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Qin C, Lu YX, Borch T, Yang LL, Li YW, Zhao HM, Hu X, Gao Y, Xiang L, Mo CH, Li QX. Interactions between Extracellular DNA and Perfluoroalkyl Acids (PFAAs) Decrease the Bioavailability of PFAAs in Pakchoi ( Brassica chinensis L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:14622-14632. [PMID: 36375011 DOI: 10.1021/acs.jafc.2c04597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Perfluoroalkyl acids (PFAAs) are emerging ionic organic pollutants worldwide. Great amounts of extracellular DNA (∼mg/kg) coexist with PFAAs in the environment. However, PFAA-DNA interactions and effects of such interactions have not been well studied. Herein, we used isothermal titration calorimetry (ITC), spectroscopy, and computational simulations to investigate the PFAA-DNA interactions. ITC assays showed that specific binding affinities of PFHxA-DNA, PFOA-DNA, PFNA-DNA, and PFOS-DNA were 5.14 × 105, 3.29 × 105, 1.99 × 105, and 2.18 × 104 L/mol, respectively, which were about 1-2 orders of magnitude stronger than those of PFAAs with human serum albumin. Spectral analysis suggested interactions of PFAAs with adenine (A), cytosine (C), guanine (G), and thymine (T), among which grooves associated with thymine were the major binding sites. Molecular dynamics simulations and quantum chemical calculations suggested that hydrogen bonds and van der Waals forces were the main interaction forces. Such a PFAA-DNA binding decreased the bioavailability of PFAAs in plant seedlings. The findings will help to improve the current understanding of the interaction between PFAAs and biomacromolecules, as well as how such interactions affect the bioavailability of PFAAs.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Ying-Xin Lu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Thomas Borch
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado80523, United States
- Department of Soil and Crop Sciences, Colorado State University, 1170 Campus Delivery, Fort Collins, Colorado80523, United States
| | - Ling-Ling Yang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou510632, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii96822, United States
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Fang J, Jin L, Meng Q, Wang D, Lin D. Interactions of extracellular DNA with aromatized biochar and protection against degradation by DNase I. J Environ Sci (China) 2021; 101:205-216. [PMID: 33334516 DOI: 10.1016/j.jes.2020.08.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/12/2023]
Abstract
With increasing environmental application, biochar (BC) will inevitably interact with and impact environmental behaviors of widely distributed extracellular DNA (eDNA), which however still remains to be studied. Herein, the adsorption/desorption and the degradation by nucleases of eDNA on three aromatized BCs pyrolyzed at 700 °C were firstly investigated. The results show that the eDNA was irreversibly adsorbed by aromatized BCs and the pseudo-second-order and Freundlich models accurately described the adsorption process. Increasing solution ionic strength or decreasing pH below 5.0 significantly increased the eDNA adsorption on BCs. However, increasing pH from 5.0 to 10.0 faintly decreased eDNA adsorption. Electrostatic interaction, Ca ion bridge interaction, and π-π interaction between eDNA and BC could dominate the eDNA adsorption, while ligand exchange and hydrophobic interactions were minor contributors. The presence of BCs provided a certain protection to eDNA against degradation by DNase I. BC-bound eDNA could be partly degraded by nuclease, while BC-bound nuclease completely lost its degradability. These findings are of fundamental significance for the potential application of biochar in eDNA dissemination management and evaluating the environmental fate of eDNA.
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Affiliation(s)
- Jing Fang
- Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Liang Jin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Qingkang Meng
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dengjun Wang
- Oak Ridge Institute for Science and Education (ORISE) Resident Research Associate, United States Environmental Protection Agency, Ada, OK 74820, USA
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China.
