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Kitamura M, Umemura K. Hybridization of papain molecules and DNA-wrapped single-walled carbon nanotubes evaluated by atomic force microscopy in fluids. Sci Rep 2023; 13:4833. [PMID: 36964258 PMCID: PMC10039081 DOI: 10.1038/s41598-023-31927-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/20/2023] [Indexed: 03/26/2023] Open
Abstract
Although various conjugates of single-walled carbon nanotubes (SWNTs) and biomolecules, such as nanobiosensors and nanobiodevices, have been reported, the conjugation of papain and SWNTs have not been reported because of the formation of unexpected aggregates. In this study, atomic force microscopy (AFM) in liquid was used to investigate the interactions between papain and DNA-wrapped SWNTs (DNA-SWNTs) at two different pH values (pH 3.0 and 10.5). The direct AFM observation of the mixture of papain and DNA-SWNTs confirmed the aggregation of papain molecules with DNA-SWNTs in the buffer solutions. The numerous and non-uniform adsorption of papain molecules onto DNA-SWNTs was more pronounced at pH 3.0 than that at pH 10.5. Furthermore, thick conjugates appeared when papain and DNA-SWNTs were simultaneously mixed. The near-infrared photoluminescence spectra of the SWNTs drastically changed when the papain molecules were injected into the DNA-SWNT suspension at pH 3.0. Thus, the regulation of electrostatic interactions is a key aspect in preparing optimal conjugates of papain and DNA-SWNTs. Furthermore, although previous papers reported AFM images of dried samples, this study demonstrates the potential of AFM in liquid in evaluating individual bioconjugates of SWNTs.
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Affiliation(s)
- Masaki Kitamura
- Department of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, 1628601, Japan.
| | - Kazuo Umemura
- Department of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, 1628601, Japan
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2
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Hirayama K, Kitamura M, Lin NS, Nguyen MH, Le BD, Mai AT, Mayama S, Umemura K. Attachment of DNA-Wrapped Single-Walled Carbon Nanotubes (SWNTs) for a Micron-Sized Biosensor. ACS OMEGA 2022; 7:47148-47155. [PMID: 36570289 PMCID: PMC9774338 DOI: 10.1021/acsomega.2c06278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
We fabricated a micron-sized biodevice based on the near-infrared photoluminescence (PL) response of single-walled carbon nanotubes (SWNTs). Various biosensors using the unique optical responses of SWNTs have been proposed by many research groups. Most of these employed either colloidal suspensions of dispersed SWNTs or SWNT films on flat surfaces, such as electrodes. In this study, we attached DNA-wrapped SWNTs (DNA-SWNTs) to frustule (micron-sized nanoporous biosilica) surfaces, which were purified from cultured isolated diatoms. After the injection of an oxidant and a reductant, the SWNTs on the frustules showed prominent PL responses. This suggests that the biodevice functions as a micron-sized redox sensor. Frustules can be easily suspended in aqueous solutions because of their porous structures and can easily be collected as pellets by low-speed centrifugation. Thus, the removal of unbound SWNTs and the recovery of the fabricated DNA-SWNT frustules for reuse were achieved by gentle centrifugation. Our proposal for micron-sized SWNT biodevices would be helpful for various biological applications.
