1
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Gutiérrez-Gálvez L, García-Mendiola T, Lorenzo E, Nuez-Martinez M, Ocal C, Yan S, Teixidor F, Pinheiro T, Marques F, Viñas C. Compelling DNA intercalation through 'anion-anion' anti-coulombic interactions: boron cluster self-vehicles as promising anticancer agents. J Mater Chem B 2024. [PMID: 39141010 DOI: 10.1039/d4tb01177e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Anticancer drugs inhibit DNA replication by intercalating between DNA base pairs, forming covalent bonds with nucleotide bases, or binding to the DNA groove. To develop safer drugs, novel molecular structures with alternative binding mechanisms are essential. Stable boron hydrides offer a promising alternative for cancer therapy, opening up additional options like boron neutron capture therapy based on 10B and thermal neutron beams or proton boron fusion therapy using 11B and proton beams. These therapies are more efficient when the boron compound is ideally located inside cancer cells, particularly in the nucleus. Current cancer treatments often utilize small, polycyclic, aromatic, planar molecules that intercalate between ds-DNA base pairs, requiring only a spacing of approximately 0.34 nm. In this paper, we demonstrate another type of intercalation. Notably, [3,3'-Fe(1,2-C2B9H11)2]-, ([o-FESAN]-), a compact 3D molecule measuring 1.1 nm × 0.6 nm, can as well intercalate by strong non-bonding interactions preferentially with guanine. Unlike known intercalators, which are positive or neutral, [o-FESAN]- is a negative species and when an [o-FESAN]- molecule approaches the negatively charged DNA phosphate chain an anion-anion interaction consistently anti-electrostatic via Ccluster-H⋯O-P bonds occurs. Then, when more molecules approach, an elongated outstandingly self-assembled structure of [o-FESAN]--[o-FESAN]- forms moving anions towards the interthread region to interact with base pairs and form aggregates of four [o-FESAN]- anions per base pair. These aggregates, in this environment, are generated by Ccluster-H⋯O-C, N-H⋯H-B and Ccluster-H⋯H-B interactions. The ferrabis(dicarbollide) boron-rich small molecules not only effectively penetrate the nucleus but also intercalate with ds-DNA, making them promising for cancer treatment. This amphiphilic anionic molecule, used as a carrier-free drug, can enhance radiotherapy in a multimodal perspective, providing healthcare professionals with improved tools for cancer treatment. This work demonstrates these findings with a plethora of techniques.
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Affiliation(s)
- Laura Gutiérrez-Gálvez
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Tania García-Mendiola
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Encarnación Lorenzo
- Departamento de Química Analítica y Análisis Instrumental, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- IMDEA-Nanociencia, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain
| | - Miquel Nuez-Martinez
- Institut de Ciència de Materials de Barcelona (C.S.I.C.) Campus U.A.B, 08193 Bellaterra, Barcelona, Spain.
| | - Carmen Ocal
- Institut de Ciència de Materials de Barcelona (C.S.I.C.) Campus U.A.B, 08193 Bellaterra, Barcelona, Spain.
| | - Shunya Yan
- Institut de Ciència de Materials de Barcelona (C.S.I.C.) Campus U.A.B, 08193 Bellaterra, Barcelona, Spain.
| | - Francesc Teixidor
- Institut de Ciència de Materials de Barcelona (C.S.I.C.) Campus U.A.B, 08193 Bellaterra, Barcelona, Spain.
| | - Teresa Pinheiro
- iBB - Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
| | - Fernanda Marques
- Departamento de Engenharia e Ciências Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
- C2TN - Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10, 2695-066 Bobadela LRS, Portugal
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (C.S.I.C.) Campus U.A.B, 08193 Bellaterra, Barcelona, Spain.
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2
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Stanko ŠT, Schawe JE, Spieckermann F, Eckert J, Löffler JF. Energy Absorption and Beam Damage during Microfocus Synchrotron X-ray Diffraction. J Phys Chem Lett 2024; 15:6286-6291. [PMID: 38848352 PMCID: PMC11194812 DOI: 10.1021/acs.jpclett.4c00497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 06/09/2024]
Abstract
In this study, we combine in situ fast differential scanning calorimetry (FDSC) with synchrotron X-ray measurements to study simultaneously the structure and thermophysical properties of materials. Using the example of the organic compound BCH-52, we show that the X-ray beam can heat the sample and induce a shift of the heat-flow signal. The aim of this paper is to investigate the influence of radiation on sample behavior. The calorimetric data is used to quantify the absorbed beam energy and, together with the diffraction data, reveal an irreversible damage of the sample. The results are especially important for materials with high absorption coefficients and for high-energy X-ray and electron beams. Our findings illustrate that FDSC combined with X-ray diffraction is a suitable characterization method when beam damage must be minimized.
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Affiliation(s)
- Štefan T. Stanko
- Laboratory
of Metal Physics and Technology, Department of Materials, ETH Zurich, 8093 Zurich, Switzerland
| | - Jürgen E.
K. Schawe
- Laboratory
of Metal Physics and Technology, Department of Materials, ETH Zurich, 8093 Zurich, Switzerland
- Mettler-Toledo
GmbH, Analytical, 8606 Nänikon, Switzerland
| | - Florian Spieckermann
- Department
of Materials Science Chair of Materials Physics, Montanuniversität Leoben, 8700 Leoben, Austria
| | - Jürgen Eckert
- Department
of Materials Science Chair of Materials Physics, Montanuniversität Leoben, 8700 Leoben, Austria
- Erich
Schmid Institute of Materials Science, Austrian Academy of Sciences, 8700 Leoben, Austria
| | - Jörg F. Löffler
- Laboratory
of Metal Physics and Technology, Department of Materials, ETH Zurich, 8093 Zurich, Switzerland
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3
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Santra S, Streibel V, Wagner LI, Cheng N, Ding P, Zhou G, Sirotti E, Kisslinger R, Rieth T, Zhang S, Sharp ID. Tuning Carbon Dioxide Reduction Reaction Selectivity of Bi Single-Atom Electrocatalysts with Controlled Coordination Environments. CHEMSUSCHEM 2024; 17:e202301452. [PMID: 38224562 DOI: 10.1002/cssc.202301452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/24/2023] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Control over product selectivity of the electrocatalytic CO2 reduction reaction (CO2RR) is a crucial challenge for the sustainable production of carbon-based chemical feedstocks. In this regard, single-atom catalysts (SACs) are promising materials due to their tunable coordination environments, which could enable tailored catalytic activities and selectivities, as well as new insights into structure-activity relationships. However, direct evidence for selectivity control via systematic tuning of the SAC coordination environment is scarce. In this work, we have synthesized two differently coordinated Bi SACs anchored to the same host material (carbon black) and characterized their CO2RR activities and selectivities. We find that oxophilic, oxygen-coordinated Bi atoms produce HCOOH, while nitrogen-coordinated Bi atoms generate CO. Importantly, use of the same support material assured that alternation of the coordination environment is the dominant factor for controlling the CO2RR product selectivity. Overall, this work demonstrates the structure-activity relationship of Bi SACs, which can be utilized to establish control over CO2RR product distributions, and highlights the promise for engineering atomic coordination environments of SACs to tune reaction pathways.
