affiliations

  1. Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125, Turin, Italy

    Arianna Marengo, Carlo Bicchi, Patrizia Rubiolo & Cecilia Cagliero

  2. Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, IA, 50011, USA

    Miranda N. Emaus & Jared L. Anderson

  3. Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, via Quarello 15/A, 10135, Turin, Italy

    Cinzia M. Bertea

Authors
  1. Arianna Marengo
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  2. Miranda N. Emaus
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  3. Cinzia M. Bertea
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  4. Carlo Bicchi
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  5. Patrizia Rubiolo
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  6. Cecilia Cagliero
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  7. Jared L. Anderson
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Correspondence to Cecilia Cagliero.

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Marengo, A., Emaus, M.N., Bertea, C.M. et al. Arabidopsis thaliana ITS sequence-specific DNA extraction by ion-tagged oligonucleotides coupled with a magnetic ionic liquid. Anal Bioanal Chem 411, 6583–6590 (2019). https://doi.org/10.1007/s00216-019-02054-z

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  • DOI: https://doi.org/10.1007/s00216-019-02054-z

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