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Affiliation(s)
- Kota Hirayama
- Biophysics
Section, Department of Physics, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka,
Shinjuku, Tokyo 162-8601, Japan
| | - Masaki Kitamura
- Biophysics
Section, Department of Physics, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka,
Shinjuku, Tokyo 162-8601, Japan
| | - Nay San Lin
- Biophysics
Section, Department of Physics, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka,
Shinjuku, Tokyo 162-8601, Japan
| | - Minh Hieu Nguyen
- VNU
University of Science, 334 Nguyen Trai, Thanh Xuan, Hanoi 10000, Vietnam
| | - Binh Duong Le
- National
Center for Technological Progress, 25 Le Thanh Tong, Hoan Kiem, Hanoi 100000, Vietnam
| | - Anh Tuan Mai
- VNU
University of Engineering and Technology, 144 Xuan Thuy, Cau Giay, Hanoi G2-206, Vietnam
| | - Shigeki Mayama
- Tokyo
Diatomology Lab, 2−3-2
Nukuikitamachi, Koganei, Tokyo 184-0015, Japan
| | - Kazuo Umemura
- Biophysics
Section, Department of Physics, Faculty of Science Division II, Tokyo University of Science, 1-3 Kagurazaka,
Shinjuku, Tokyo 162-8601, Japan
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Nißler R, Müller AT, Dohrman F, Kurth L, Li H, Cosio EG, Flavel BS, Giraldo JP, Mithöfer A, Kruss S. Detektion und Visualisierung der Pflanzen‐Pathogen‐Response durch Nah‐Infrarot‐fluoreszente Polyphenolsensoren. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Robert Nißler
- Physikalische Chemie II Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Deutschland
- Institut für Physikalische Chemie Georg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
| | - Andrea T. Müller
- Research Group Plant Defense Physiology Max-Planck-Institut für Chemische Ökologie Hans-Knöll-Straße 8 07745 Jena Deutschland
| | - Frederike Dohrman
- Institut für Physikalische Chemie Georg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
| | - Larissa Kurth
- Institut für Physikalische Chemie Georg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
| | - Han Li
- Institute of Nanotechnology Karlsruhe Institute of Technology (KIT) 76344 Eggenstein-Leopoldshafen Deutschland
| | - Eric G. Cosio
- Institute for Nature Earth and Energy (INTE-PUCP) Pontifical Catholic University of Peru Av. Universitaria 1801, San Miguel 15088 Lima Peru
| | - Benjamin S. Flavel
- Institute of Nanotechnology Karlsruhe Institute of Technology (KIT) 76344 Eggenstein-Leopoldshafen Deutschland
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences University of California Riverside CA 92507 USA
| | - Axel Mithöfer
- Research Group Plant Defense Physiology Max-Planck-Institut für Chemische Ökologie Hans-Knöll-Straße 8 07745 Jena Deutschland
| | - Sebastian Kruss
- Physikalische Chemie II Ruhr-Universität Bochum Universitätsstraße 150 44801 Bochum Deutschland
- Institut für Physikalische Chemie Georg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
- Fraunhofer-Institut für Mikroelektronische Schaltungen Finkenstraße 61 47057 Duisburg Deutschland
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Hirayama K, Kitamura M, Hamano R, Umemura K. Stable Near-Infrared Photoluminescence of Single-Walled Carbon Nanotubes Dispersed Using a Coconut-Based Natural Detergent. ACS OMEGA 2021; 6:30708-30715. [PMID: 34805698 PMCID: PMC8603184 DOI: 10.1021/acsomega.1c04615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
We prepared single-walled carbon nanotube (SWNT) suspensions in phosphate buffer solutions containing 1% of a coconut-based natural detergent (COCO) or 1% of sodium dodecyl sulfate (SDS). The suspensions exhibited strong photoluminescence (PL) in the near-infrared region, suggesting that the SWNTs, such as those with (9, 4) and (7, 6) chiralities, were monodispersed. Upon diluting the suspensions with a detergent-free phosphate buffer solution, the PL intensity of the SDS-containing SWNT suspension was significantly lower than that of the COCO-containing SWNT suspension. The COCO-containing SWNT suspension was more stable than the SDS-containing SWNT suspension. The SWNT concentration of the suspensions prepared via bath-type sonication was lower than that of the suspensions prepared via probe-type sonication. However, near-infrared (NIR) PL intensity of the SWNT suspensions prepared via bath-type sonication was much higher than that of the SWNT suspensions prepared via probe-type sonication regardless of the detergent. This suggested that the fraction of monodispersed SWNTs of the suspensions prepared via bath-type sonication was larger than that of the suspensions prepared via probe-type sonication, although the SWNT concentration was low. Our results indicated that COCO favored the fabrication of SWNT suspensions with stable and strong NIR PL, which are useful for various biological applications.
