DNA adsorption characteristics of hollow spherule allophane nano-particles

Matsuura, Yoko; Iyoda, Fumitoshi; Arakawa, Shuichi; John, Baiju; Okamoto, Masami; Hayashi, Hidetomo

doi:10.1016/j.msec.2013.08.040

Cited by 20 publications

(11 citation statements)

References 17 publications

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“…In a recent study of the interaction of DNA with allophane, Matsuura et al . [ 47 ] showed that allophane was adsorbed on single-stranded DNA (ss-DNA). The authors also mentioned that the phosphate group of ss-DNA strongly associated with Al-OH group of allophane.…”

Section: Allophane and Other Silicatesmentioning

confidence: 99%

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

Hashizume

2015

Life

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Besides having a large capacity for taking up organic molecules, clay minerals can catalyze a variety of organic reactions. Derived from rock weathering, clay minerals would have been abundant in the early Earth. As such, they might be expected to play a role in chemical evolution. The interactions of clay minerals with biopolymers, including RNA, have been the subject of many investigations. The behavior of RNA components at clay mineral surfaces needs to be assessed if we are to appreciate how clays might catalyze the formation of nucleosides, nucleotides and polynucleotides in the “RNA world”. The adsorption of purines, pyrimidines and nucleosides from aqueous solution to clay minerals is affected by suspension pH. With montmorillonite, adsorption is also influenced by the nature of the exchangeable cations. Here, we review the interactions of some clay minerals with RNA components.

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Section: Allophane and Other Silicatesmentioning

confidence: 99%

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

Hashizume

2015

Life

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“…9) so that the size of allophane nanoaggregates increased to micron-sized aggregates (microaggregates). This phenomenon has been attributed to the chemical adsorption of allophane nanoaggregates on DNA strands, as described by Matsuura et al (2013), followed by conjoining of these aggregates by the polymeric DNA, with porous allophane microaggregates formed as a result. The microaggregates comprised assemblages of allophane nanoaggregates with numerous spaces (pores) of both nano-and submicron scale.…”

Section: Formation Of Allophane Nano-and Microaggregates and Physicalmentioning

confidence: 97%

“…Furthermore, Matsuura et al (2014) have hypothesised that allophane is able to protect DNA and ribonucleic acid (RNA) from ultraviolet light and, using computer modelling, simulated the interaction between DNA and allophane. Their simulations illustrated that the DNA strands underwent elongation and the phosphate backbone of DNA altered after bonding to allophane (Matsuura et al, 2013), possibly as a result of chemical adsorption of DNA through its phosphate groups to aluminol groups at the wall perforations of allophane (Huang et al, 2014). However, a more detailed understanding of the adsorption mechanism of DNA on allophane has not been developed, and the driving factor allowing allophane to adsorb more DNA than other clay minerals has remained vague, thus providing impetus for the studies reported here.…”

Section: Introductionmentioning

confidence: 99%

DNA adsorption by nanocrystalline allophane spherules and nanoaggregates, and implications for carbon sequestration in Andisols

Huang

Lowe

Churchman

et al. 2016

Applied Clay Science

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This study provides fundamental knowledge about the interaction of allophane, deoxyribonucleic acid (DNA), and organic matter in soils, and how allophane sequesters DNA. The adsorption capacities of salmon-sperm DNA on pure synthetic allophane (characterised morphologically and chemically) and on humic-acid-rich synthetic allophane were determined, and the resultant DNAallophane complexes were characterised using synchrotron-radiation-derived P X-ray absorption near-edge fine structure (XANES) spectroscopy and infrared (IR) spectroscopy. The synthetic allophane adsorbed up to 34 µg mg-1 of salmon-sperm DNA. However, the presence of humic acid significantly lowered the DNA uptake on the synthetic allophane to 3.5 µg mg-1 by occupying the active sites on allophane so that DNA was repulsed. Both allophane and humic acid adsorbed DNA chemically through its phosphate groups. IR spectra for the allophane-DNA complex showed a chemical change of the Si−O−Al stretching of allophane after DNA adsorption, possibly because of the alteration of the steric distance of the allophane outer wall, or because of the precipitation of aluminium phosphate on allophane after DNA adsorption on it, or both. The aluminol groups of synthetic allophane almost completely reacted with additions of small amounts of DNA (~2−6 µg mg-1), but the chemical adsorption of DNA on allophane simultaneously led to the formation of very porous allophane aggregates up to ~500 µm in diameter. The formation of the allophane nanoand microaggregates enabled up to 28 µg mg-1 of DNA to be adsorbed (~80% of total) within spaces (pores) between allophane spherules and allophane nanoaggregates (as "physical adsorption"), giving a total of 34 g mg-1 of DNA adsorbed by the allophane. The stability of the allophane-DNA nano-and microaggregates likely prevents encapsulated DNA from exposure to oxidants, and DNA within small pores between allophane spherules and nanoaggregates may not be accessible to enzymes or microbes, hence enabling DNA protection and preservation in such materials. By implication, substantial organic carbon is therefore likely to be sequestered and protected in allophanic soils (Andisols) in the same way as demonstrated here for DNA, that is, 3 predominantly by encapsulation within a tortuous network of nanopores and submicropores amidst stable nanoaggregates and microaggregates, rather than by chemisorption alone.

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“…Nanoparticles have been observed ubiquitously in volcanic soils with TEM (Kitagawa, 1971;Henmi & Wada, 1976;Karube et al, 1996;Jongmans et al, 2000;Woignier et al, 2007Woignier et al, , 2008Matsuura et al, 2013). Some amorphous aluminium silicates synthesized below 373 K also contain large quantities of nanoparticles (Suzuki et al, 2009).…”

Section: Nanoparticles In Clays and Soilsmentioning

confidence: 99%

Quantifying nanoparticles in clays and soils with a small-angle X-ray scattering method

Tsukimura

Suzuki

2020

J Appl Crystallogr

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Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3-10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and -aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.

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DNA adsorption characteristics of hollow spherule allophane nano-particles

Cited by 20 publications

References 17 publications

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

Adsorption of Nucleic Acid Bases, Ribose, and Phosphate by Some Clay Minerals

DNA adsorption by nanocrystalline allophane spherules and nanoaggregates, and implications for carbon sequestration in Andisols

Quantifying nanoparticles in clays and soils with a small-angle X-ray scattering method

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