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Sit I, Young MA, Kubicki JD, Grassian VH. Distinguishing different surface interactions for nucleotides adsorbed onto hematite and goethite particle surfaces through ATR-FTIR spectroscopy and DFT calculations. Phys Chem Chem Phys 2023. [PMID: 37470700 PMCID: PMC10395000 DOI: 10.1039/d3cp01200j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
Geochemical interfaces can impact the fate and transport of aqueous species in the environment including biomolecules. In this study, we investigate the surface chemistry of adsorbed nucleotides on two different minerals, hematite and goethite, using infrared spectroscopy and density functional theory (DFT) calculations. Attenuated total reflectance-Fourier transform infrared spectroscopy is used to probe the adsorption of deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxycytidine monophosphate (dCMP), and deoxythymidine monophosphate (dTMP) onto either hematite or goethite particle surfaces. The results show preferential adsorption of the phosphate group to either surface. Remarkably, surface adsorption of the four nucleotides onto either hematite or goethite have nearly identical experimental spectra in the phosphate region (900 to 1200 cm-1) for each mineral surface yet are distinctly different between the two minerals, suggesting differences in binding of these nucleotides to the two mineral surfaces. The experimental absorption frequencies in the phosphate region were compared to DFT calculations for nucleotides adsorbed through the phosphate group to binuclear clusters in either a monodentate or bidentate bridging coordination. Although the quality of the fits suggests that both binding modes may be present, the relative amounts differ on the two surfaces with preferential bonding suggested to be monodentate coordination on hematite and bidentate bridging on goethite. Possible reasons for these differences are discussed.
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Affiliation(s)
- Izaac Sit
- Department of Nanoengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark A Young
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
| | - James D Kubicki
- Department of Earth, Environmental & Resource Sciences, The University of Texas at El Paso, El Paso, TX 79968, USA.
| | - Vicki H Grassian
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA 92093, USA.
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2
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Vlasova N, Markitan O. Nucleotide Interaction with Nanocrystalline Ceria Surface. CHEMISTRY & CHEMICAL TECHNOLOGY 2022. [DOI: 10.23939/chcht16.04.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The adsorption of nucleotides on the surface of nanocrystalline cerium dioxide (pHpzc = 6.3) in NaCl solutions was investigated using multi-batch adsorption experiments over a wide range of pH. The obtained results were interpreted as a formation of outer and inner sphere surface complexes with the participation of phosphate moieties. The Basic Stern surface complexation model was applied to obtain quantitative equilibrium reaction constants.
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3
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Sit I, Quirk E, Hettiarachchi E, Grassian VH. Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15038-15049. [PMID: 36445255 PMCID: PMC9753757 DOI: 10.1021/acs.langmuir.2c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO2 particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO2 surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.
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Affiliation(s)
- Izaac Sit
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleanor Quirk
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eshani Hettiarachchi
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Vicki H. Grassian
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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4
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Vlasova N, Markitan O. Phosphate–nucleotide–nucleic acid: Adsorption onto nanocrystalline ceria surface. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Baú JPT, Villafañe-Barajas SA, da Costa ACS, Negrón-Mendoza A, Colín-Garcia M, Zaia DAM. Adenine Adsorbed onto Montmorillonite Exposed to Ionizing Radiation: Essays on Prebiotic Chemistry. ASTROBIOLOGY 2020; 20:26-38. [PMID: 31549853 DOI: 10.1089/ast.2018.1909] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most adsorption and radiolysis experiments related to prebiotic chemistry studies are performed in distilled water or sodium chloride solutions. However, distilled water and sodium chloride solutions do not represent the composition of the primitive seas of Earth. In this work, an artificial seawater with ion abundances Mg2+ > Ca2+ >> Na+ ≈ K+ and SO42- >> Cl- was used, one that is different from the average composition of seawater today. This artificial seawater is named seawater 4.0 Ga, since it better represents the composition of the major constituents of seawater of primitive Earth. The radiolysis of adenine adsorbed onto montmorillonite was studied. The most important result is that adenine is adsorbed onto montmorillonite, when it is dissolved in artificial seawater 4.0 Ga, and the clay protects adenine against gamma radiation decomposition. However, desorption of adenine from montmorillonite was possible only with 0.10 mol L-1 of KOH. This result indicates that adenine was strongly bonded to montmorillonite. Fourier transform infrared spectroscopy showed that NH2 group and electrostatic interactions, between negatively charged montmorillonite and positively charged adenine, are responsible for adsorption of adenine onto montmorillonite. In addition, X-ray diffractograms showed that adenine enters in the interlayer space of montmorillonite.
