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.
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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.
The authors declare no competing financial interests.
Supplementary text, figures and tables. (PDF 4966 kb)
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)
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)
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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