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DNA-directed assembly of copper nanoblocks with inbuilt fluorescent and electrochemical properties: Application in simultaneous amplification-free analysis of multiple RNA species

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Abstract

The intrinsic affinity of DNA molecules toward metallic ions can drive the specific formation of copper nanostructures within the nucleic acid helix structure in a sequence-dependent manner. The resultant nanostructures have interesting fluorescent and electrochemical properties, which are attractive for novel biosensing applications. However, the potential of using DNA-templated nanostructures for precision disease diagnosis remains unexplored. Particularly, DNAtemplated nanostructures show high potential for the universal amplification-free detection of different RNA biomarker species. Because of their low cellular levels and differing species-dependent length and sequence features, simultaneous detection of different messenger RNAs, microRNAs, and long non-coding RNAs species with a single technique is challenging. Here, we report a contemporary technique for facile in situ assembly of DNA-templated copper nanoblocks (CuNBs) on various RNA species targets after hybridization-based magnetic isolation. Our approach circumvents the typical limitations associated with amplification and labeling procedures of current RNA assays. The synthesized CuNBs enabled amplification-free fM-level RNA detection with flexible fluorescence or electrochemical readouts. Furthermore, our nanosensing technique displays potential for clinical application, as demonstrated by non-invasive analysis of three diagnostic RNA biomarkers from a cohort of 10 prostate cancer patient urinary samples with 100%-concordance (quantitative reverse transcriptionpolymerase chain reaction (PCR) validation). The good analytical performance and versatility of our method may be useful in both diagnostics and research fields.

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Acknowledgements

This work was supported by the UQ Postdoctoral Research Fellowship (No. 2012001456). Although not directly funding the research work in this paper, we acknowledge funding received by our laboratory from the National Breast Cancer Foundation of Australia (No. CG-12-07). This grant has significantly contributed to the environment to stimulate the research described here. K. M. K. acknowledges support from the Australian Government Research Training Program Scholarship. We thank Robert “Frank” Gardiner, Aine Farrell, Robyn Medcraft, and Clement Chow for collecting and providing clinical urine samples. We thank Junrong Li for TEM imaging.

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  1. Kevin M. Koo and Laura G. Carrascosa contributed equally to this work.

Authors and Affiliations

  1. Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia

    Kevin M. Koo, Laura G. Carrascosa & Matt Trau

  2. School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia

    Matt Trau

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  1. Kevin M. Koo
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  2. Laura G. Carrascosa
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Correspondence to Matt Trau.

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DNA-directed assembly of copper nanoblocks with inbuilt fluorescent and electrochemical properties: Application in simultaneous amplification-free analysis of multiple RNA species

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Koo, K.M., Carrascosa, L.G. & Trau, M. DNA-directed assembly of copper nanoblocks with inbuilt fluorescent and electrochemical properties: Application in simultaneous amplification-free analysis of multiple RNA species. Nano Res. 11, 940–952 (2018). https://doi.org/10.1007/s12274-017-1706-0

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