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Affiliation(s)
- Saswati Santra
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Verena Streibel
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Laura I Wagner
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Ningyan Cheng
- Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Pan Ding
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Guanda Zhou
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Elise Sirotti
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Ryan Kisslinger
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Tim Rieth
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
| | - Siyuan Zhang
- Max-Planck-Institut für Eisenforschung, Max-Planck-Straße 1, 40237, Düsseldorf, Germany
| | - Ian D Sharp
- Walter Schottky Institute, Technical University of Munich, 85748, Garching, Germany
- TUM School of Natural Sciences, Technical University of Munich, 85748, Garching, Germany
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4
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Hoang J, Patil SL, Srinoi P, Liu T, Marquez MD, Khantamat O, Tuntiwechapikul W, Gunaratne PH, Lee TR. Transfection of Unmodified MicroRNA Using Monolayer-Coated Au Nanoparticles as Gene-Delivery Vehicles. ACS APPLIED BIO MATERIALS 2024; 7:230-237. [PMID: 38133569 DOI: 10.1021/acsabm.3c00837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This article describes a monolayer-coated gold nanoparticle-based transfection system for the delivery of microRNA (miRNA) into human osteosarcoma (HOS) cells. Two distinct ammonium-terminated adsorbates were used in this study, which provided a platform for ionic bonding of the miRNA onto gold nanoparticles (AuNPs). The custom-designed monolayer-coated gold nanoparticles were characterized by dynamic light scattering, gel mobility shift assay, transmission electron microscopy, ultraviolet-visible spectrometry, zeta potential, and X-ray photoelectron spectroscopy. The miRNA-loaded gold nanoparticles were transfected, and the level of intracellular miRNA delivered and taken up by cells was measured by Taqman qPCR. The overall analysis indicated a successful delivery of miRNA into the HOS cells at an ∼11,000-fold increase compared to nontreated cells.
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Affiliation(s)
- Johnson Hoang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, United States
| | - Sagar L Patil
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, United States
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Pannaree Srinoi
- Departments of Chemistry and Chemical Engineering and the Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5003, United States
- Department of Chemistry and Centre of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Tingting Liu
- Departments of Chemistry and Chemical Engineering and the Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5003, United States
| | - Maria D Marquez
- Departments of Chemistry and Chemical Engineering and the Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5003, United States
| | - Orawan Khantamat
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wirote Tuntiwechapikul
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Preethi H Gunaratne
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, United States
| | - T Randall Lee
- Departments of Chemistry and Chemical Engineering and the Texas Center for Superconductivity, University of Houston, Houston, Texas 77204-5003, United States
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5
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Low-Energy Electron Generation for Biomolecular Damage Inquiry: Instrumentation and Methods. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Technological advancement has produced a variety of instruments and methods to generate electron beams that have greatly assisted in the extensive theoretical and experimental efforts devoted to investigating the effect of secondary electrons with energies approximately less than 100 eV, which are referred as low-energy electrons (LEEs). In the past two decades, LEE studies have focused on biomolecular systems, which mainly consist of DNA and proteins and their constituents as primary cellular targets of ionizing radiation. These studies have revealed that compared to other reactive species produced by high-energy radiation, LEEs have distinctive pathways and considerable efficiency in inducing lethal DNA lesions. The present work aims to briefly discuss the current state of LEE production technology and to motivate further studies and improvements of LEE generation techniques in relation to biological electron-driven processes associated with such medical applications as radiation therapy and cancer treatment.
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6
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Sinha R, Das SK, Ghosh M, Chowdhury J. Fabrication of gold nanoparticles tethered in heat-cooled calf thymus-deoxyribonucleic acid Langmuir-Blodgett film as effective surface-enhanced Raman scattering sensing platform. Front Chem 2022; 10:1034060. [DOI: 10.3389/fchem.2022.1034060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
SERS active substrate fabricated through self-assembly of Gold nanoparticles on the disjointed networks of Heat-cooled Calf Thymus DNA (HC-Ct DNA) Langmuir-Blodgett (LB) film has been reported. Adsorption kinetics of HC-Ct DNA molecules at the air-water interface has been studied explicitly. The UV-Vis electronic absorption spectra in conjunction with the FESEM images collectively suggest the presence of H- type aggregated domains most likely owing to plane-to-plane self-association of the HC-Ct DNA molecules aligned vertically on the surface of the LB film. Elemental composition and the morphological features of the as-prepared substrate (APS) are explored from XPS analysis and the FESEM, AFM images respectively. The SERS efficacy of the APS has been tested with trace concentrations of 4-Mercaptopyridine molecule. Finally, this SERS active substrate has also been used for the detection of malathion at ultrasensitive concentrations.
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7
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Cordsmeier L, Hahn MB. DNA Stability in Biodosimetry, Pharmacy and DNA Based Data-Storage: Optimal Storage and Handling Conditions. Chembiochem 2022; 23:e202200391. [PMID: 35972228 PMCID: PMC9826032 DOI: 10.1002/cbic.202200391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/12/2022] [Indexed: 01/11/2023]
Abstract
DNA long-term stability and integrity is of importance for applications in DNA based bio-dosimetry, data-storage, pharmaceutical quality-control, donor insemination and DNA based functional nanomaterials. Standard protocols for these applications involve repeated freeze-thaw cycles of the DNA, which can cause detrimental damage to the nucleobases, as well as the sugar-phosphate backbone and therefore the whole molecule. Throughout the literature three hypotheses can be found about the underlying mechanisms occurring during freeze-thaw cycles. It is hypothesized that DNA single-strand breaks during freezing can be induced by mechanical stress leading to shearing of the DNA molecule, by acidic pH causing damage through depurination and beta elimination or by the presence of metal ions catalyzing oxidative damage via reactive oxygen species (ROS). Here we test these hypotheses under well defined conditions with plasmid DNA pUC19 in high-purity buffer (1xPBS) at physiological salt and pH 7.4 conditions, under pH 6 and in the presence of metal ions in combination with the radical scavengers DMSO and Ectoine. The results show for the 2686 bp long plasmid DNA, that neither mechanical stress, nor pH 6 lead to degradation during repeated freeze-thaw cycles. In contrast, the presence of metal ions (Fe2+ ) leads to degradation of DNA via the production of radical species.
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Affiliation(s)
- Leo Cordsmeier
- Bundesanstalt für Materialforschung und Prüfung12205BerlinGermany
- Freie Universität BerlinInstitut für Chemie14195BerlinGermany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und Prüfung12205BerlinGermany
- Freie Universität BerlinInstitut für Chemie14195BerlinGermany
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8
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Olgaç N, Şahin Y, Liv L. Development and characterisation of cysteine-based gold electrodes for the electrochemical biosensing of the SARS-CoV-2 spike antigen. Analyst 2022; 147:4462-4472. [PMID: 36052711 DOI: 10.1039/d2an01225a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This article describes three novel electrochemical biosensing platforms developed to determine the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) spike antigen protein: glutaraldehyde, SARS-CoV-2 spike antibody and bovine serum albumin; N,N-dicyclohexyl carbodiimide/4-(dimethylamino)pyridine functionalised SARS-CoV-2 spike antibody and bovine serum albumin; and 1-ethyl-3-[3-dimethylaminopropyl]-carbodiimide hydrochloride/N-hydroxysuccinimide functionalised SARS-CoV-2 spike antibody and bovine serum albumin modified cysteine-based gold-flower modified glassy carbon electrodes. Two of the produced biosensors having better signals were used to determine the SARS-CoV-2 spike antigen in spiked-saliva and clinical samples containing gargle and mouthwash liquids and characterised using cyclic voltammetry, scanning electron microscopy, energy dispersive X-ray spectroscopy and X-ray photoelectron spectroscopy. The study provides highly significant information in terms of how coupling reagents ought to be used with linkers consisting of both amine and carboxylic acid terminals (i.e. cysteine). The electrochemical cathodic signals based on antibody-antigen protein interactions at approximately -270 mV were evaluated as a response using square wave voltammetry, and they increased in proportion to the SARS-CoV-2 spike antigen. The limit of detection values were 0.93 and 46.3 ag mL-1 in a linear range from 1 ag mL-1 to 100 pg mL-1 and from 100 ag mL-1 to 10 ng mL-1 and the recovery and relative standard deviation values for spiked-saliva samples were 99.50% and 99.40%, and 3.87% and 0.13% for BSA/S-AB/GluAl/Cys/Au/GCE and BSA/S-AB/f-Cys/Au/GCE, respectively. The results showed that both biosensing platforms could be selectively and accurately used to diagnose COVID-19 in RT-PCR-approved clinical samples.
