Interactions of DNA with Clay Minerals and Soil Colloidal Particles and Protection against Degradation by DNase

Cai, Peng; Huang, Qiaoyun; Zhang, Xuewen

doi:10.1021/es0522985

Cited by 158 publications

(139 citation statements)

References 26 publications

(30 reference statements)

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“…Kaolinite is a dioctahedral phyllosilicate clay produced by the chemical weathering of aluminum silicate minerals, some of the most common minerals on earth. It readily binds to naked DNA and, when bound, forces a shift in the DNA conformation from the righthanded B form to the left-handed Z form (35). The findings in this study indicate that these interactions interfere with DNA recovery and/or amplification, introducing bias in Sketa22, HF183/ BacR287, and HumM2 C q measurements.…”

Section: Discussionmentioning

confidence: 77%

“…To evaluate the ability of the SPC to identify samples with matrix interference, each participating laboratory was provided blinded, paired filter sets with one set containing 100 ml of treated sewage-impaired stream water and the other, including the same 100-ml impaired stream sample plus a substance reported to bind DNA (3 filters, 9 total test reactions per lab for each sample type) (35). Extraction blank Sketa22 qPCR measurements and 100-ml impaired water sample values were indistinguishable (Fig.…”

Section: Calibration Curve Model Performancementioning

confidence: 99%

See 1 more Smart Citation

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

Shanks

Kelty

Oshiro

et al. 2016

Appl Environ Microbiol

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There is growing interest in the application of human-associated fecal source identification quantitative real-time PCR (qPCR) technologies for water quality management. The transition from a research tool to a standardized protocol requires a high degree of confidence in data quality across laboratories. Data quality is typically determined through a series of specifications that ensure good experimental practice and the absence of bias in the results due to DNA isolation and amplification interferences. However, there is currently a lack of consensus on how best to evaluate and interpret human fecal source identification qPCR experiments. This is, in part, due to the lack of standardized protocols and information on interlaboratory variability under conditions for data acceptance. The aim of this study is to provide users and reviewers with a complete series of conditions for data acceptance derived from a multiple laboratory data set using standardized procedures. To establish these benchmarks, data from HF183/BacR287 and HumM2 human-associated qPCR methods were generated across 14 laboratories. Each laboratory followed a standardized protocol utilizing the same lot of reference DNA materials, DNA isolation kits, amplification reagents, and test samples to generate comparable data. After removal of outliers, a nested analysis of variance (ANOVA) was used to establish proficiency metrics that include lab-to-lab, replicate testing within a lab, and random error for amplification inhibition and sample processing controls. Other data acceptance measurements included extraneous DNA contamination assessments (notemplate and extraction blank controls) and calibration model performance (correlation coefficient, amplification efficiency, and lower limit of quantification). To demonstrate the implementation of the proposed standardized protocols and data acceptance criteria, comparable data from two additional laboratories were reviewed. The data acceptance criteria proposed in this study should help scientists, managers, reviewers, and the public evaluate the technical quality of future findings against an established benchmark. Fecal pollution remains a significant challenge for ambient water quality managers worldwide. In the United States alone, it is estimated that 39.2% of all rivers, lakes, and streams are unsafe for recreational use, with fecal pathogens as the number one cause of impairment (1). General fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, shed by nearly all warm-blooded animals, are routinely used to assess water quality. However, general FIB cannot discriminate between different animal groups, making it challenging to pinpoint the origin of fecal pollution. Researchers and managers alike recognize the advantages of animal source information to help solve long-standing ambient water quality problems. As a result, a number of fecal source identification technologies have been developed (2-9). These methods have been employed to address challenges such as the identification ...

