DNA adsorption on synthetic and natural allophanes

Saeki, Kazutoshi; Sakai, Masao; Wada, Shin Ichiro

doi:10.1016/j.clay.2010.09.015

Cited by 52 publications

(45 citation statements)

References 33 publications

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“…17.3 Salmon-sperm DNA adsorption isotherm for humic-acid (HA)-free and for HA-rich synthetic allophane. This experiment was based on work by Saeki et al (2010), and DNA in the supernatant was measured by UV spectrophotometry at 260 and 280 nm.…”

Section: Discussionmentioning

confidence: 99%

“…Allophane adsorbs more DNA than other minerals in soils (Saeki et al, 2010;Harsh, 2012), and may be capable of preserving DNA as well. Greaves and Wilson (1970) suggested that nucleic acids in the centre of expandable montmorillonite crystal structures may be protected from attack by microbial enzymes, and hence we hypothesise that aDNA may also be physically protected and preserved within intra-and inter-nanoaggregate interstices of allophane in Andisols and andic paleosols.…”

Section: Dna Adsorption On Allophanementioning

confidence: 99%

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Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

et al. 2014

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Andisols and andic paleosols dominated by the nanocrystalline mineral allophane sequester large amounts of carbon (C), attributable mainly to its chemical bonding with charged hydroxyl groups on the surface of allophane together with its physical protection in nanopores within and between allophane nanoaggregates. C near-edge X-ray absorption fine structure (NEXAFS) spectra for a New Zealand Andisol (Tirau series) showed that the organic matter (OM) mainly comprises quinonic, aromatic, aliphatic, and carboxylic C. In different buried horizons from several other Andisols, C contents varied but the C species were similar, attributable to pedogenic processes operating during developmental upbuilding, downward leaching, or both. The presence of OM in natural allophanic soils weakened the adsorption of DNA on clay; an adsorption isotherm experiment involving humic acid (HA) showed that HA-free synthetic allophane adsorbed seven times more DNA than HA-rich synthetic allophane. Phosphorus X-ray absorption near-edge structure (XANES) spectra for salmonsperm DNA and DNA-clay complexes indicated that DNA was bound to the allophane clay through the phosphate group, but it is not clear if DNA was chemically bound to the surface of the allophane or to OM, or both. We plan more experiments to investigate interactions among DNA, allophane (natural and synthetic), and OM. Because DNA shows a high affinity to allophane, we are studying the potential to reconstruct late Quaternary palaeoenvironments by attempting to extract and characterise ancient DNA from allophanic paleosols.

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Section: Discussionmentioning

confidence: 99%

Section: Dna Adsorption On Allophanementioning

confidence: 99%

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

et al. 2014

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“…Additionally, Saeki et al suggested that double-strand DNA adsorption on allophane decreased considerably with increasing suspension pH values in the range between 3 and 9 [6]. However, to the best of our knowledge, single-strand DNA (ss-DNA) assumed ancient DNA was not used as adsorbate, and the mechanism of DNA adsorption and its sustenance in allophane clusters was not fully revealed yet.…”

Section: Introductionmentioning

confidence: 99%

DNA adsorption characteristics of hollow spherical allophane nano-particles

Matsuura

Iyoda

Hayashi

et al. 2014

AIP Conference Proceedings

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To understand the propensity of the natural allophane to adsorb the DNA molecules, the adsorption characteristics were assessed against a natural allophane, using single-stranded DNA (ss-DNA) and adenosine 5'-monophosphate (5'-AMP) as a reference molecule. The adsorption capacity of ss-DNA on AK70 exhibited one order of magnitude lower value as compared with that of 5'-AMP. The adsorption capacity of ss-DNA decreased with increasing pH due to the interaction generated between phosphate groups of ss-DNA and functional Al-OH groups on the wall perforations through deprotonation, associated with higher energy barrier for the adsorption of ss-DNA. The adsorption morphologies consisting of the individual ss-DNA with mono-layer coverage of the allophane clustered particle was successfully observed through TEM analysis.