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Affiliation(s)
- João Paulo T Baú
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, Londrina, Brasil
| | - Sául A Villafañe-Barajas
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
| | | | - Alicia Negrón-Mendoza
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
| | - María Colín-Garcia
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, México
| | - Dimas A M Zaia
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, Londrina, Brasil
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6
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Sand KK, Jelavić S. Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life? Front Microbiol 2018; 9:2217. [PMID: 30319562 PMCID: PMC6167411 DOI: 10.3389/fmicb.2018.02217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.
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Affiliation(s)
- Karina Krarup Sand
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Fornaro T, Brucato JR, Feuillie C, Sverjensky DA, Hazen RM, Brunetto R, D'Amore M, Barone V. Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite. ASTROBIOLOGY 2018; 18:989-1007. [PMID: 30048146 DOI: 10.1089/ast.2017.1784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.
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Affiliation(s)
- Teresa Fornaro
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
- 3 Scuola Normale Superiore , Pisa, Italy
| | - John R Brucato
- 2 INAF-Astrophysical Observatory of Arcetri , Firenze, Italy
| | - Cécile Feuillie
- 4 Louvain Institute of Biomolecular Science and Technology, University Catholique de Louvain , Louvain-la-Neuve, Belgium
| | - Dimitri A Sverjensky
- 5 Department of Earth and Planetary Sciences, Johns Hopkins University , Baltimore, Maryland, United States
| | - Robert M Hazen
- 1 Geophysical Laboratory, Carnegie Institution for Science , Washington, District of Columbia, United States
| | - Rosario Brunetto
- 6 Institut d'Astrophysique Spatiale, UMR8617 CNRS-Univ. Paris-Sud, Université Paris-Saclay , Orsay, France
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Villafañe-Barajas SA, Baú JPT, Colín-García M, Negrón-Mendoza A, Heredia-Barbero A, Pi-Puig T, Zaia DAM. Salinity Effects on the Adsorption of Nucleic Acid Compounds on Na-Montmorillonite: a Prebiotic Chemistry Experiment. ORIGINS LIFE EVOL B 2018; 48:181-200. [PMID: 29392543 DOI: 10.1007/s11084-018-9554-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals. In this work, the adsorption of adenine, adenosine, and 5'AMP onto Na+montmorillonite was studied using a primitive ocean analog (4.0 Ga) from experimental and computational approaches. The order of sorption of the molecules was: 5'AMP > adenine > adenosine. Infrared spectra showed that the interaction between these molecules and montmorillonite occurs through the NH2 group. In addition, electrostatic interaction between negatively charged montmorillonite and positively charge N1 of these molecules could occur. Results indicate that dissolved salts affect the sorption in all cases; the size and structure of each organic molecule influence the amount sorbed. Specifically, the X-ray diffraction patterns show that dissolved salts occupy the interlayer space in Na-montmorillonite and compete with organic molecules for available sites. The adsorption capacity is clearly affected by dissolved salts in thermodynamic terms as deduced by isotherm models. Indeed, molecular dynamic models suggest that salts are absorbed in the interlamellar space and can interact with oxygen atoms exposed in the edges of clay or in its surface, reducing the sorption of the organic molecules. This research shows that the sorption process could be affected by high concentration of salts, since ions and organic molecules may compete for available sites on inorganic surfaces. Salt concentration in primitive oceans may have strongly affected the sorption, and hence the concentration processes of organic molecules on minerals.