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Affiliation(s)
- Nursel Olgaç
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey. .,Yildiz Technical University, Faculty of Arts and Science, Department of Chemistry, 34210, Istanbul, Turkey.
| | - Yücel Şahin
- Yildiz Technical University, Faculty of Arts and Science, Department of Chemistry, 34210, Istanbul, Turkey.
| | - Lokman Liv
- Electrochemistry Laboratory, Chemistry Group, The Scientific and Technological Research Council of Turkey, National Metrology Institute (TUBITAK UME), 41470, Gebze, Kocaeli, Turkey.
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9
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X-ray photoelectron spectroscopy of Thymine and 5-Bromouracil studied by Symmetry-Adapted-Cluster Configuration-Interaction (SAC-CI) theory. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Gao Y, Kong A, Peng M, Lv Y, Liu M, Li W, Zhang J, Fu Y. Tuning electrochemical environment enables unexpected C=O selectivity for cinnamaldehyde hydrogenation over self-standing palladium cathode. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Singh A, Meena R. Feasibility study of DNA-based porous membranes as gravity-driven purifications. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-022-04372-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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12
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Ahsan MS, Kochetov V, Hein D, Bokarev SI, Wilkinson I. Probing the molecular structure of aqueous triiodide via X-ray photoelectron spectroscopy and correlated electron phenomena. Phys Chem Chem Phys 2022; 24:15540-15555. [PMID: 35713286 DOI: 10.1039/d1cp05840a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liquid-microjet-based X-ray photoelectron spectroscopy was applied to aqueous triiodide solutions, I3-(aq.), to investigate the anion's valence- and core-level electronic structure, ionization dynamics, associated electron-correlation effects, and nuclear geometric structure. The roles of multi-active-electron (shake-up) ionization processes - with noted sensitivity to the solute geometric structure - were investigated through I3-(aq.) solution valence, I 4d, and I 3d core-level measurements. The experimental spectra were interpreted with the aid of simulated photoelectron spectra, built upon multi-reference ab initio electronic structure calculations associated with different I3-(aq.) molecular geometries. A comparison of the single-to-multi-active-electron ionization signal ratios extracted from the experimental and theoretical core-level photoemission spectra suggests that the ground state of the solute adopts a near-linear average geometry in aqueous solutions. This contrasts with the interpretation of time-resolved X-ray solution scattering studies, but is found to be fully consistent with the rest of the solution-phase I3-(aq.) literature. Comparing the results of low- and high-photon-energy photoemission measurements, we further suggest that the aqueous anion adopts a more asymmetric geometry at the aqueous-solution-gas interface than in the aqueous bulk.
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Affiliation(s)
- Md Sabbir Ahsan
- Department of Locally-Sensitive and Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany. .,Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Vladislav Kochetov
- Institut für Physik, Universität Rostock, Albert Einstein Str. 23-24, D-18059 Rostock, Germany
| | - Dennis Hein
- Operando Interfacial Photochemistry, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-platz. 1, D-14109 Berlin, Germany.,Department of Physics, Humboldt-Universität zu Berlin, Newtonstrasse 15, D-12489 Berlin, Germany
| | - Sergey I Bokarev
- Institut für Physik, Universität Rostock, Albert Einstein Str. 23-24, D-18059 Rostock, Germany
| | - Iain Wilkinson
- Department of Locally-Sensitive and Time-Resolved Spectroscopy, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany.
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Bağda E, Kızılyar Y, İnci ÖG, Ghaffarlou M, Barsbay M. One-pot modification of oleate-capped UCNPs with AS1411 G-quadruplex DNA in a fully aqueous medium. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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14
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Hahn MB, Dietrich PM, Radnik J. In situ monitoring of the influence of water on DNA radiation damage by near-ambient pressure X-ray photoelectron spectroscopy. Commun Chem 2021; 4:50. [PMID: 36697687 PMCID: PMC9814248 DOI: 10.1038/s42004-021-00487-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/10/2021] [Indexed: 02/01/2023] Open
Abstract
Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS experiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.
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Affiliation(s)
- Marc Benjamin Hahn
- grid.14095.390000 0000 9116 4836Institut für Experimentalphysik, Freie Universität Berlin, Berlin, Germany ,grid.71566.330000 0004 0603 5458Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
| | | | - Jörg Radnik
- grid.71566.330000 0004 0603 5458Bundesanstalt für Materialforschung und -prüfung, Berlin, Germany
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15
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Highly Sensitive and Cost-Effective Portable Sensor for Early Gastric Carcinoma Diagnosis. SENSORS 2021; 21:s21082639. [PMID: 33918707 PMCID: PMC8069728 DOI: 10.3390/s21082639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 11/17/2022]
Abstract
Facile and efficient early detection of cancer is a major challenge in healthcare. Herein we developed a novel sensor made from a polycarbonate (PC) membrane with nanopores, followed by sequence-specific Oligo RNA modification for early gastric carcinoma diagnosis. In this design, the gastric cancer antigen CA72-4 is specifically conjugated to the Oligo RNA, thereby inhibiting the electrical current through the PC membrane in a concentration-dependent manner. The device can determine the concentration of cancer antigen CA72-4 in the range from 4 to 14 U/mL, possessing a sensitivity of 7.029 µAU-1mLcm-2 with a linear regression (R2) of 0.965 and a lower detection limit of 4 U/mL. This device has integrated advantages including high specificity and sensitivity and being simple, portable, and cost effective, which collectively enables a giant leap for cancer screening technologies towards clinical use. This is the first report to use RNA aptamers to detect CA72-4 for gastric carcinoma diagnosis.
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Haque J, Jafar Mazumder MA, Quraishi MA, Ali SA, Aljeaban NA. Pyrrolidine-based quaternary ammonium salts containing propargyl and hydrophobic C-12 and C-16 alkyl chains as corrosion inhibitors in aqueous acidic media. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114473] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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17
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Wittmar J, Meyer S, Sieling T, Kunte J, Smiatek J, Brand I. What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute-Biopolymer Interactions. J Phys Chem B 2020; 124:7999-8011. [PMID: 32816487 DOI: 10.1021/acs.jpcb.0c05273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and double-stranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.