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“…However, the difference is not likely to affect the adsorption of DNA by the solid samples because it was within the variation in ionic strength at which adsorption was almost constant in andosol (29) and allophanes (30). The natural allophane, gibbsite, and kaolinite adsorbed significantly more DNA in the Tris-HCl buffer than NaCl solution (t-test, P<0.005), as did the synthetic allophane, humic acid A, and the TA soil sample (P<0.05) ( Table 1).…”

mentioning

confidence: 99%

“…Whichever mechanism occurs, Tris acts as a bridge between DNA and solid surfaces. However the frequency and strength of the bridge binding are much reduced in comparison to that with divalent cations such as Mg 2+ and Ca 2+ , because no positive effects of Tris on DNA adsorption were observed for several minerals such as montmorillonite while even small amounts of divalent cations remarkably enhanced the adsorption by montmorillonite, kaolinite, goethite (2), soils (29) and allophane (30).…”

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confidence: 99%

Effect of Tris-HCl Buffer on DNA Adsorption by a Variety of Soil Constituents

2011

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We investigated the effect of tris(hydroxymethyl)aminomethane hydrochloride (Tris-HCl) buffer (pH 7.0) as a bulk solution on the adsorption of DNA by gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols. The natural allophane, gibbsite, kaolinite and an andosol adsorbed significantly more DNA in a 0.1 M Tris-HCl buffer than in a 0.1 M NaCl solution (t-test, P<0.005). In contrast, montmorillonite adsorbed significantly less DNA in the Tris-HCl than NaCl solution (P<0.05). Care should be taken when using TrisHCl in studies on the adsorption of extracellular DNA molecules by soil particles.Key words: DNA adsorption, Tris-HCl buffer, allophane, soil, montmorilloniteNucleic acid adsorption at soil-solution interfaces is important in understanding many subjects such as the biosafety of genetically modified organisms (17), protection of DNA against nucleases in soil (13, 22), genetic transformation of competent bacteria in situ (5,6,11,22) and extraction of DNA from soil for the study of microbial communities (e.g. 34).The adsorption of DNA molecules by phyllosilicate minerals is affected by several factors including DNA size (6), mineral types (2), the pH of buffer solutions (7,8,11), the ionic strength of solutions (12), the presence of other cellular components (21, 22) and electrolytes (7). The adsorption of DNA by phyllosilicate minerals can differ from that by variable-charge soils such as andosol. There have been several studies on the retention of DNA in natural soils (18,19,26,28,29).Tris(hydroxymethyl)aminomethane (Tris) solutions are used widely as buffers due to their stabilizing effects on biomolecules (16). There have been several studies about the adsorption of DNA on soil particles using Tris-HCl buffers as background solutions (e.g. 2, 3, 4). Recently, Wei et al. (36) reported that a Tris-HCl buffer (pH 7.4) increased protein adsorption on germanium (Ge) surface. To grasp how much Tris-HCl affects on the adsorption of DNA by soils, we investigated the effect of a Tris-HCl buffer (pH 7.0) as a bulk solution on DNA adsorption by a variety of materials (gibbsite, goethite, montmorillonite, kaolinite, synthetic and natural allophanes, two humic acids and two andosols).The mineral samples used in this study were: Gibbsite, provided by Showa Denko (Tokyo, Japan); goethite, synthesized by the method of Atkinson et al.(1); montmorillonite K10, provided by Sigma-Aldrich (St Louis, USA); kaolinite, collected from Iriki, Kagoshima, Japan; a synthetic allophane produced by the method of Ohashi et al. (20) and a natural allophane supplied by Shinagawa Chemicals (Tokyo, Japan). The properties of these solids have been reported recently (14,24,25). Humic acid A and B were purified from reagents provided by Wako Pure Chemical Industries (Osaka, Japan) and Sigma-Aldrich. The purification process was based on the IHSS method (33). The properties of humic acids were described previously (10,15,27). Two surface humic andosols were also used; Chiran soil (CR ...

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DNA adsorption on synthetic and natural allophanes

Cited by 52 publications

References 33 publications

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

DNA adsorption characteristics of hollow spherical allophane nano-particles

Effect of Tris-HCl Buffer on DNA Adsorption by a Variety of Soil Constituents

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