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Wang Z, Huang Z, Han J, Xie G, Liu J. Polyvalent Metal Ion Promoted Adsorption of DNA Oligonucleotides by Montmorillonite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1037-1044. [PMID: 33435677 DOI: 10.1021/acs.langmuir.0c02529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Montmorillonite (MMT) is a two-dimensional (2D) clay material. Its abundance on the early earth has attracted studies for its role in prebiotic reactions, and adsorption of DNA to MMT is potentially important for understanding the origin of life. Although several possible models of DNA adsorption on MMT have been established, a consensus on the adsorption mechanism has yet to be formed, thereby a fundamental adsorption study is performed here. Adding up to 300 mM NaCl failed to promote DNA adsorption on MMT, Al2O3, or SiO2 nanoparticles. For polyvalent metals, DNA adsorption was achieved following the order Ce3+ > Cu2+ > Ni2+ > Zn2+. Among them, Ce3+ and Cu2+ inverted the surface charge of MMT to positive. In addition, using washing experiments, Cu2+- and Ce3+-mediated adsorption mainly depended on the DNA phosphate backbone, while Ni2+ and Zn2+ interacted with the backbone phosphate groups and adenine bases of DNA. Overall, these polyvalent metal ions promoted DNA adsorption via a cation bridge model. This research provides new insights into the surface interactions of MMT and DNA, which is conducive to future work on the interaction between clays and biopolymers.
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Affiliation(s)
- Zhen Wang
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Jing Han
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Gang Xie
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Zhang L, Gadd GM, Li Z. Microbial biomodification of clay minerals. ADVANCES IN APPLIED MICROBIOLOGY 2020; 114:111-139. [PMID: 33934851 DOI: 10.1016/bs.aambs.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clay minerals are important reactive centers in the soil system. Their interactions with microorganisms are ubiquitous and wide-ranging, affecting growth and function, interactions with other organisms, including plants, biogeochemical processes and the fate of organic and inorganic pollutants. Clay minerals have a large specific surface area and cation exchange capacity (CEC) per unit mass, and are abundant in many soil systems, especially those of agricultural significance. They can adsorb microbial cells, exudates, and enzymes, organic and inorganic chemical species, nutrients, and contaminants, and stabilize soil organic matter. Bacterial modification of clays appears to be primarily due to biochemical mechanisms, while fungi can exhibit both biochemical and biomechanical mechanisms, the latter aided by their exploratory filamentous growth habit. Such interactions between microorganisms and clays regulate many critical environmental processes, such as soil development and transformation, the formation of soil aggregates, and the global cycling of multiple elements. Applications of biomodified clay minerals are of relevance to the fields of both agricultural management and environmental remediation. This review provides an overview of the interactions between bacteria, fungi and clay minerals, considers some important gaps in current knowledge, and indicates perspectives for future research.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China; Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom; State Key Laboratory of Heavy Oil Processing, State Key Laboratory of Petroleum Pollution Control, College of Science and Environment, China University of Petroleum, Beijing, China
| | - Zhen Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China; Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.