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Affiliation(s)
- Julia Wittmar
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Susann Meyer
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Thorben Sieling
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Jörg Kunte
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Izabella Brand
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
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Ge H, Wang D, Pan Y, Guo Y, Li H, Zhang F, Zhu X, Li Y, Zhang C, Huang L. Sequence‐Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Huan Ge
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Dongya Wang
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Yue Pan
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Hongyu Li
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Fan Zhang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuehua Li
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Ling Huang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
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Ge H, Wang D, Pan Y, Guo Y, Li H, Zhang F, Zhu X, Li Y, Zhang C, Huang L. Sequence‐Dependent DNA Functionalization of Upconversion Nanoparticles and Their Programmable Assemblies. Angew Chem Int Ed Engl 2020; 59:8133-8137. [DOI: 10.1002/anie.202000831] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/17/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Huan Ge
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Dongya Wang
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Yue Pan
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Yuanyuan Guo
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Hongyu Li
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Fan Zhang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
| | - Xinyuan Zhu
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Yuehua Li
- Departments of Radiology and CardiologyShanghai Jiao Tong University Affiliated Sixth People's HospitalShanghai Jiao Tong University School of Medicine 600 Yishan Road Shanghai 200233 China
| | - Chuan Zhang
- School of Chemistry and Chemical EngineeringState Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University 800 Dongchuan Road Shanghai 200240 China
| | - Ling Huang
- Key Laboratory of Flexible Electronics (KLOFE) &, Institute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced, Materials (SICAM)Nanjing Tech University (NJTECH) 30 South Puzhu Road Nanjing 211816 China
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20
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Basu S, Pacelli S, Paul A. Self-healing DNA-based injectable hydrogels with reversible covalent linkages for controlled drug delivery. Acta Biomater 2020; 105:159-169. [PMID: 31972367 DOI: 10.1016/j.actbio.2020.01.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/11/2020] [Accepted: 01/14/2020] [Indexed: 01/08/2023]
Abstract
Injectable hydrogels represent a valuable tool for the delivery of therapeutic molecules aimed to restore the functionality of damaged tissues. In this study, we report the design of a nanocomposite DNA-based hydrogel crosslinked with oxidized alginate (OA) via the formation of reversible imine linkages. The formulated hydrogel functioned as an injectable carrier for the sustained delivery of a small molecule drug, simvastatin. The degree of oxidation of alginate and the concentration of silicate-based nanoparticles (nSi) were varied to modulate the rheological properties of the hydrogels. Specifically, the formulations consisting of OA with higher degree of oxidation displayed the highest value of storage moduli, yield stress, yield strain, and rapid recovery after removal of cyclic stress. The hydrogel formulations exhibited self-healing and shear-thinning properties due to the reversible nature of the covalent imine bonds formed between the aldehyde groups of OA and the amine groups present in the DNA nucleotides. Moreover, the incorporation of charged nSi further enhanced the shear strength of the formulated hydrogels by establishing electrostatic interactions with the phosphate groups of the DNA network. The optimized hydrogel was able to promote the sustained release of simvastatin for more than a week. The bioactivity of the released drug was confirmed by testing its ability to induce osteogenic differentiation and migration of human adipose-derived stem cells in vitro. Overall, the results obtained from this study demonstrate that DNA could be used as a natural biopolymer to fabricate self-healing injectable hydrogels with sustained release properties for minimally invasive therapeutic approaches. STATEMENT OF SIGNIFICANCE: Dynamic covalent chemistry, especially Schiff base reactions have emerged as a promising route for the formation of injectable hydrogels. Our study demonstrated the development of a DNA-based self-healing hydrogel formed via Schiff base reaction occurring at physiological conditions. The hydrogels functioned as sustained delivery vehicles for the hydrophobic drug simvastatin, which requires a polymeric carrier for controlled delivery of therapeutic concentrations of the drug without exhibiting cytotoxic effects. Presently available hydrogel-based drug delivery systems encounter major challenges for the delivery of hydrophobic drugs due to the hydrophilic nature of the base matrix. Our strategy presents a platform technology for the design of minimally invasive approaches for the sustained delivery of hydrophobic drugs similar to simvastatin.
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Affiliation(s)
- Sayantani Basu
- Department of Chemical and Petroleum Engineering, School of Engineering, University of Kansas, Lawrence, KS, USA
| | - Settimio Pacelli
- Department of Biomedical Engineering, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada.
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Kesama MR, Dugasani SR, Jung SG, Gnapareddy B, Park T, Park SH. Band gap, dielectric constant, and susceptibility of DNA layers as controlled by vanadium ion concentration. NANOTECHNOLOGY 2019; 31:085705. [PMID: 31675737 DOI: 10.1088/1361-6528/ab53b0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Deoxyribonucleic acid (DNA) doped with transition metal ions shows great versatility for molecular-based biosensors and bioelectronics. Methodologies for developing DNA lattices (formed by synthetic double-crossover tiles) and DNA layers (used by natural salmon) doped with vanadium ions (V3+), as well as an understanding of the physical characteristics of V3+-doped DNA nanostructures, are essential in practical applications in interdisciplinary research fields. Here, DNA lattices and layers doped with V3+ are constructed through substrate-assisted growth and drop-casting methods. In addition, enhanced physical characteristics such as the band gap energy, work function, dielectric constant, and susceptibility of V3+-doped DNA nanostructures with varying V3+ concentration ([V 3+ ]) are investigated. The critical concentration ([V 3+ ]C ) at a given amount of DNA was predicted based on an analysis of the phase transition of DNA lattices from crystalline to amorphous with specific [V 3+ ]. Generally, the [V 3+ ]C provided crucial information on the structural stability and extremum physical characteristics of V3+-doped DNA nanostructures due to the optimum incorporation of V3+ into DNA. We obtained the optical absorption spectra for energy band gap estimation; Raman spectra for identifying the preferential coordination sites of V3+ in DNA; x-ray photoelectron spectra to examine the chemical state, chemical composition, and functional groups; and ultraviolet photoelectron spectra to estimate the work function. In addition, we addressed the electrical properties (i.e. current, capacitance, dielectric constant, and storage energy) and magnetic properties (magnetic field-dependent and temperature-dependent magnetizations and susceptibility) of DNA layers in the presence of V3+. The development of biocompatible materials with specific optical, electrical, and magnetic properties is required for future applications because they must have designated functionality, high efficiency, and affordability.
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Affiliation(s)
- Mallikarjuna Reddy Kesama
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea. Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea. Center for Integrated Nanostructure Physics (CINP), Institute for Basic Sciences (IBS) and Department of Biophysics, Institute of Quantum Biophysics (IQB), Sungkyunkwan University, Suwon 16419, Republic of Korea
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22
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New, Amino Acid Based Zwitterionic Polymers as Promising Corrosion Inhibitors of Mild Steel in 1 M HCl. COATINGS 2019. [DOI: 10.3390/coatings9100675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The zwitterionic monomers, N,N’-diallylamino propanephosphonate and amino acid residual N,N’-diallyl-l-methionine hydrochloride were synthesized, with excellent yields. These monomers were utilized in the preparation of zwitterionic homo and co-cyclopolymers 5–7 in aqueous solution using 2,2′-azobis (2-methylpropionamidine) dihydrochloride as an initiator. The polymers were characterized by FT-IR, NMR, and TGA. The performance of these synthesized polymers on mild steel in acidic solution was investigated by gravimetric method, Tafel extrapolation, linear polarization resistance, and electrochemical impedance spectroscopy. At 313 K, the maximum inhibition efficiencies of corrosion inhibitors 5–7 at 4.50 × 10−4 mol L−1 were found to be 85.2%, 83.3%, and 99.5%, respectively. The inhibition efficiencies obtained from gravimetric weight loss, potentiodynamic polarization, and electrochemical impedance spectroscopy measurements were in good agreement. Different adsorption isotherms were also explored to find the best fit, and found to obey Langmuir adsorption isotherm. The thermodynamic parameters, such as activation energy (Ea), standard enthalpy of activation (ΔH*), standard entropy of activation (ΔS*), adsorption–desorption equilibrium constant (Kads), and standard free energy of adsorption (ΔGoads), were determined. Electrochemical data indicated that the zwitterionic copolymer 7 acts as a mixed type inhibitor under the influence of anodic control. The surface morphology of mild steel corrosion was evaluated without and with corrosion inhibitors by AFM, SEM-EDX, and XPS, which confirmed the adsorption of inhibitor molecules on the metal surface.
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McKee AD, Schaible MJ, Rosenberg RA, Kundu S, Orlando TM. Low energy secondary electron induced damage of condensed nucleotides. J Chem Phys 2019; 150:204709. [PMID: 31153208 DOI: 10.1063/1.5090491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10-18 cm2) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.