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Affiliation(s)
- Saúl A Villafañe-Barajas
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México
| | - João Paulo T Baú
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, Londrina, PR, 86051-990, Brazil
| | - María Colín-García
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México.
| | - Alicia Negrón-Mendoza
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México
| | - Alejandro Heredia-Barbero
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México
| | - Teresa Pi-Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Cd. Mx., México
| | - Dimas A M Zaia
- Laboratório de Química Prebiótica, Departamento de Química-CCE, Universidade Estadual de Londrina, Londrina, PR, 86051-990, Brazil.
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9
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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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10
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Amorphous Silica-Promoted Lysine Dimerization: a Thermodynamic Prediction. ORIGINS LIFE EVOL B 2017; 48:23-34. [DOI: 10.1007/s11084-017-9548-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
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11
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Jelavić S, Tobler DJ, Hassenkam T, De Yoreo JJ, Stipp SLS, Sand KK. Prebiotic RNA polymerisation: energetics of nucleotide adsorption and polymerisation on clay mineral surfaces. Chem Commun (Camb) 2017; 53:12700-12703. [DOI: 10.1039/c7cc04276k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A set of experimentally measured and internally consistent Gibbs free energies of binding between different model nucleotides and mineral surfaces is reported.
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Affiliation(s)
- S. Jelavić
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- Copenhagen OE 2100
- Denmark
| | - D. J. Tobler
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- Copenhagen OE 2100
- Denmark
| | - T. Hassenkam
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- Copenhagen OE 2100
- Denmark
| | - J. J. De Yoreo
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
- Department of Materials Science and Engineering
| | - S. L. S. Stipp
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- Copenhagen OE 2100
- Denmark
| | - K. K. Sand
- Nano-Science Center
- Department of Chemistry
- University of Copenhagen
- Copenhagen OE 2100
- Denmark
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12
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Insights to Achieve a Better Control of Silicon-Aluminum Ratio and ZSM-5 Zeolite Crystal Morphology through the Assistance of Biomass. Catalysts 2016. [DOI: 10.3390/catal6020030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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13
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Liu B, Liu J. Comprehensive Screen of Metal Oxide Nanoparticles for DNA Adsorption, Fluorescence Quenching, and Anion Discrimination. ACS APPLIED MATERIALS & INTERFACES 2015; 7:24833-8. [PMID: 26491955 DOI: 10.1021/acsami.5b08004] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Although DNA has been quite successful in metal cation detection, anion detectioin remains challenging because of the charge repulsion. Metal oxides represent a very important class of materials, and different oxides might interact with anions differently. In this work, a comprehensive screen of common metal oxide nanoparticles (MONPs) was carried out for their ability to adsorb DNA, quench fluorescence, and release adsorbed DNA in the presence of target anions. A total of 19 MONPs were studied, including Al2O3, CeO2, CoO, Co3O4, Cr2O3, Fe2O3, Fe3O4, In2O3, ITO, Mn2O3, NiO, SiO2, SnO2, a-TiO2 (anatase), r-TiO2 (rutile), WO3, Y2O3, ZnO, ZrO2. These MONPs have different DNA adsorption affinity. Some adsorb DNA without quenching the fluorescence, while others strongly quench adsorbed fluorophores. They also display different affinity toward anions probed by DNA desorption. Finally, CeO2, Fe3O4, and ZnO were used to form a sensor array to discriminate phosphate, arsenate, and arsenite from the rest using linear discriminant analysis. This study not only provides a solution for anion discrimination using DNA as a signaling molecule but also provides insights into the interface of metal oxides and DNA.
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Affiliation(s)
- Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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14
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Iqubal MA, Sharma R, Kamaluddin. Studies on interaction of ribonucleotides with zinc ferrite nanoparticles using spectroscopic and microscopic techniques. KARBALA INTERNATIONAL JOURNAL OF MODERN SCIENCE 2015. [DOI: 10.1016/j.kijoms.2015.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
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