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Facile Fabrication of Natural Polyelectrolyte-Nanoclay Composites: Halloysite Nanotubes, Nucleotides and DNA Study. Molecules 2020; 25:molecules25153557. [PMID: 32759785 PMCID: PMC7436255 DOI: 10.3390/molecules25153557] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/16/2020] [Accepted: 07/31/2020] [Indexed: 12/22/2022] Open
Abstract
Complexation of biopolymers with halloysite nanotubes (HNTs) can greatly affect their applicability as materials building blocks. Here we have performed a systematic investigation of fabrication of halloysite nanotubes complexes with nucleotides and genomic DNA. The binding of DNA and various nucleotide species (polyAU, UMP Na2, ADP Na3, dATP Na, AMP, uridine, ATP Mg) by halloysite nanotubes was tested using UV-spectroscopy. The study revealed that binding of different nucleotides to the nanoclay varied but was low both in the presence and absence of MgCl2, while MgCl2 facilitated significantly the binding of longer molecules such as DNA and polyAU. Modification of the nanotubes with DNA and nucleotide species was further confirmed by measurements of ζ-potentials. DNA-Mg-modified nanotubes were characterized using transmission electron (TEM), atomic force (AFM) and hyperspectral microscopies. Thermogravimetric analysis corroborated the sorption of DNA by the nanotubes, and the presence of DNA on the nanotube surface was indicated by changes in the surface adhesion force measured by AFM. DNA bound by halloysite in the presence of MgCl2 could be partially released after addition of phosphate buffered saline. DNA binding and release from halloysite nanotubes was tested in the range of MgCl2 concentrations (10–100 mM). Even low MgCl2 concentrations significantly increased DNA sorption to halloysite, and the binding was leveled off at about 60 mM. DNA-Mg-modified halloysite nanotubes were used for obtaining a regular pattern on a glass surface by evaporation induced self-assembly process. The obtained spiral-like pattern was highly stable and resisted dissolution after water addition. Our results encompassing modification of non-toxic clay nanotubes with a natural polyanion DNA will find applications for construction of gene delivery vehicles and for halloysite self-assembly on various surfaces (such as skin or hair).
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Pedreira-Segade U, Michot LJ, Daniel I. Effects of salinity on the adsorption of nucleotides onto phyllosilicates. Phys Chem Chem Phys 2018; 20:1938-1952. [PMID: 29297910 DOI: 10.1039/c7cp07004g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
In the context of the origin of life, phyllosilicate surfaces might favor the adsorption, concentration and reactivity of otherwise diluted prebiotic molecules. The primitive oceanic seafloor was certainly rich in Fe-Mg-rich phyllosilicates. The salinity of the primitive seawater remains largely unknown. Values ranging from 1 to 15 times modern salinity have been proposed and the salt composition of the primitive ocean also remains elusive although it may have played a role in the interactions between nucleotides and mineral surfaces. Therefore we studied the adsorption of 5'-monophosphate deoxyguanosine (dGMP) as a model nucleotide onto a Fe-rich swelling clay, i.e. nontronite, and an Al-rich phyllosilicate, i.e. pyrophyllite, for comparison. Experiments were carried out at atmospheric pressure, 25 °C and natural pH, with a series of salts NaCl, MgCl2, CaCl2, MgSO4, NaH2PO4 and LaCl3 in order to evaluate the effect of cations and anions on dGMP adsorption. The present study shows that nucleotides are adsorbed on both phyllosilicates via a ligand exchange mechanism. The phosphate group of the nucleotide is adsorbed on the lateral metal hydroxyls of the broken edges of phyllosilicates. The presence of divalent cations or molecular anions, such as phosphate or sulfate, tends to inhibit this interaction on mineral surfaces. However, in the presence of divalent cations, cationic bridging on the basal surfaces of the swelling clay also occurs and could induce a higher retention capacity of the swelling clays compared to non-swelling phyllosilicates in primitive and modern natural environments.
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Affiliation(s)
- Ulysse Pedreira-Segade
- Univ Lyon, Ens de Lyon, Université Lyon 1, CNRS, UMR 5276 LGL-TPE, F-69342, Lyon, France.
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Pihlasalo S, Mariani L, Härmä H. Quantitative and discriminative analysis of nucleic acid samples using luminometric nonspecific nanoparticle methods. NANOSCALE 2016; 8:5902-5911. [PMID: 26912463 DOI: 10.1039/c5nr09252c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Homogeneous simple assays utilizing luminescence quenching and time-resolved luminescence resonance energy transfer (TR-LRET) were developed for the quantification of nucleic acids without sequence information. Nucleic acids prevent the adsorption of a protein to europium nanoparticles which is detected as a luminescence quenching of europium nanoparticles with a soluble quencher or as a decrease of TR-LRET from europium nanoparticles to the acceptor dye. Contrary to the existing methods based on fluorescent dye binding to nucleic acids, equal sensitivities for both single- (ssDNA) and double-stranded DNA (dsDNA) were measured and a detection limit of 60 pg was calculated for the quenching assay. The average coefficient of variation was 5% for the quenching assay and 8% for the TR-LRET assay. The TR-LRET assay was also combined with a nucleic acid dye selective to dsDNA in a single tube assay to measure the total concentration of DNA and the ratio of ssDNA and dsDNA in the mixture. To our knowledge, such a multiplexed assay is not accomplished with commercially available assays.