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Affiliation(s)
- A D McKee
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R A Rosenberg
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - S Kundu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Momtazi L, Sønsteby HH, Nilsen O. Biocompatible organic-inorganic hybrid materials based on nucleobases and titanium developed by molecular layer deposition. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2019; 10:399-411. [PMID: 30800579 PMCID: PMC6369986 DOI: 10.3762/bjnano.10.39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/03/2019] [Indexed: 05/31/2023]
Abstract
We have constructed thin films of organic-inorganic hybrid character by combining titanium tetra-isopropoxide (TTIP) and the nucleobases thymine, uracil or adenine using the molecular layer deposition (MLD) approach. Such materials have potential as bioactive coatings, and the bioactivity of these films is described in our recent work [Momtazi, L.; Dartt, D. A.; Nilsen, O.; Eidet, J. R. J. Biomed. Mater. Res., Part A 2018, 106, 3090-3098. doi:10.1002/jbm.a.36499]. The growth was followed by in situ quartz crystal microbalance (QCM) measurements and all systems exhibited atomic layer deposition (ALD) type of growth. The adenine system has an ALD temperature window between 250 and 300 °C, while an overall reduction in growth rate with increasing temperature was observed for the uracil and thymine systems. The bonding modes of the films have been further characterized by Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy and X-ray diffraction, confirming the hybrid nature of the as-deposited films with an amorphous structure where partial inclusion of the TTIP molecule occurs during growth. The films are highly hydrophilic, while the nucleobases do leach in water providing an amorphous structure mainly of TiO2 with reduced density and index of refraction.
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Affiliation(s)
- Leva Momtazi
- Centre for Materials Science and Nanotechnology (SMN), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Henrik H Sønsteby
- Centre for Materials Science and Nanotechnology (SMN), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Ola Nilsen
- Centre for Materials Science and Nanotechnology (SMN), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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Abstract
Extracellular deoxyribonucleic acid (eDNA) exists in biological environments such as those around medical implants since prokaryotic or eukaryotic cells can undergo processes such as autolysis, necrosis, and apoptosis. For bacteria, eDNA has been shown to be involved in biofilm formation and gene transfer and acts as a nutrient source. In terms of biofilm formation, eDNA in solution has been shown to be very important in increasing attachment; however, very little is known about the role played by surface immobilized eDNA in initiating bacterial attachment and whether the nature of a DNA layer (physically adsorbed or covalently attached, and molecular weight) influences biofilm formation. In this study, the authors shed light on the role that surface attached DNA plays in the early biofilm formation by using Si wafers (Si) and allylamine plasma polymer (AAMpp) coated Si wafers to adsorb and covalently immobilize salmon sperm DNA of three different molecular weights. Pseudomonas aeruginosa was chosen to study the bacterial interactions with these DNA functionalized surfaces. Characterization of surface chemistry and imaging of attached bacteria were performed via x-ray photoelectron spectroscopy (XPS), scanning electron microscopy, and epi-fluorescence microscopy. XPS results confirmed the successful grafting of DNA on the AAMpp and Si surfaces, and surprisingly the results showed that the surface attached DNA actually reduced initial bacterial attachment, which was contrary to the initial hypothesis. This adds speculation about the specific role played by DNA in the dynamics of how it influences biofilm formation, with the possibility that it could actually be used to make bacterial resistant surfaces.
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Kesama MR, Yun BK, Dugasani SR, Jung JH, Park SH. Enhancing the electrical, optical, and magnetic characteristics of DNA thin films through Mn2+ fortification. Colloids Surf B Biointerfaces 2018; 167:197-205. [DOI: 10.1016/j.colsurfb.2018.04.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 01/24/2023]
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Herrera S, Tasca F, Williams FJ, Calvo EJ, Carro P, Salvarezza RC. Surface Structure of 4-Mercaptopyridine on Au(111): A New Dense Phase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9565-9572. [PMID: 28849939 DOI: 10.1021/acs.langmuir.7b01627] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
4-Mercaptopyridine (4MPy) self-assembled on Au(111) has been studied by in situ electrochemical scanning tunneling microscopy (EC-STM) in HClO4, cyclic voltammetry, X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). Samples prepared by varying the immersion time at constant concentration named short time (30 s) and long time (3 min) adsorption have been studied. Cyclic voltammetry and XPS showed that the chemistry of the adsorbed molecules does not depend on the adsorption time resulting in a well established chemisorbed thiol self-assembled monolayer on Au(111). EC-STM study of the short time adsorption sample revealed a new self-assembled structure after a cathodic desorption/readsorption sweep, which remains stable only if the potential is kept negative to the Au(111) zero charge potential (EPZC). DFT calculations have shown a correlation between the observed structure and a dense weakly adsorbed phase with a surface coverage of θ = 0.4 and a (5 × √3) lattice configuration. At potentials positive to the EPZC, the weakly adsorbed state becomes unstable, and a different structure is formed due to the chemisorption driven by the electrostatic interaction. Long time adsorption experiments, on the other hand, have shown the typical (5 × √3) structure with θ = 0.2 surface coverage (chemisorbed phase) and are stable over the whole potential range. The difference observed in long time and short time immersion can be explained by the optimization of molecular interactions during the self-assembly process.
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Affiliation(s)
- Santiago Herrera
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón 2, Buenos Aires C1428EHA, Argentina
| | - Federico Tasca
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón 2, Buenos Aires C1428EHA, Argentina
| | - Federico J Williams
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón 2, Buenos Aires C1428EHA, Argentina
| | - Ernesto J Calvo
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Facultad Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria , Pabellón 2, Buenos Aires C1428EHA, Argentina
| | - Pilar Carro
- Área de Química Física, Departamento de Química, Facultad de Ciencias, Universidad de La Laguna, Instituto de Materiales y Nanotecnología , Avenida Francisco Sánchez, s/n 38200-La Laguna, Tenerife, Spain
| | - Roberto C Salvarezza
- INIFTA Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET- Sucursal 4 Casilla de Correo 16, 1900) La Plata, Argentina
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Phal S, Lindholm-Sethson B, Geladi P, Shchukarev A, Tesfalidet S. Determination of methotrexate in spiked human blood serum using multi-frequency electrochemical immittance spectroscopy and multivariate data analysis. Anal Chim Acta 2017; 987:15-24. [PMID: 28916036 DOI: 10.1016/j.aca.2017.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/07/2017] [Accepted: 08/15/2017] [Indexed: 02/01/2023]
Abstract
This article describes an attempt to develop a sensor based on multi-frequency immittance spectroscopy for the determination of methotrexate (MTX) in blood serum using gold electrodes modified with antibodies. The attachment of antibodies was monitored with electrochemical immittance spectroscopy (EIS) and X-ray photoelectron spectroscopy (XPS). The EIS measurements of MTX resulted in a data matrix of size 39 × 55. The data were analysed using multivariate data analysis and showed a concentration dependence and time dependence that could be separated. This allowed the calculation of a multivariate calibration model. The model showed good linear behavior on a logarithmic scale offering a detection limit of 5 × 10-12 mol L-1.
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Affiliation(s)
| | | | - Paul Geladi
- Corpus Data & Image Analysis AB, Rålambsvägen 66 B, Suit 1408, SE 112 56 Stockholm, Sweden
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Camacho AS, Martín-García I, Contreras-Celedón C, Chacón-García L, Alonso F. DNA-supported palladium nanoparticles as a reusable catalyst for the copper- and ligand-free Sonogashira reaction. Catal Sci Technol 2017. [DOI: 10.1039/c7cy00001d] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Palladium nanoparticles on DNA have been shown to be an effective and reusable heterogeneous catalyst for the copper- and ligand-free Sonogashira coupling reaction of aryl iodides under mild conditions in air.
