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Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

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Abstract

MicroRNAs (miRNAs) are small RNAs that bind to mRNA targets and regulate their translation. A functional study of miRNAs and exploration of their utility as disease markers require miRNA extraction from biological samples, which contain large amounts of interfering compounds for downstream RNA identification and quantification. The most common extraction methods employ silica columns or the TRIzol reagent but give out low recovery for small RNAs probably due to their short strand lengths. Herein, we fabricated the titanium dioxide nanofibers using electrospinning to facilitate miRNA extraction and developed the optimal buffer conditions to improve miRNA recovery from biological matrices of cell lysate and serum. We found that our TiO2 fibers could obtain a recovery of 18.0 ± 3.6% for miRNA fibers while carrying out the extraction in the more complex medium of cell lysate, much higher than the 0.02 ± 0.0001% recovery from the commercial kit. The much improved extraction of miRNAs from our fibers could be originated from the strong coordination between TiO2 and RNA’s phosphate backbone. In addition, the binding, washing, and elution buffers judiciously developed in the present study can achieve selective extraction of small RNA shorter than 500 nucleotides in length. Our results demonstrate that TiO2 nanofibers can work as a valuable tool for extraction of miRNAs from biological samples with high recovery.

Schematic for extraction of small RNAs using TiO2 nanofibers

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Acknowledgments

We are thankful for the kind assistance from Mr. Joshua Belardes on the early stage of buffer optimization for DNA extraction with SiO2 fibers.

Funding

The authors acknowledge the support by the National Cancer Institute of the National Institutes of Health under Award Number R01CA188991 to WZ. This award also provided support (3R01CA188991-02S1) under the Research Supplements to Promote Diversity in Health-Related Research Program for LAJ. MAG was supported by MARCU-STAR training grant from NIH. SS and YM were supported by the Research in Science and Engineering (RISE) undergraduate summer research program at UC Riverside. JGC was supported by UC Riverside’s office of Undergraduate Education (UE).

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Authors and Affiliations

  1. Program in Biomedical Sciences, University of California, 900 University Ave., Riverside, CA, 92521, USA

    Luis A. Jimenez

  2. Department of Chemistry, University of California, 900 University Ave., Riverside, CA, 92521, USA

    Marissa A. Gionet-Gonzales, Sabrina Sedano, Jocelyn G. Carballo, Yomara Mendez & Wenwan Zhong

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  1. Luis A. Jimenez
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  2. Marissa A. Gionet-Gonzales
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  3. Sabrina Sedano
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  4. Jocelyn G. Carballo
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  5. Yomara Mendez
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  6. Wenwan Zhong
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Correspondence to Wenwan Zhong.

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The authors declare that they have no competing interests.

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The serum samples were obtained from commercial sources with the individual information unknown to the researchers.

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Published in the topical collection celebrating ABCs 16th Anniversary.

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Jimenez, L.A., Gionet-Gonzales, M.A., Sedano, S. et al. Extraction of microRNAs from biological matrices with titanium dioxide nanofibers. Anal Bioanal Chem 410, 1053–1060 (2018). https://doi.org/10.1007/s00216-017-0649-3

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  • DOI: https://doi.org/10.1007/s00216-017-0649-3

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