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Affiliation(s)
- S Pihlasalo
- Laboratory of Materials Chemistry and Chemical Analysis, Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland.
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Feuillie C, Sverjensky DA, Hazen RM. Attachment of ribonucleotides on α-alumina as a function of pH, ionic strength, and surface loading. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 31:240-248. [PMID: 25469864 DOI: 10.1021/la504034k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The interactions between nucleic acids and mineral surfaces have been the focus of many studies in environmental sciences, in biomedicine, as well as in origin of life studies for the prebiotic formation of biopolymers. However, few studies have focused on a wide range of environmental conditions and the likely modes of attachment. Here we investigated the adsorption of ribonucleotides onto α-alumina surfaces over a wide range of pH, ionic strength, and ligand-to-solid ratio, by both an experimental and a theoretical approach. The adsorption of ribonucleotides is strongly affected by pH, with a maximum adsorption at pH values around 5. Alumina adsorbs high amounts of nucleotides >2 μmol/m(2). We used the extended triple-layer model (ETLM) to predict the speciation of the surface complexes formed as well as the stoichiometry and equilibrium constants. We propose the formation of two surface species: a monodentate inner-sphere complex, dominant at pH <7, and a bidentate outer-sphere complex, dominant at higher pH. Both complexes would involve interactions between the negatively charged phosphate group and the positively charged surface of alumina. Our results provide a better understanding of how nucleic acids attach to mineral surfaces under varying environmental conditions. Moreover, the predicted configuration of nucleotide surface species, bound via the phosphate group, could have implications for the abiotic formation of nucleic acids in the context of the origin of life.
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Affiliation(s)
- Cécile Feuillie
- Geophysical Laboratory, Carnegie Institution of Washington , 5251 Broad Branch Road North West, Washington, DC 20015, United States
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Kumari B, Banerjee SS, Singh V, Das P, Bhowmick AK. Processing of abasic site damaged lesions by APE1 enzyme on DNA adsorbed over normal and organomodified clay. CHEMOSPHERE 2014; 112:503-510. [PMID: 25048946 DOI: 10.1016/j.chemosphere.2014.05.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/09/2014] [Accepted: 05/11/2014] [Indexed: 06/03/2023]
Abstract
The efficiency of the apurinic/apyrimidinic endonuclease (APE1) DNA repair enzyme in the processing of abasic site DNA damage lesions at precise location in DNA oligomer duplexes that are adsorbed on clay surfaces was evaluated. Three different forms of clay namely montmorillonite, quaternary ammonium salt modified montmorillonite and its boiled counterpart i.e. partially devoid of organic moiety were used for a comparative study of adsorption, desorption and DNA repair efficiency on their surfaces. The interaction between the DNA and the clay was analysed by X-ray diffraction, Atomic force microscopy, UV-Vis spectroscopy and Infrared spectroscopy. The abasic site cleavage efficiency of APE1 enzyme was quantitatively evaluated by polyacrylamide gel electrophoresis. Apart from the difference in the DNA adsorption or desorption capacity of the various forms of clay, substantial variation in the repair efficiency of abasic sites initiated by the APE1 enzyme on the clay surfaces was observed. The incision efficiency of APE1 enzyme at abasic sites was found to be greatly diminished, when the DNA was adsorbed over organomodified montmorillonite. The reduced repair activity indicates an important role of the pendant surfactant groups on the clay surfaces in directing APE1 mediated cleavage of abasic site DNA damage lesions.
