A carbon nanotube reporter of microRNA hybridization events in vivo

Harvey, Jackson D.; Jena, Prakrit V.; Baker, Hanan; Zerze, Gül H.; Williams, R. T.; Galassi, Thomas V.; Roxbury, Daniel; Mittal, Jeetain; Heller, Daniel A.

doi:10.1038/s41551-017-0041

Cited by 187 publications

(302 citation statements)

References 67 publications

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“…8 Similarly, screening DNA-chirality pairs for analyte specificity 9 led to the development of optical biosensors for a range of small molecule analytes. 10 The ability to integrate molecular recognition into DNA-nanotube hybrids has been achieved via base-pair hybridization, 11 antibody-coupling, 12 and oligonucleotide aptamers. 13 …”

Section: Introductionmentioning

confidence: 99%

DNA–Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent

Jena

Safaee

Heller

et al. 2017

ACS Appl. Mater. Interfaces

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109

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Short single-stranded DNA (ssDNA) has emerged as the natural polymer of choice for non-covalently functionalizing photoluminescent single-walled carbon nanotubes. In addition, specific empirically identified DNA sequences can be used to separate single species (chiralities) of nanotubes with exceptionally high purity. Currently, only limited general principles exist for designing DNA-nanotube hybrids amenable to separation processes, due in part to an incomplete understanding of the fundamental interactions between a DNA sequence and a specific nanotube structure, while even less is known in the design of nanotube-based sensors with determined optical properties. We therefore developed a combined experimental and analysis platform, based on time-resolved near-infrared fluorescence spectroscopy, to extract the complete set of photoluminescence parameters that characterize DNA-nanotube hybrids. Here, we systematically investigated the affinity of the d(GT)n oligonucleotide family for structurally-defined carbon nanotubes by measuring photoluminescence response of the nanotube upon oligonucleotide displacement. We found, surprisingly, that the rate of displacement of oligonucleotides is independent of the coverage on the nanotube, as inferred through intrinsic optical properties of the hybrid. The kinetics of intensity modulation are essentially single exponentials, and the time constants, which quantify the stability of DNA binding, span an order of magnitude. Surprisingly, these time constants do not depend on the intrinsic optical parameters within the hybrids, suggesting that DNA-nanotube stability is not due to increased nanotube surface coverage by DNA. Further, a principal component analysis of the excitation and emission shifts, along with intensity enhancement at equilibrium accurately identified the (8,6) nanotube as the partner chirality to (GT)6 ssDNA. Combined, the chirality-resolved equilibrium and kinetics data can guide the development of DNA-nanotube pairs with tunable stability and optical modulation. Additionally, this high-throughput optical platform could function as a primary screen for mapping the DNA-chirality recognition phase space.

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Section: Introductionmentioning

confidence: 99%

DNA–Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent

Jena

Safaee

Heller

et al. 2017

ACS Appl. Mater. Interfaces

Self Cite

109

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“…14 An alternative method that permits the study of SWCNTs in solution takes advantage of SWCNT sensitivity to their local dielectric environment 15-17 by monitoring SWCNT fluorescence intensity changes and solvatochromic shifts upon corona exchange. 18,19 This technique is applied to study polymer-surfactant exchange kinetics, [20][21][22][23] whereby SWCNTs suspended with surfactant exhibit higher quantum yield and optical transition energy (i.e. blue-shifted spectra) compared to SWCNTs suspended with most biomolecules such as protein or ssDNA.…”

Section: Introductionmentioning

confidence: 99%

Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring

Pinals¹,

Yang²,

Lui³

et al. 2019

Preprint

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Noncovalent adsorption of DNA on nanoparticles has led to their widespread implementation as gene delivery tools and optical probes. Yet, the behavior and stability of DNA-nanoparticle complexes once applied in biomolecule-rich, in vivo environments remains unpredictable, whereby biocompatibility testing usually occurs in serum. Here, we demonstrate time-resolved measurements of exchange dynamics between solution-phase and adsorbed corona-phase DNA and protein biomolecules on single-walled carbon nanotubes (SWCNTs). We capture real-time binding of fluorophore-labeled biomolecules, utilizing the SWCNT surface as a fluorescence quencher, and apply this corona exchange assay to study protein corona dynamics on ssDNA-SWCNT-based dopamine sensors. We study exchange of two blood proteins, albumin and fibrinogen, adsorbing to and competitively displacing (GT)6 vs. (GT)15 ssDNA from ssDNA-SWCNTs. We find that (GT)15 binds to SWCNTs with a higher affinity than (GT)6 and that fibrinogen interacts with ssDNA-SWCNTs more strongly than albumin. Albumin and fibrinogen cause a 52.2% and 78.2% attenuation of the dopamine nanosensor response, coinciding with 0.5% and 3.7% desorption of (GT)6, respectively. Concurrently, the total surface-adsorbed fibrinogen mass is 168% greater than that of albumin. Binding profiles are fit to a competitive surface exchange model which recapitulates the experimental observation that fibrinogen has a higher affinity for SWCNTs than albumin, with a fibrinogen on-rate constant 1.61-fold greater and an off-rate constant 0.563-fold smaller than that of albumin. Our methodology presents a generic route to assess real-time corona exchange on nanoparticles in solution phase, and more broadly motivates testing of nanoparticle-based technologies in blood plasma rather than the more ubiquitously-tested serum conditions.

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“…Of the potential nanomaterials for detecting ions and biomolecules, semiconducting carbon nanotubes exhibit exciting properties that include ballistic transport, biocompatibility, and size compatibility. [1][2][3] In recent years, therefore, CNT-ISFETs have received increasing interest as transducer in many diverse fields. [3][4][5] CNT has also high compatibility with high-κ dielectric that opened a new route to advanced miniature devices.…”

Section: Introductionmentioning

confidence: 99%

Modeling of carbon nanotube ISFETs with high‐κ gate dielectrics for biosensing applications

Thakur

Dutta

2019

Int J Numerical Modelling

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An electrochemical model for two fabricated CNT‐ISFETs has been developed by considering all chemical and physical parameters of the device and then simulated in MATLAB environment. Model has been developed by studying on some aspects of carbon nanotube‐based ion sensitive field effect transistor (CNT‐ISFET) with two high‐κ dielectric materials (HfO2 and ZrO2) fabricated by chemical solution process at low temperature. DC experiments have been performed on pH of the solution to determine the dependence of surface potential, threshold voltage, and drain current. Sensitivities of the devices have also been determined experimentally and found to be 57.5 and 60 mV/pH compared with theoretical values of 56.6 and 58.6 mV/pH for HfO2 and ZrO2 CNT‐ISFETs, respectively in the pH range of 5 to 9. Time domain experiments have been performed to determine the memory effects of the devices. Experiments showed drift rate of 0.52 and 0.683 mV/h at pH 7 for HfO2 and ZrO2 as gate oxides, respectively. The hysteresis widths are found to be 5.88 and 5.26 mV in a pH loop of 7 → 9 → 7 → 5 → 7 for loop time of 60 minutes, respectively, for HfO2 and ZrO2 dielectrics. The simulated results of the developed model are compared with experimentally obtained data and found to be in good agreement.

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A carbon nanotube reporter of microRNA hybridization events in vivo

Cited by 187 publications

References 67 publications

DNA–Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent

DNA–Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent

Corona exchange dynamics on carbon nanotubes by multiplexed fluorescence monitoring

Modeling of carbon nanotube ISFETs with high‐κ gate dielectrics for biosensing applications

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