Dissociation of Single-Strand DNA: Single-Walled Carbon Nanotube Hybrids by Watson−Crick Base-Pairing

Jung, Seungwon; Cha, Misun; Park, Jiyong; Jeong, Namjo; Kim, Gunn; Park, Changwon; Ihm, Jisoon; Lee, Junghoon

doi:10.1021/ja102673m

Cited by 39 publications

(30 citation statements)

References 23 publications

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“…These observations can be reconciled with the observations of Jung et al, 28 who suggested that the energy released by a 17 bp duplex formation is enough to facilitate desorption of the dsDNA. The values estimated by the authors predict that the 24 bp dsDNA used in our simulation would have a desorption energy of around 56 kcal/mol, which is 2 orders of magnitude larger than thermal fluctuation at ambient conditions.…”

Section: ■ Resultssupporting

confidence: 72%

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

Schuergers

Lin

et al. 2018

ACS Appl. Mater. Interfaces

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Nanoprobes such as single-walled carbon nanotubes (SWCNTs) are capable of label-free detection that benefits from intrinsic and photostable near-infrared fluorescence. Despite the growing number of SWCNT-based applications, uncertainty surrounding the nature of doublestranded DNA (dsDNA) immobilization on pristine SWCNTs has limited their use as optical sensors for probing DNA−protein interactions. To address this limitation, we study enzyme activity on unmodified dsDNA strands immobilized on pristine SWCNTs. Restriction enzyme activity on various dsDNA sequences was used to verify the retention of the dsDNA's native conformation on the nanotube surface and to quantitatively compare the degree of dsDNA accessibility. We report a 2.8-fold enhancement in initial enzyme activity in the presence of surfactants. Forster resonance electron transfer (FRET) analysis attributes this enhancement to increased dsDNA displacement from the SWCNT surface. Furthermore, the accessibility of native dsDNA was found to vary with DNA configuration and the spacing between the restriction site and the nanotube surface, with a minimum spacing of four base pairs (bp) from the anchoring site needed to preserve enzyme activity. Molecular dynamics (MD) simulations verify that the anchored dsDNA remains within the vicinity of the SWCNT, revealing an unprecedented bimodal displacement of the bp nearest to SWCNT surface. Together, these findings illustrate the successful immobilization of native dsDNA on pristine SWCNTs, offering a new near-infrared platform for exploring vital DNA processes.

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Section: ■ Resultssupporting

confidence: 72%

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

Schuergers

Lin

et al. 2018

ACS Appl. Mater. Interfaces

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“…As one of the most powerful building blocks for self‐assembled nanostructures,10 DNA has the potential to play a major role in any such development. Although the selective dispersion of SWNTs with pristine DNA was realized,11 the subsequent controlled assembly through hybridization with complementary DNA (cDNA) is unfeasible because of the unwrapping of DNA attached to the tube 12. Other studies that combine DNA and SWNTs have entailed covalent bond formation between the two moieties13 or the chemical modification of DNA wrapped around the nanotubes 14.…”

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confidence: 99%

In vitro antioxidant activity of protein hydrolysates prepared from corn gluten meal

2008

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BACKGROUND: Corn gluten meal (CGM), a major by-product of corn wet milling, is mainly used as forage in China. Because of its particular amino acid composition, in which there are large amounts of hydrophobic amino acids such as leucine, alanine and phenylalanine, CGM protein was thought to be a good resource to obtain antioxidant peptides. CGM protein was hydrolysed with a biochemical grade alcalase and the derived hydrolysates were assessed for their antioxidant properties in different in vitro assay systems, including inhibiting activity on lipid peroxidation, by reducing power, hydroxyl radical scavenging activity, and DPPH radical scavenging activity. The effects of concentration and molecular weight (MW) of hydrolysates on antioxidant activity were investigated.

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“…Karachevtsev et al prepared DNA-SWNT hybrids with polynuclueotides and studied aggregate formation of the hybrids [38,39]. Jung et al also demonstrated detachment of DNA molecules from SWNT surfaces through DNA hybridization [40]. Jeng et al estimated the kinetic parameters of DNA hybridization on SWNT surfaces [41].…”

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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Dissociation of Single-Strand DNA: Single-Walled Carbon Nanotube Hybrids by Watson−Crick Base-Pairing

Cited by 39 publications

References 23 publications

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

Restriction Enzyme Analysis of Double-Stranded DNA on Pristine Single-Walled Carbon Nanotubes

In vitro antioxidant activity of protein hydrolysates prepared from corn gluten meal

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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