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Affiliation(s)
- Ana Silvia Camacho
- Instituto de Síntesis Orgánica (ISO) and Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Alicante
- 03080 Alicante
- Spain
| | - Iris Martín-García
- Instituto de Síntesis Orgánica (ISO) and Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Alicante
- 03080 Alicante
- Spain
| | - Claudia Contreras-Celedón
- Laboratorio de Diseño Molecular
- Instituto de Investigaciones Químico-Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- Morelia
- México
| | - Luis Chacón-García
- Laboratorio de Diseño Molecular
- Instituto de Investigaciones Químico-Biológicas
- Universidad Michoacana de San Nicolás de Hidalgo
- Morelia
- México
| | - Francisco Alonso
- Instituto de Síntesis Orgánica (ISO) and Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad de Alicante
- 03080 Alicante
- Spain
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31
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Lobo Maza F, Grumelli D, Carro P, Vericat C, Kern K, Salvarezza RC. The role of the crystalline face in the ordering of 6-mercaptopurine self-assembled monolayers on gold. NANOSCALE 2016; 8:17231-17240. [PMID: 27714158 DOI: 10.1039/c6nr06148f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Well-ordered molecular films play an important role in nanotechnology, from device fabrication to surface patterning. Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on the Au(100)-(1 × 1) and Au(111)-(1 × 1) have been used to understand the interplay of molecule-substrate interactions for heterocyclic thiols capable of binding to the surface by two anchors, which spontaneously form a highly disordered film on Au(111). Our results reveal that for the same surface coverage the simple change of the substrate from Au(111)-(1 × 1) to Au(100)-(1 × 1) eliminates molecular disorder and yields well-ordered SAMs. We discuss these findings in terms of differences in the surface mobility of 6MP species on these surfaces, the energetics of the adsorption sites, and the number of degrees of freedom of these substrates for a molecule with reduced surface mobility resulting from its two surface anchors. These results reveal the presence of subtle molecule-substrate interactions involving the heteroatom that drastically alter SAM properties and therefore strongly impact on our ability to control physical properties and to build devices at the nanoscale.
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Affiliation(s)
- Flavia Lobo Maza
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET- Sucursal 4 Casilla de Correo 16, (1900) La Plata, Argentina.
| | - Doris Grumelli
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET- Sucursal 4 Casilla de Correo 16, (1900) La Plata, Argentina.
| | - Pilar Carro
- Área de Química Física, Departamento de Química, Facultad de Ciencias, Universidad de La Laguna, Instituto de Materiales y Nanotecnología, Avda. Francisco Sánchez, s/n 38071-La Laguna, Tenerife, Spain
| | - Carolina Vericat
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET- Sucursal 4 Casilla de Correo 16, (1900) La Plata, Argentina.
| | - Klaus Kern
- Max Planck Institute FKF, Stuttgart, Germany and EPFL, Lausanne, Switzerland
| | - Roberto C Salvarezza
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET- Sucursal 4 Casilla de Correo 16, (1900) La Plata, Argentina.
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32
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Schlathölter T, Reitsma G, Egorov D, Gonzalez-Magaña O, Bari S, Boschman L, Bodewits E, Schnorr K, Schmid G, Schröter CD, Moshammer R, Hoekstra R. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Schlathölter
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Geert Reitsma
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Max-Born-Institute; Max Born Strasse 2A 12489 Berlin Germany
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Olmo Gonzalez-Magaña
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sadia Bari
- European XFEL GmbH; Holzkoppel 4 22869 Schenefeld Germany
- DESY; Notkestraße 85 22607 Hamburg Germany
| | - Leon Boschman
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Kapteyn Institute; Landleven 12 9747 AD Groningen The Netherlands
| | - Erwin Bodewits
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kirsten Schnorr
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Georg Schmid
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | | | - Robert Moshammer
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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33
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Schlathölter T, Reitsma G, Egorov D, Gonzalez-Magaña O, Bari S, Boschman L, Bodewits E, Schnorr K, Schmid G, Schröter CD, Moshammer R, Hoekstra R. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses. Angew Chem Int Ed Engl 2016; 55:10741-5. [DOI: 10.1002/anie.201605335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Schlathölter
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Geert Reitsma
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Max-Born-Institute; Max Born Strasse 2A 12489 Berlin Germany
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Olmo Gonzalez-Magaña
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sadia Bari
- European XFEL GmbH; Holzkoppel 4 22869 Schenefeld Germany
- DESY; Notkestraße 85 22607 Hamburg Germany
| | - Leon Boschman
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Kapteyn Institute; Landleven 12 9747 AD Groningen The Netherlands
| | - Erwin Bodewits
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kirsten Schnorr
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Georg Schmid
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | | | - Robert Moshammer
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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Myers BD, Lin QY, Wu H, Luijten E, Mirkin CA, Dravid VP. Size-Selective Nanoparticle Assembly on Substrates by DNA Density Patterning. ACS NANO 2016; 10:5679-5686. [PMID: 27192324 DOI: 10.1021/acsnano.6b02246] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The vision of nanoscale self-assembly research is the programmable synthesis of macroscale structures with controlled long and short-range order that exhibit a desired set of properties and functionality. However, strategies to reliably isolate and manipulate the nanoscale building blocks based on their size, shape, or chemistry are still in their infancy. Among the promising candidates, DNA-mediated self-assembly has enabled the programmable assembly of nanoparticles into complex architectures. In particular, two-dimensional assembly on substrates has potential for the development of integrated functional devices and analytical systems. Here, we combine the high-resolution patterning capabilities afforded by electron-beam lithography with the DNA-mediated assembly process to enable direct-write grayscale DNA density patterning. This method allows modulation of the functionally active DNA surface density to control the thermodynamics of interactions between nanoparticles and the substrate. We demonstrate that size-selective directed assembly of nanoparticle films from solutions containing a bimodal distribution of particles can be realized by exploiting the cooperativity of DNA binding in this system. To support this result, we study the temperature-dependence of nanoparticle assembly, analyze the DNA damage by X-ray photoelectron spectroscopy and fluorescence microscopy, and employ molecular dynamics simulations to explore the size-selection behavior.
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Affiliation(s)
- Benjamin D Myers
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University , Evanston, Illinois 60208, United States
| | - Qing-Yuan Lin
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Huanxin Wu
- Department of Physics and Astronomy, Northwestern University , Evanston, Illinois 60208, United States
| | - Erik Luijten
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
- Department of Physics and Astronomy, Northwestern University , Evanston, Illinois 60208, United States
- Department of Engineering Sciences and Applied Mathematics, Northwestern University , Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University , Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Vinayak P Dravid
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
- NUANCE Center, Northwestern University , Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University , Evanston, Illinois 60208, United States
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35
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Narita A, Fujii K, Baba Y, Shimoyama I. Use of a DNA film on a self-assembled monolayer for investigating the physical process of DNA damage induced by core electron ionization. Int J Radiat Biol 2016; 92:733-738. [PMID: 27192925 DOI: 10.1080/09553002.2016.1179812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE A novel two-layer sample composed of a deoxyribonucleic acid (DNA) film and self-assembled monolayer (SAM) was prepared on an inorganic surface to mimic the processes in which DNA is damaged by soft X-ray irradiation. MATERIALS AND METHODS A mercaptopropyltrimethoxysilane (MPTS) SAM was formed on a sapphire surface, then oligonucleotide (OGN) molecules were adsorbed on the MPTS-SAM. The thicknesses and chemical states of the layers were determined by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) around the phosphorus (P) and sulfur (S) K-edges. To induce the damage to the OGN molecules, the sample was irradiated with synchrotron soft X-rays. The chemical state of the OGN molecules before and after irradiation was examined by NEXAFS around the nitrogen (N) K-edge region. RESULTS The thickness of the MPTS-OGN layer was approximately 7.7 nm. The S atom of the OGN molecules was located at the bottom of the OGN layer. The peak shape of the N K-edge NEXAFS spectra of the MPTS-OGN layers clearly changed following irradiation. CONCLUSIONS The MPTS-OGN layer formed on the sapphire surface. The chemical states and the structure of the interface were elucidated using synchrotron soft X-rays. The OGN molecules adsorbed on the MPTS films decomposed upon exposure to soft X-ray irradiation.