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Section: Discussionmentioning

confidence: 77%

Section: Calibration Curve Model Performancementioning

confidence: 99%

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

Shanks

Kelty

Oshiro

et al. 2016

Appl Environ Microbiol

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“…Pietramellara et al speculated that the decrease in transformation rates they observed upon repeated wetting and drying cycles of adsorbed DNA was due to conformational changes (28). Cai et al also speculated that differences in the conformation of adsorbed DNA could be responsible for lower transformation efficiencies for DNA bound to kaolinte and inorganic clays (2), based on their previous work characterizing adsorption to different surfaces (3). Detailed characterizations of the conformation of adsorbed DNA only recently became feasible, and the influence of the conformation of adsorbed DNA on transformation frequencies has not, to our knowledge, been systematically investigated.…”

mentioning

confidence: 99%

Adsorption of Extracellular Chromosomal DNA and Its Effects on Natural Transformation of Azotobacter vinelandii

Zilles

Nguyen

2010

Appl Environ Microbiol

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To better understand the influence of environmental conditions on the adsorption of extracellular chromosomal DNA and its availability for natural transformation, the amount and conformation of adsorbed DNA were monitored under different conditions in parallel with transformation assays using the soil bacterium Azotobacter vinelandii. DNA adsorption was monitored using the technique of quartz crystal microbalance with dissipation (QCM-D). Both silica and natural organic matter (NOM) surfaces were evaluated in solutions containing either 100 mM NaCl or 1 mM CaCl 2 . The QCM-D data suggest that DNA adsorbed to silica surfaces has a more compact and rigid conformation in Ca 2؉ solution than in Na ؉ solution and that the reverse is true when DNA is adsorbed to NOM surfaces. While the amounts of DNA adsorbed on a silica surface were similar for Ca 2؉ and Na ؉ solutions, the amount of DNA adsorbed on an NOM-coated surface was higher in Ca 2؉ solution than in Na ؉ solution. Transformation frequencies for dissolved DNA and DNA adsorbed to silica and to NOM were 6 ؋ 10 ؊5 , 5 ؋ 10 ؊5 , and 2.5 ؋ 10 ؊4 , respectively. For NOM-coated surfaces, transformation frequencies from individual experiments were 2-to 50-fold higher in the presence of Ca 2؉ than in the presence of Na ؉ . The results suggest that groundwater hardness (i.e., Ca 2؉ concentration) will affect the amount of extracellular DNA adsorbed to the soil surface but that neither adsorption nor changes in the conformation of the adsorbed DNA will have a strong effect on the frequency of natural transformation of A. vinelandii.

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“…The adsorption of DNA on soil particles plays a major role in protecting extracellular DNA from degradation in soils (Paget and Simonet, 1994), and the interactions between DNA and common clay minerals have been investigated using FTIR spectroscopy (Cai et al, 2006a). Allophane adsorbs more DNA than other minerals in soils (Saeki et al, 2010;Harsh, 2012), and may be capable of preserving DNA as well.…”

Section: Dna Adsorption On Allophanementioning

confidence: 99%

“…A DNA strand comprises heterocyclic bases and a pentose-phosphodiester backbone, and it has been suggested that DNA binds to clays through the phosphate group (Cai et al, 2006a) but there was no direct evidence. We propose three main mechanisms for DNA adsorption on allophane: (1) direct chemical adsorption on the organic matter-free and protonated surface of allophane, (2) indirect chemical adsorption/dissolution on/into the SOM-rich allophane, and (3) physical adsorption in interstices/nanopores of allophane nanoaggregates (Figs.…”

Section: Dna Adsorption On Allophanementioning

confidence: 99%

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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Interactions of DNA with Clay Minerals and Soil Colloidal Particles and Protection against Degradation by DNase

Cited by 158 publications

References 26 publications

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

Data Acceptance Criteria for Standardized Human-Associated Fecal Source Identification Quantitative Real-Time PCR Methods

Adsorption of Extracellular Chromosomal DNA and Its Effects on Natural Transformation of Azotobacter vinelandii

Carbon Storage and DNA Adsorption in Allophanic Soils and Paleosols

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