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Nißler R, Müller AT, Dohrman F, Kurth L, Li H, Cosio EG, Flavel BS, Giraldo JP, Mithöfer A, Kruss S. Detection and Imaging of the Plant Pathogen Response by Near-Infrared Fluorescent Polyphenol Sensors. Angew Chem Int Ed Engl 2021; 61:e202108373. [PMID: 34608727 PMCID: PMC9298901 DOI: 10.1002/anie.202108373] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/28/2021] [Indexed: 12/17/2022]
Abstract
Plants use secondary metabolites such as polyphenols for chemical defense against pathogens and herbivores. Despite their importance in plant pathogen interactions and tolerance to diseases, it remains challenging to detect polyphenols in complex plant tissues. Here, we create molecular sensors for plant polyphenol imaging that are based on near-infrared (NIR) fluorescent single-wall carbon nanotubes (SWCNTs). We identified polyethylene glycol-phospholipids that render (6,5)-SWCNTs sensitive (Kd =90 nM) to plant polyphenols (tannins, flavonoids, …), which red-shift (up to 20 nm) and quench their emission (ca. 1000 nm). These sensors report changes in total polyphenol level after herbivore or pathogen challenge in crop plant systems (Soybean Glycine max) and leaf tissue extracts (Tococa spp.). We furthermore demonstrate remote chemical imaging of pathogen-induced polyphenol release from roots of soybean seedlings over the time course of 24 h. This approach allows in situ visualization and understanding of the chemical plant defense in real time and paves the way for plant phenotyping for optimized polyphenol secretion.
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Affiliation(s)
- Robert Nißler
- Physical Chemistry II, Bochum University, Universitätsstrasse 150, 44801, Bochum, Germany.,Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077, Göttingen, Germany
| | - Andrea T Müller
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Frederike Dohrman
- Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077, Göttingen, Germany
| | - Larissa Kurth
- Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077, Göttingen, Germany
| | - Han Li
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Eric G Cosio
- Institute for Nature Earth and Energy (INTE-PUCP), Pontifical Catholic University of Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru
| | - Benjamin S Flavel
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344, Eggenstein-Leopoldshafen, Germany
| | - Juan Pablo Giraldo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745, Jena, Germany
| | - Sebastian Kruss
- Physical Chemistry II, Bochum University, Universitätsstrasse 150, 44801, Bochum, Germany.,Institute of Physical Chemistry, Georg-August Universität Göttingen, Tammannstrasse 6, 37077, Göttingen, Germany.,Fraunhofer Institute for Microelectronic Circuits and Systems, Finkenstrasse 61, 47057, Duisburg, Germany
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Matsukawa Y, Umemura K. Optical Response Characteristics of Single-Walled Carbon Nanotube Chirality Exposed to Oxidants with Different Oxidizing Power. Molecules 2021; 26:molecules26041091. [PMID: 33669602 PMCID: PMC7922499 DOI: 10.3390/molecules26041091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Semiconductor single-walled carbon nanotubes (SWNTs) have unique characteristics owing to differences in the three-dimensional structure (chirality) expressed by the chiral index (n,m), and many studies on the redox characteristics of chirality have been reported. In this study, we investigated the relationship between the chirality of SWNTs and the oxidizing power of oxidants by measuring the near-infrared (NIR) absorption spectra of two double-stranded DNA-SWNT complexes with the addition of three oxidants with different oxidizing powers. A dispersion was prepared by mixing 0.5 mg of SWNT powder with 1 mg/mL of DNA solution. Different concentrations of hydrogen peroxide (H2O2), potassium hexachloroidylate (IV) (K2IrCl6), or potassium permanganate (KMnO4) were added to the dispersion to induce oxidation. Thereafter, a catechin solution was added to observe if the absorbance of the oxidized dispersion was restored by the reducing action of the catechin. We found that the difference in the oxidizing power had a significant effect on the detection sensitivity of the chiralities of the SWNTs. Furthermore, we revealed a detectable range of oxidants with different oxidizing powers for each chirality.
