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A carbon nanotube reporter of microRNA hybridization events in vivo

Nature Biomedical Engineering volume 1, Article number: 0041 (2017) Cite this article

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Abstract

MicroRNAs and other small oligonucleotides in biofluids are promising disease biomarkers, yet conventional assays require complex processing steps that are unsuitable for point-of-care testing or for implantable or wearable sensors. Single-walled carbon nanotubes are an ideal material for implantable sensors, owing to their emission in the near-infrared spectral region, photostability and exquisite sensitivity. Here, we report an engineered carbon-nanotube-based sensor capable of real-time optical quantification of hybridization events of microRNA and other oligonucleotides. The mechanism of the sensor arises from competitive effects between displacement of both oligonucleotide charge groups and water from the nanotube surface, which result in a solvatochromism-like response. The sensor, which allows for detection via single-molecule sensor elements and for multiplexing by using multiple nanotube chiralities, can monitor toehold-based strand-displacement events, which reverse the sensor response and regenerate the sensor complex. We also show that the sensor functions in whole urine and serum, and can non-invasively measure DNA and microRNA after implantation in live mice.

The detection of oligonucleotide hybridization is important for a broad range of applications, from devices based on dynamic DNA nanotechnology to clinical point-of-care diagnostics. Oligonucleotides in biofluids, such as serum, urine and peritoneal fluid1,2, are a promising source of biomarkers for a variety of pathologies, including cancer3,4. Of the potential biomarker oligonucleo­tides5–7, microRNA (miRNA) is highly stable in body fluids, and many studies have identified specific patterns of miRNA expression indicative of disease states3,8–13. Devices that can measure changes in biomarker miRNA14 or cell-free DNA15 concentrations in biofluids such as urine, serum or ascitic fluid in patients with risk factors for a disease or its relapse may improve early detection and treatment. Implantable or wearable devices that enable minimally invasive continuous biomarker monitoring may extend this strategy to detect biomarkers at the earliest possible stages of disease.

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Figure 1: Carbon nanotube sensor for the detection of miRNA hybridization events.
Figure 2: Characterization of miRNA detection limit, kinetics and functionality.
Figure 3: Single-nanotube response to miRNA hybridization.
Figure 4: Sensor multiplexing.
Figure 5: Monitoring toehold-mediated strand displacement.
Figure 6: Detection of miRNA in biofluids and non-invasively in live mice.

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Acknowledgements

This work was supported by the US National Institutes of Health (NIH) Director’s New Innovator Award (DP2-HD075698), NIH/National Cancer Institute (NCI) Cancer Center Support Grant (P30-CA008748), the Center for Molecular Imaging and Nanotechnology, the Louis V. Gerstner Jr. Young Investigator’s Fund, the Experimental Therapeutics Center, the Alan and Sandra Gerry Metastasis Research Initiative, Cycle for Survival, the Frank A. Howard Scholars Program, the Honorable Tina Brozman Foundation for Ovarian Cancer Research, the Byrne Research Fund, the Anna Fuller Fund, Mr William H. Goodwin and Mrs Alice Goodwin and the Commonwealth Foundation for Cancer Research, and the Imaging and Radiation Sciences Program at Memorial Sloan Kettering Cancer Center. Molecular simulation work was performed at Lehigh University and is supported by the US Department of Energy (DOE) Office of Science, Basic Energy Sciences (BES), and Division of Material Sciences and Engineering, under award DE-SC0013979. Use of the high-performance computing capabilities of the Extreme Science and Engineering Discovery Environment (XSEDE) was supported by the US National Science Foundation under grant number TG-MCB-120014. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported under contract no. DE-AC02-05CH11231. P.V.J. was supported by the NCI Grant NIH T32 Training Grant 2T32CA062948-21. H.A.B. was supported by a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award number T32GM007739 to the Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program. R.M.W. was supported by the Ovarian Cancer Research Fund Alliance (Anna Schreiber Mentored Investigator Award 370463). D.R. was supported by an American Cancer Society 2013 Roaring Fork Valley Research Fellowship and grant no. P20GM103430 from the National Institute of General Medical Sciences of the NIH. We thank the Molecular Cytology Core Facility at Memorial Sloan Kettering Cancer Center and N. Paknejad for the atomic force microscopy measurements.

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Authors and Affiliations

  1. Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA

    Jackson D. Harvey, Prakrit V. Jena, Hanan A. Baker, Ryan M. Williams, Thomas V. Galassi & Daniel A. Heller

  2. Department of Pharmacology, Weill Cornell Medical College, New York, New York 10065, USA

    Jackson D. Harvey, Hanan A. Baker, Thomas V. Galassi & Daniel A. Heller

  3. Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA

    Gül H. Zerze & Jeetain Mittal

  4. Department of Chemical Engineering, University of Rhode Island, Kingston, Rhode Island 02881, USA

    Daniel Roxbury

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Contributions

J.D.H., P.V.J. and D.A.H. conceived the research, designed the experiments and analysed the data. J.D.H. and H.A.B. performed the experiments. Programs to facilitate data analysis were written by P.V.J. and D.R. Molecular dynamics simulations and analysis were designed and conducted by G.H.Z., D.R. and J.M. Assistance with in vivo work was provided by R.M.W. The probe system for in vivo measurements was designed and built by T.V.G. and D.A.H. The manuscript was prepared and written by J.D.H. and D.A.H.; all authors contributed to editing the manuscript. D.A.H. supervised the project.

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Correspondence to Daniel A. Heller.

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Supplementary information

Supplementary Information

Supplementary text, figures and tables. (PDF 4966 kb)

Supplementary Video 1

Molecular dynamics simulation showing that a single-stranded portion of the GT15mir19 oligomer is bound to the nanotube, and that the hybridized construct remains stable on the nanotube surface. (MPG 59544 kb)

Supplementary Video 2

Molecular dynamics simulation showing that the entire GT15mir19 oligomer is bound to the surface and wraps the nanotube, with the nucleobases orienting closely to the nanotube surface in a parallel orientation. (MPG 38660 kb)

Supplementary Video 3

Molecular dynamics simulations of hybridized miR-19, without the (GT)15 nanotube binding domain, in the presence of the nanotube. (MPG 19152 kb)

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Harvey, J., Jena, P., Baker, H. et al. A carbon nanotube reporter of microRNA hybridization events in vivo. Nat Biomed Eng 1, 0041 (2017). https://doi.org/10.1038/s41551-017-0041

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