Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

Umemura, Kazuo; Izumi, Katsuki; Oura, Shusuke

doi:10.3390/nano6100180

Cited by 13 publications

(9 citation statements)

References 95 publications

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“…We first took advantage of the unique fluorescence quenching effect of SWNTs on the adsorbed fluorescently labelled DNA, which provided an effective way to quantify the amount of DNA molecules adsorbed onto the SWNT surfaces. Secondly, as DNA adsorption onto SWNT surfaces causes an increase in SWNT diameter [5, 15, 30], we utilized AFM to measure the dimensions of individual DNA-SWNT hybrids based on their cross-section values in the images. This approach allowed us to directly assess the effects of sonication on the DNA-SWNT hybridization process.…”

Section: Resultsmentioning

confidence: 99%

“…Samples were sonicated using either a probe-type sonicator (VCX 130 630-0423: ϕ = 2 mm, 130W; Sonics & Materials Inc., Newtown USA) or a bath-type sonicator (80W; EOL80; Steady Ultrasonic Sdn. Bhd., Selangor Malaysia) [28–30]. The different sonication conditions were as follows: (a) sonication at 60% maximum amplitude of the probe-type sonicator (P60), (b) sonication at 20% maximum amplitude of the probe-type sonicator (P20), (c) bath-type sonication (B), and (d) control (no sonication).…”

Section: Methodsmentioning

confidence: 99%

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Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces

Umemura

Sato

Bustamante

et al. 2017

Colloids and Surfaces B: Biointerfaces

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Surface modification of single-walled carbon nanotubes (SWNTs) with DNA molecules has attracted much attention in recent years to increase SWNT solubility and make various SWNT-based nanobiodevices. Therefore, there is a critical need to quantify the interaction between DNA molecules and SWNT surfaces, particularly the intermediate structures during DNA adsorption. In this study, we demonstrate the ability to detect the adsorption of DNA oligomers on SWNT surfaces by fluorescence spectroscopy. Fluorescein-labelled, 30 mer, thymine oligonucleotides (F-T30) were employed as a fluorescent probe to study the interaction of DNA with SWNTs. A clear quenching effect was observed when F-T30 was adsorbed onto SWNT surfaces. Using this method, the amount of DNA adsorbed onto the SWNT surfaces was measured under different sonication conditions to correlate absorption efficiency with sonication strength and duration. When a bath-type sonicator was used, mild adsorption of F-T30 on SWNT surfaces was observed. Furthermore, a two-step adsorption was observed in this condition. In contrast, we observed rapid adsorption of F-T30 to SWNT surfaces at the higher sonication amplitude (60% maximal) using a probe-type sonicator, while only slight adsorption of DNA molecules was observed at the lower amplitude (20% maximal). Our data revealed that the quenching effect can be used to evaluate DNA adsorption onto SWNT surfaces. In addition, atomic force microscopy (AFM) and photoacoustic spectroscopy (PAS) were conducted to provide complementary information on the DNA-SWNT nanoconjugates.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces

Umemura

Sato

Bustamante

et al. 2017

Colloids and Surfaces B: Biointerfaces

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“…Carbon nanotubes (CNTs) are promising nanomaterials because of their extraordinary mechanical, electrical, and optical properties [ 1 , 2 , 3 , 4 ]. To apply CNTs to various applications such as nanodevices and nanobiodevices, preparing suspensions of CNTs is one of the primary techniques [ 5 , 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Dispersion of Carbon Nanotubes with “Green” Detergents

et al. 2021

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Solubilization of carbon nanotubes (CNTs) is a fundamental technique for the use of CNTs and their conjugates as nanodevices and nanobiodevices. In this work, we demonstrate the preparation of CNT suspensions with “green” detergents made from coconuts and bamboo as fundamental research in CNT nanotechnology. Single-walled CNTs (SWNTs) with a few carboxylic acid groups (3–5%) and pristine multi-walled CNTs (MWNTs) were mixed in each detergent solution and sonicated with a bath-type sonicator. The prepared suspensions were characterized using absorbance spectroscopy, scanning electron microscopy, and Raman spectroscopy. Among the eight combinations of CNTs and detergents (two types of CNTs and four detergents, including sodium dodecyl sulfate (SDS) as the standard), SWNTs/MWNTs were well dispersed in all combinations except the combination of the MWNTs and the bamboo detergent. The stability of the suspensions prepared with coconut detergents was better than that prepared with SDS. Because the efficiency of the bamboo detergents against the MWNTs differed significantly from that against the SWNTs, the natural detergent might be useful for separating CNTs. Our results revealed that the use of the “green” detergents had the advantage of dispersing CNTs as well as SDS.

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“…Evaluating DNA molecules is important for developing biological applications. Many authors have reported the physical and chemical characterizations of DNA-SWNT hybrids using microscopy [9][10][11] and spectroscopy [12][13][14][15][16][17]. Furthermore, theoretical models of the hybrid structures have been proposed by several authors [18][19][20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Interactions of Secondary DNA and Initial DNA on Single-Walled Carbon Nanotube Surfaces Studied by Photoluminescence, Atomic Force Microscopy, and Electrophoresis

Toyofuku

Ohura

Ito

et al. 2019

Journal of Nanomaterials

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We examined the interactions of initial single-stranded DNA (ssDNA) and secondary ssDNA molecules on single-walled carbon nanotubes (SWNTs). Thymine 30-mers (T30) and 30-mers from a partial sequence of φx174 DNA (φ30) were used to prepare the DNA-SWNT hybrids. First, the hybrids were annealed at various temperatures without secondary DNA to evaluate the stability of the hybrids. As a result, aggregates of SWNTs were formed in the T30-SWNT hybrids, even at 54°C, although the φ30-SWNT hybrids were stable up to 84°C. Second, we added secondary DNA molecules during the annealing procedure. We reacted adenine 30-mers (A30) with the T30-SWNT hybrids and characterized the samples by combining agarose gel electrophoresis with/without ethidium bromide and atomic force microscopy (AFM) as well as near-infrared photoluminescence (PL) spectroscopy. Cross-links appeared to form among the SWNTs because of nonspecific hybridization of T30 and A30. PL measurements revealed clear shifts in the PL emission wavelength of SWNTs. However, when complementary φ30 DNA (cφ30) was reacted with φ30-SWNT hybrids, there was no significant difference in the PL spectra after the reaction, although electrophoresis suggested the hybridization of the cφ30 and φ30 DNA molecules. Our results suggest that the hybridization manner of DNA molecules with unnatural sequences greatly differs from that of natural DNA molecules.

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Probe Microscopic Studies of DNA Molecules on Carbon Nanotubes

Cited by 13 publications

References 95 publications

Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces

Using a fluorescence quenching method to detect DNA adsorption onto single-walled carbon nanotube surfaces

Dispersion of Carbon Nanotubes with “Green” Detergents

Interactions of Secondary DNA and Initial DNA on Single-Walled Carbon Nanotube Surfaces Studied by Photoluminescence, Atomic Force Microscopy, and Electrophoresis

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