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Affiliation(s)
- Ayumi Narita
- a Japan Atomic Energy Agency , Shirakata, Tokai , Naka , Ibaraki , Japan
| | - Kentaro Fujii
- a Japan Atomic Energy Agency , Shirakata, Tokai , Naka , Ibaraki , Japan
| | - Yuji Baba
- a Japan Atomic Energy Agency , Shirakata, Tokai , Naka , Ibaraki , Japan
| | - Iwao Shimoyama
- a Japan Atomic Energy Agency , Shirakata, Tokai , Naka , Ibaraki , Japan
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36
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Mankos M, Persson HHJ, N’Diaye AT, Shadman K, Schmid AK, Davis RW. Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy. PLoS One 2016; 11:e0154707. [PMID: 27149617 PMCID: PMC4858156 DOI: 10.1371/journal.pone.0154707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 11/19/2022] Open
Abstract
DNA sequencing by imaging in an electron microscope is an approach that holds promise to deliver long reads with low error rates and without the need for amplification. Earlier work using transmission electron microscopes, which use high electron energies on the order of 100 keV, has shown that low contrast and radiation damage necessitates the use of heavy atom labeling of individual nucleotides, which increases the read error rates. Other prior work using scattering electrons with much lower energy has shown to suppress beam damage on DNA. Here we explore possibilities to increase contrast by employing two methods, X-ray photoelectron and Auger electron spectroscopy. Using bulk DNA samples with monomers of each base, both methods are shown to provide contrast mechanisms that can distinguish individual nucleotides without labels. Both spectroscopic techniques can be readily implemented in a low energy electron microscope, which may enable label-free DNA sequencing by direct imaging.
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Affiliation(s)
- Marian Mankos
- Electron Optica Inc., 1000 Elwell Court #110, Palo Alto, California, 94303, United States of America
| | - Henrik H. J. Persson
- Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA, 94304, United States of America
| | - Alpha T. N’Diaye
- NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
| | - Khashayar Shadman
- Electron Optica Inc., 1000 Elwell Court #110, Palo Alto, California, 94303, United States of America
| | - Andreas K. Schmid
- NCEM, Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
| | - Ronald W. Davis
- Stanford Genome Technology Center, Stanford University School of Medicine, 855 California Avenue, Palo Alto, CA, 94304, United States of America
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37
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Hassanien R, Almaky MM, Houlton A, Horrocks BR. Preparation and electrical properties of a copper-conductive polymer hybrid nanostructure. RSC Adv 2016. [DOI: 10.1039/c6ra20325f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Conductive copper–polymer hybrid nanowires prepared by templating on DNA.
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Affiliation(s)
- Reda Hassanien
- Department of Chemistry
- Faculty of Science
- Assiut University
- Egypt
| | - Mahdi M. Almaky
- Department of Chemistry
- Faculty of Science
- Sebha University
- Sebha
- Libya
| | - Andrew Houlton
- Chemical Nanoscience Laboratory
- School of Chemistry
- Newcastle University
- UK
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38
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Iliafar S, Mittal J, Vezenov D, Jagota A. Interaction of single-stranded DNA with curved carbon nanotube is much stronger than with flat graphite. J Am Chem Soc 2014; 136:12947-57. [PMID: 25162693 DOI: 10.1021/ja5055498] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We used single molecule force spectroscopy to measure the force required to remove single-stranded DNA (ssDNA) homopolymers from single-walled carbon nanotubes (SWCNTs) deposited on methyl-terminated self-assembled monolayers (SAMs). The peeling forces obtained from these experiments are bimodal in distribution. The cluster of low forces corresponds to peeling from the SAM surface, while the cluster of high forces corresponds to peeling from the SWCNTs. Using a simple equilibrium model of the single molecule peeling process, we calculated the free energy of binding per nucleotide. We found that the free energy of ssDNA binding to hydrophobic SAMs decreases as poly(A) > poly(G) ≈ poly(T) > poly(C) (16.9 ± 0.1; 9.7 ± 0.1; 9.5 ± 0.1; 8.7 ± 0.1 kBT, per nucleotide). The free energy of ssDNA binding to SWCNT adsorbed on this SAM also decreases in the same order poly(A) > poly(G) > poly(T) > poly(C), but its magnitude is significantly greater than that of DNA-SAM binding energy (38.1 ± 0.2; 33.9 ± 0.1; 23.3 ± 0.1; 17.1 ± 0.1 kBT, per nucleotide). An unexpected finding is that binding strength of ssDNA to the curved SWCNTs is much greater than to flat graphite, which also has a different ranking (poly(T) > poly(A) > poly(G) ≥ poly(C); 11.3 ± 0.8, 9.9 ± 0.5, 8.3 ± 0.2, and 7.5 ± 0.8 kBT, respectively, per nucleotide). Replica-exchange molecular dynamics simulations show that ssDNA binds preferentially to the curved SWCNT surface, leading us to conclude that the differences in ssDNA binding between graphite and nanotubes arise from the spontaneous curvature of ssDNA.
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Affiliation(s)
- Sara Iliafar
- Department of Chemical and Biomolecular Engineering and ‡Bioengineering Program, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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39
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Rosenberg RA, Symonds JM, Vijayalakshmi K, Mishra D, Orlando TM, Naaman R. The relationship between interfacial bonding and radiation damage in adsorbed DNA. Phys Chem Chem Phys 2014; 16:15319-25. [DOI: 10.1039/c4cp01649a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Illustration showing that secondary electrons have a higher damage probability for thiolated DNA as opposed to unthiolated DNA, due to the former's higher density of LUMO states, which leads to more efficient capture of the low energy electrons.
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Affiliation(s)
- R. A. Rosenberg
- Advanced Photon Source
- Argonne National Laboratory
- Argonne, USA
| | - J. M. Symonds
- School of Chemistry and Biochemistry and School of Physics
- Georgia Institute of Technology
- Atlanta, USA
| | | | - Debabrata Mishra
- Department of Chemical Physics
- Weizmann Institute
- Rehovot 76100, Israel
| | - T. M. Orlando
- School of Chemistry and Biochemistry and School of Physics
- Georgia Institute of Technology
- Atlanta, USA
| | - R. Naaman
- Department of Chemical Physics
- Weizmann Institute
- Rehovot 76100, Israel
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40
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Khan MN, Tjong V, Chilkoti A, Zharnikov M. Spectroscopic study of a DNA brush synthesized in situ by surface initiated enzymatic polymerization. J Phys Chem B 2013; 117:9929-38. [PMID: 23899324 DOI: 10.1021/jp404774x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We used a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the chemical integrity, purity, and possible internal alignment of single-strand (ss) adenine deoxynucleotide (poly(A)) DNA brushes. The brushes were synthesized by surface-initiated enzymatic polymerization (SIEP) on a 25-mer of adenine self-assembled monolayer (SAM) on gold (A25-SH), wherein the terminal 3'-OH of the A25-SH serve as the initiation sites for SIEP of poly(A). XPS and NEXAFS spectra of poly(A) brushes were found to be almost identical to those of A25-SH initiator, with no unambiguous traces of contamination. Apart from the well-defined chemical integrity and contamination-free character, the brushes were found to have a high degree of orientational order, with an upright orientation of individual strands, despite their large thickness up to ~55 nm, that corresponds to a chain length of at least several hundred nucleotides for individual ssDNA molecules. The orientational order exhibited by these poly(A) DNA brushes, mediated presumably by base stacking, was found to be independent of the brush thickness as long as the packing density was high enough. The well-defined character and orientational ordering of the ssDNA brushes make them a potentially promising system for different applications.