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Fu Y, You Z, Xiao A, Liu L. Magnetic molecularly imprinting polymers, reduced graphene oxide, and zeolitic imidazolate frameworks modified electrochemical sensor for the selective and sensitive detection of catechin. Mikrochim Acta 2021; 188:71. [PMID: 33547976 DOI: 10.1007/s00604-021-04724-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
Abstract
A glassy carbon electrode (GCE) was modified with magnetic molecularly imprinted polymers (mMIPs) using catechin as a template, reduced graphene oxide (rGO), and zeolitic imidazolate frameworks-8 (ZIF-8) for the sensitive detection of catechin (mMIPs/rGO-ZIF-8/GCE). The prepared rGO, ZIF-8, and mMIPs exhibited typical structures and properties determined by various characterizations. The mMIPs showed good selectivity for catechin among several structural analogs. The mMIPs/rGO-ZIF-8/GCE showed a higher maximum peak current for catechin than that of a single component modified GCE. After the optimization of the material ratio, coating amounts, pH, and scan rate, the mMIPs/rGO-ZIF-8/GCE exhibited good selectivity, good linearity, and a low detection limit (LOD) for catechin. The linear range was 0.01 nmol/L-10 μmol/L and the LOD was 0.003 nmol/L (S/N = 3). The relative standard deviations for reproducibility and stability tests (n = 6) were 5.2% and 6.1%, respectively. A recovery between 99.1 and 101.3% was obtained in the detection of catechin in spiked samples. Based on these findings, the proposed mMIPs/rGO-ZIF-8/GCE could be developed further, and future research could be conducted on alternate fabrication strategies and methods to create more portable and practical electrochemical sensors. Graphical Abstract.
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Affiliation(s)
- Yafen Fu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, People's Republic of China
| | - Zongyi You
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, People's Republic of China
| | - Aiping Xiao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, People's Republic of China
| | - Liangliang Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, People's Republic of China.
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Horii Y, Ohura S, Umemura K. An efficient method to quantitatively detect competitive adsorption of DNA on single-walled carbon nanotube surfaces. Anal Biochem 2020; 601:113776. [PMID: 32450060 DOI: 10.1016/j.ab.2020.113776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 04/24/2020] [Accepted: 05/10/2020] [Indexed: 11/29/2022]
Abstract
In this study, we quantitatively detected adsorption and desorption of DNA molecules that competed with sodium cholate (SC) molecules on single-walled carbon nanotubes (SWNTs) by fluorescence spectroscopy. In previous studies, competitive adsorption and/or replacement were studied based on techniques such as near-infrared (NIR) absorbance and photoluminescence (PL) spectroscopy of SWNTs. In those studies, adsorption of organic molecules was detected as spectral changes in SWNTs, but not in organic molecules. In this study, we employed fluorescent-labeled DNA (Fc-DNA) to detect competitive adsorption through quenching of fluorescent dyes that were attached to DNA molecules. Through this approach, the adsorption behaviors of DNA molecules could be directly determined. Hence, we found that Fc-DNA molecules adsorbed on SWNT surfaces that were pre-wrapped with SC when the SC concentration was reduced. However, when SC concentrations recovered after three days of incubation, detachment of Fc-DNA molecules was observed. In addition, our method could be applied to evaluate the adsorption of fluorescent dyes on SWNT surfaces instead of DNA molecules. Hence, our method is effective in studying competitive adsorption of organic molecules on SWNT surfaces. The obtained information is complementary to that obtained from NIR spectroscopy of SWNTs.
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Affiliation(s)
- Yuhei Horii
- Department of Physics, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Shusuke Ohura
- Department of Physics, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan
| | - Kazuo Umemura
- Department of Physics, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 162-8601, Japan.
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Prajapati SK, Malaiya A, Kesharwani P, Soni D, Jain A. Biomedical applications and toxicities of carbon nanotubes. Drug Chem Toxicol 2020; 45:435-450. [DOI: 10.1080/01480545.2019.1709492] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Payal Kesharwani
- Ram-Eesh Institute of Vocational and Technical Education, Knowledge Park I, Greater Noida, Uttar Pradesh, India
| | - Deeksha Soni
- Rawatpura Sarkar Institute of Pharmacy, Datia, Madhya Pradesh, India
| | - Aakanchha Jain
- Bhagyodaya Tirth Pharmacy College, Sagar, Madhya Pradesh, India
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