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Affiliation(s)
- Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, Bihar, India
| | - Shib Shankar Banerjee
- Department of Materials Science and Engineering, Indian Institute of Technology Patna, Patna 800013, Bihar, India
| | - Vandana Singh
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, Bihar, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Patna 800013, Bihar, India.
| | - Anil K Bhowmick
- Department of Materials Science and Engineering, Indian Institute of Technology Patna, Patna 800013, Bihar, India
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Ramírez Jiménez SI. The early Earth atmosphere and early life catalysts. Met Ions Life Sci 2014; 14:1-14. [PMID: 25416388 DOI: 10.1007/978-94-017-9269-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Homochirality is a property of living systems on Earth. The time, the place, and the way in which it appeared are uncertain. In a prebiotic scenario two situations are of interest: either an initial small bias for handedness of some biomolecules arouse and progressed with life, or an initial slight excess led to the actual complete dominance of the known chiral molecules. A definitive answer can probably never be given, neither from the fields of physics and chemistry nor biology. Some arguments can be advanced to understand if homochirality is necessary for the initiation of a prebiotic homochiral polymer chemistry, if this homochirality is suggesting a unique origin of life, or if a chiral template such as a mineral surface is always required to result in an enantiomeric excess. A general description of the early Earth scenario will be presented in this chapter, followed by a general description of some clays, and their role as substrates to allow the concentration and amplification of some of the building blocks of life.
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Affiliation(s)
- Sandra Ignacia Ramírez Jiménez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad # 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, Mexico,
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Hou Y, Wu P, Zhu N. The protective effect of clay minerals against damage to adsorbed DNA induced by cadmium and mercury. CHEMOSPHERE 2014; 95:206-212. [PMID: 24047649 DOI: 10.1016/j.chemosphere.2013.08.069] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/03/2013] [Accepted: 08/16/2013] [Indexed: 06/02/2023]
Abstract
The adsorption of Salmon Sperm DNA on three kinds of raw clay (rectorite, montmorillonite and sericite) was investigated as a function of pH, ionic strength and the concentrations of DNA and phosphate ions in solution. The DNA adsorption was reduced in the following order: rectorite>montmorillonite>sericite. Based on these findings, there is a strong evidence that the mechanisms for DNA adsorption on clay involve electrostatic forces, cation bridging and ligand exchange. Cyclic voltammetry (CV) and UV-vis absorption and fluorescence spectroscopy were used to compare the properties of unbound DNA and the absorbed DNA on rectorite, both in the absence and presence of Cd(2+) and Hg(2+) inaqueous solutions. The interaction of heavy metals with the unbound DNA was evidenced by the disappearance of reduction peaks in CV, a small bathochromic shift in UV-vis spectroscopy and an incomplete quenching in the emission spectra. Such changes were not observed in the DNA-rectorite hybrids, which is evidence that adsorption on the clay can reduce the extent of the DNA damage caused by heavy metals. Therefore, in these experience the rectorite played an important role in protecting DNA against Cd(2+) and Hg(2+) induced damage.
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Affiliation(s)
- Yakun Hou
- College of Environment and Energy, South China University of Technology, Guangzhou 510006, China
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12
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Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. Environmental conditions influence eDNA persistence in aquatic systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:1819-27. [PMID: 24422450 DOI: 10.1021/es404734p] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental DNA (eDNA) surveillance holds great promise for improving species conservation and management. However, few studies have investigated eDNA dynamics under natural conditions, and interpretations of eDNA surveillance results are clouded by uncertainties about eDNA degradation. We conducted a literature review to assess current understanding of eDNA degradation in aquatic systems and an experiment exploring how environmental conditions can influence eDNA degradation. Previous studies have reported macrobial eDNA persistence ranging from less than 1 day to over 2 weeks, with no attempts to quantify factors affecting degradation. Using a SYBR Green quantitative PCR assay to observe Common Carp ( Cyprinus carpio ) eDNA degradation in laboratory mesocosms, our rate of Common Carp eDNA detection decreased over time. Common Carp eDNA concentration followed a pattern of exponential decay, and observed decay rates exceeded previously published values for aquatic macrobial eDNA. Contrary to our expectations, eDNA degradation rate declined as biochemical oxygen demand, chlorophyll, and total eDNA (i.e., from any organism) concentration increased. Our results help explain the widely divergent, previously published estimates for eDNA degradation. Measurements of local environmental conditions, consideration of environmental influence on eDNA detection, and quantification of local eDNA degradation rates will help interpret future eDNA surveillance results.