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Affiliation(s)
- M Nuruzzaman Khan
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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41
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Xiao F, Luo X, Fu X, Zheng Y. Cleavage Enhancement of Specific Chemical Bonds in DNA by Cisplatin Radiosensitization. J Phys Chem B 2013; 117:4893-900. [DOI: 10.1021/jp400852p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Fangxing Xiao
- Fujian Provincial Key Laboratory of Photocatalysis,
State Key Laboratory Breeding Base, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xinglan Luo
- Fujian Provincial Key Laboratory of Photocatalysis,
State Key Laboratory Breeding Base, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Xianzhi Fu
- Fujian Provincial Key Laboratory of Photocatalysis,
State Key Laboratory Breeding Base, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
| | - Yi Zheng
- Fujian Provincial Key Laboratory of Photocatalysis,
State Key Laboratory Breeding Base, College of Chemistry
and Chemical Engineering, Fuzhou University, Fuzhou 350002, People’s Republic of China
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42
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Molecular Scale Simulation of Ionizing Particles Tracks for Radiobiology and Hadrontherapy Studies. ADVANCES IN QUANTUM CHEMISTRY 2013. [DOI: 10.1016/b978-0-12-396455-7.00004-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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Oka T, Yokoya A, Fujii K, Fukuda Y, Ukai M. Unpaired electron species in thin films of calf-thymus DNA molecules induced by nitrogen and oxygen K-shell photoabsorption. PHYSICAL REVIEW LETTERS 2012; 109:213001. [PMID: 23215591 DOI: 10.1103/physrevlett.109.213001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 09/05/2012] [Indexed: 06/01/2023]
Abstract
The mechanism of DNA modification induced by K-shell photoabsorption of nitrogen and oxygen atoms was investigated by electron paramagnetic resonance and x-ray absorption near edge structure measurements of calf thymus DNA. A g factor of 2.000 for the unpaired electron species, which only arises during irradiation, was measured. The EPR intensities for DNA zwere twofold times larger than those estimated based on the photoabsorption cross section. This suggests that the DNA film itself forms unpaired electron species through the excitation of enhanced electron recapturing, known as the postcollision interaction process.
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Affiliation(s)
- T Oka
- Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan.
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44
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Sensitive Marker of the Cisplatin-DNA Interaction: X-Ray Photoelectron Spectroscopy of CL. Bioinorg Chem Appl 2012; 2012:649640. [PMID: 23133406 PMCID: PMC3485869 DOI: 10.1155/2012/649640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 01/19/2023] Open
Abstract
The development of cisplatin and Pt-based analogues anticancer agents requires knowledge concerning the molecular mechanisms of interaction between such drugs with DNA. However, the binding dynamics and kinetics of cisplatin reactions with DNA determined by traditional approaches are far from satisfactory. In this study, a typical 20-base oligonucleotide (CGTGACAGTTATTGCAGGCG), as a simplified model representing DNA, was mixed with cisplatin in different molar ratios and incubation time. High-resolution XPS spectra of the core elements C, N, O, P, and Cl were recorded to explore the interaction between cisplatin and DNA. From deconvoluted Cl spectra we could readily differentiate the covalently bound chlorine from ionic chloride species in the cisplatin-oligo complexes, which displayed distinct features at various reaction times and ratios. Monitoring the magnitude and energy of the photoelectron Cl 2p signal by XPS could act as a sensitive marker to probe the interaction dynamics of chemical bonds in the reaction of cisplatin with DNA. At 37°C, the optimum incubation time to obtain a stable cisplatin-oligo complex lies around 20 hrs. This novel analysis technique could have valuable implications to understand the fundamental mechanism of cisplatin cytotoxicity and determine the efficiency of the bonds in treated cancer cells.
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45
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González-Magaña O, Reitsma G, Tiemens M, Boschman L, Hoekstra R, Schlathölter T. Near-Edge X-ray Absorption Mass Spectrometry of a Gas-Phase Peptide. J Phys Chem A 2012; 116:10745-51. [DOI: 10.1021/jp307527b] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- O. González-Magaña
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
| | - G. Reitsma
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
| | - M. Tiemens
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
| | - L. Boschman
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
- Kapteyn
Astronomical Institute, University of Groningen, Landleven 12, 9747AD Groningen,
The Netherlands
| | - R. Hoekstra
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
| | - T. Schlathölter
- KVI Atomic and Molecular Physics, University of Groningen, Zernikelaan 25, 9747AA Groningen,
The Netherlands
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Cho E, Brown A, Kuech TF. Chemical characterization of DNA-immobilized InAs surfaces using X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:11890-11898. [PMID: 22809291 DOI: 10.1021/la302313v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-stranded DNA immobilized on an III-V semiconductor is a potential high-sensitivity biosensor. The chemical and electronic changes occurring upon the binding of DNA to the InAs surface are essential to understanding the DNA-immobilization mechanism. In this work, the chemical properties of DNA-immobilized InAs surfaces were determined through high-resolution X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure (NEXAFS). Prior to DNA functionalization, HF- and NH(4)OH- based aqueous etches were used to remove the native oxide from the InAs surface. The initial chemical state of the surface resulting from these etches were characterized prior to functionalization. F-tagged thiolated single-stranded DNA (ssDNA) was used as the probe species under two different functionalization methods. The presence of DNA immobilized on the surface was confirmed from the F 1s, N 1s, and P 2p peaks in the XPS spectra. The presence of salt had a profound effect on the density of immobilized DNA on the InAs surface. To study the interfacial chemistry, the surface was treated with thiolated ssDNA with and without the mercaptohexanol molecule. An analysis of the As 3d and In 3d spectra indicates that both In-S and As-S are present on the surface after DNA functionalization. The amount of In-S and As-S was determined by the functionalization method as well as the presence of mercaptohexanol during functionalization. The orientation of the adsorbed ssDNA is determined by polarization-dependent NEXAFS utilizing the N K-edge. The immobilized ssDNA molecule has a preferred tilt angle with respect to the substrate normal, but with a random azimuthal distribution.
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Affiliation(s)
- EunKyung Cho
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, USA
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López-Donaire ML, Sussman EM, Fernández-Gutiérrez M, Méndez-Vilas A, Ratner BD, Vázquez-Lasa B, San Román J. Amphiphilic Self-Assembled “Polymeric Drugs”: Morphology, Properties, and Biological Behavior of Nanoparticles. Biomacromolecules 2012; 13:624-35. [DOI: 10.1021/bm300043f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- María Luisa López-Donaire
- Institute of Polymer Science and Technology, CSIC, C/Juan de la Cierva 3,
28006 Madrid, Spain
- CIBER-BBN, Ebro River Campus, Building R&D, Block 5, Floor 1, Poeta Mariano Esquillor s/n, 50017 Zaragoza, Spain
| | - Eric M. Sussman
- Department of Bioengineering, University of Washington, Seattle, Washington
98195-5061, United States
| | - Mar Fernández-Gutiérrez
- Institute of Polymer Science and Technology, CSIC, C/Juan de la Cierva 3,
28006 Madrid, Spain
- CIBER-BBN, Ebro River Campus, Building R&D, Block 5, Floor 1, Poeta Mariano Esquillor s/n, 50017 Zaragoza, Spain
| | - Antonio Méndez-Vilas
- CIBER-BBN, Ebro River Campus, Building R&D, Block 5, Floor 1, Poeta Mariano Esquillor s/n, 50017 Zaragoza, Spain
| | - Buddy D. Ratner
- Department of Bioengineering, University of Washington, Seattle, Washington
98195-5061, United States
| | - Blanca Vázquez-Lasa
- Institute of Polymer Science and Technology, CSIC, C/Juan de la Cierva 3,
28006 Madrid, Spain
- CIBER-BBN, Ebro River Campus, Building R&D, Block 5, Floor 1, Poeta Mariano Esquillor s/n, 50017 Zaragoza, Spain
| | - Julio San Román
- Institute of Polymer Science and Technology, CSIC, C/Juan de la Cierva 3,
28006 Madrid, Spain
- CIBER-BBN, Ebro River Campus, Building R&D, Block 5, Floor 1, Poeta Mariano Esquillor s/n, 50017 Zaragoza, Spain
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Pokapanich W, Ottosson N, Svensson S, Ohrwall G, Winter B, Björneholm O. Bond Breaking, Electron Pushing, and Proton Pulling: Active and Passive Roles in the Interaction between Aqueous Ions and Water as Manifested in the O 1s Auger Decay. J Phys Chem B 2011; 116:3-8. [PMID: 22107172 DOI: 10.1021/jp2041247] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- W Pokapanich
- Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden.
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