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Affiliation(s)
- Matthew A Barnes
- Department of Biological Sciences and Environmental Change Initiative, University of Notre Dame , Notre Dame, Indiana 46556, United States
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Silicon dioxide thin film mediated single cell nucleic acid isolation. PLoS One 2013; 8:e68280. [PMID: 23874571 PMCID: PMC3707904 DOI: 10.1371/journal.pone.0068280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 05/27/2013] [Indexed: 11/19/2022] Open
Abstract
A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube.
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Brundin M, Figdor D, Sundqvist G, Sjögren U. DNA Binding to Hydroxyapatite: A Potential Mechanism for Preservation of Microbial DNA. J Endod 2013; 39:211-6. [DOI: 10.1016/j.joen.2012.09.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/23/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
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Zhang J, Lang HP, Yoshikawa G, Gerber C. Optimization of DNA hybridization efficiency by pH-driven nanomechanical bending. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6494-6501. [PMID: 22439593 DOI: 10.1021/la205066h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The accessibility and binding affinity of DNA are two key parameters affecting the hybridization efficiency in surface-based biosensor technologies. Better accessibility will result in a higher hybridization efficiency. Often, mixed ssDNA and mercaptohexanol monolayers are used to increase the hybridization efficiency and accessibility of surface-bound oligonucleotides to complementary target DNA. Here, no mercaptohexanol monolayer was used. We demonstrate by differential microcantilever deflection measurements at different pH that the hybridization efficiency peaks between pH 7.5 and 8.5. At low pH 4.5, hydration and electrostatic forces led to tensile surface stress, implying the reduced accessibility of the bound ssDNA probe for hybridization. In contrast, at high pH 8.5, the steric interaction between neighboring ssDNA strands was decreased by higher electrostatic repulsive forces, bending the microcantilever away from the gold surface to provide more space for the target DNA. Cantilever deflection scales with pH-dependent surface hybridization efficiency because of high target DNA accessibility. Hence, by changing the pH, the hybridization efficiency is adjusted.
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Affiliation(s)
- Jiayun Zhang
- Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.
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16
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Kumar A, Prakash R. Synthesis of nano ground nutshell-like polyindole by supramolecular assembled salts of ss-DNA assisted chloroauric acid. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.05.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Ruiz-Hitzky E, Aranda P, Darder M, Ogawa M. Hybrid and biohybrid silicate based materials: molecular vs. block-assembling bottom–up processes. Chem Soc Rev 2011; 40:801-28. [DOI: 10.1039/c0cs00052c] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nguyen TH, Chen KL, Elimelech M. Adsorption Kinetics and Reversibility of Linear Plasmid DNA on Silica Surfaces: Influence of Alkaline Earth and Transition Metal Ions. Biomacromolecules 2010; 11:1225-30. [DOI: 10.1021/bm901427n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thanh H. Nguyen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
| | - Kai Loon Chen
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
| | - Menachem Elimelech
- Department of Civil and Environmental Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Chemical Engineering, Environmental Engineering Program, Yale University, New Haven, Connecticut 06520
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Survey of the year 2008: applications of isothermal titration calorimetry. J Mol Recognit 2010; 23:395-413. [DOI: 10.1002/jmr.1025] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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