1
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Chiang YJ, Huang WC, Han CH, Liu CL, Tsai CC, Hu WP. Near-edge x-ray absorption fine structure spectra and specific dissociation of small peptoid molecules. J Chem Phys 2024; 160:074305. [PMID: 38380751 DOI: 10.1063/5.0188660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
In this study, the total ion yield near-edge x-ray absorption fine structure spectra of four similar peptoid molecules, which differ in the numbers and positions of methyl groups, were investigated experimentally and theoretically. At each excitation energy, the intensity and branching ratio of each ionic product were measured. At a few resonant excitation energies, a specific dissociation of the C-CO bond at the nitrogen and oxygen K-edges and of the N-CO bond at the carbon K-edge was dominant, which correlated well with the predicted destination antibonding orbitals of the core electron excitation. These specific dissociation mechanisms of small peptoid molecules could provide insights into similar phenomena that occur in peptide molecules.
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Affiliation(s)
- Yu-Ju Chiang
- Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Wan-Chou Huang
- Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chou-Hsun Han
- Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Chen-Lin Liu
- Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Cheng-Cheng Tsai
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Wei-Ping Hu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 62102, Taiwan
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2
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Liu X, Li L, Li F, Zhao W, Luo L, Bi X, Li X, You T. An ultra-high-sensitivity electrochemiluminescence aptasensor for Pb 2+ detection based on the synergistic signal-amplification strategy of quencher abscission and G-quadruplex generation. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127480. [PMID: 34666293 DOI: 10.1016/j.jhazmat.2021.127480] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 06/13/2023]
Abstract
Signal amplification provides an effective way to improve detection performance. Herein, an ultrasensitive electrochemiluminescence (ECL) aptasensor for Pb2+ detection was developed based on a dual signal-amplification strategy of the abscission of a quencher and the generation of a G-quadruplex by one-step and simultaneous way. Nitrogen-doped carbon quantum dots linked with complementary DNA (cDNA-NCQDs) at the sensing interface was applied as the quencher of a tris(4,4'-dicarboxylic acid-2,2'-bipyridyl)ruthenium(II) (Ru(dcbpy)32+)/tripropylamine system to minimize the ECL signal due to the intermolecular hydrogen bond-induced energy-transfer process. Upon the addition of Pb2+, its specific binding with the aptamer triggered the abscission of cDNA-NCQDs, accompanied by the formation of G-quadruplex on the surface of the electrode, both of which amplified the intensity of the light emission. The ECL amplification efficiency induced by the above two mechanisms (78.6%) was valuably greater than that of their sum value (69.3%). This synergistic effect resulted in high detection sensitivity of the ECL aptasensor, which allowed to thereby obtain Pb2+ measurements in the range of 1 fM - 10 nM with an ultra-low detection limit of 0.19 fM. The Pb2+-mediated synergistic signal-amplification ECL strategy can provide a new approach for integrating various amplification strategies.
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Affiliation(s)
- Xiaohong Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Libo Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Fang Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wanlin Zhao
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lijun Luo
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaoya Bi
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xia Li
- Department of Chemistry, Liaocheng University, Liaocheng, Shandong 252059, China
| | - Tianyan You
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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3
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Yuan Z, Zhou Q, Cai L, Pan L, Sun W, Qumu S, Yu S, Feng J, Zhao H, Zheng Y, Shi M, Li S, Chen Y, Zhang X, Zhang MQ. SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment. Nat Methods 2021; 18:1223-1232. [PMID: 34608315 DOI: 10.1038/s41592-021-01276-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 08/18/2021] [Indexed: 02/08/2023]
Abstract
Spatial metabolomics can reveal intercellular heterogeneity and tissue organization. Here we report on the spatial single nuclear metabolomics (SEAM) method, a flexible platform combining high-spatial-resolution imaging mass spectrometry and a set of computational algorithms that can display multiscale and multicolor tissue tomography together with identification and clustering of single nuclei by their in situ metabolic fingerprints. We first applied SEAM to a range of wild-type mouse tissues, then delineated a consistent pattern of metabolic zonation in mouse liver. We further studied the spatial metabolic profile in the human fibrotic liver. We discovered subpopulations of hepatocytes with special metabolic features associated with their proximity to the fibrotic niche, and validated this finding by spatial transcriptomics with Geo-seq. These demonstrations highlighted SEAM's ability to explore the spatial metabolic profile and tissue histology at the single-cell level, leading to a deeper understanding of tissue metabolic organization.
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Affiliation(s)
- Zhiyuan Yuan
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Qiming Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, School of Life Sciences, Tsinghua University, Beijing, China
| | - Lesi Cai
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Lin Pan
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Weiliang Sun
- Institute of Clinical Medicine, China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Shiwei Qumu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friend Hospital, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Si Yu
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yongchang Zheng
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minglei Shi
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Shao Li
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,The State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing, China.
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Institute of TCM-X, Department of Automation, Tsinghua University, Beijing, China. .,MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, BNRist, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China. .,Department of Biological Sciences, Center for Systems Biology, The University of Texas, Richardson, TX, USA.
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In-Situ Monitoring of Real-Time Loop-Mediated Isothermal Amplification with QCM: Detecting Listeria monocytogenes. BIOSENSORS-BASEL 2021; 11:bios11090308. [PMID: 34562899 PMCID: PMC8470657 DOI: 10.3390/bios11090308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022]
Abstract
Functionalized DNA sequences are promising sensing elements to combine with transducers for bio-sensing specific target microbes. As an application example, this paper demonstrates in situ detection of loop-mediated isothermal amplification products by hybridizing them with thiolated-ssDNA covalently anchored on the electrodes of a quartz crystal microbalance (QCM). Such hybridization leads to a frequency signal, which is suitable for monitoring real-time LAMP amplification based on mass-sensing: it detects interactions between the complementary nucleobases of LAMP products in solution and the thiolated-ssDNA probe sequence on the gold surface. Target DNA LAMP products cause irreversible frequency shifts on the QCM surfaces during hybridization in the kHz range, which result from both changes in mass and charge on the electrode surface. In order to confirm the LAMP assay working in the QCM sensing system at elevated temperature, the sky blue of positive LAMP products solution was achieved by using the Hydroxy Naphthol Blue (HNB) and agarose gel electrophoresis. Since on-QCM sensing of DNA hybridization leads to irreversible sensor responses, this work shows characterization by X-ray photoelectron spectroscopy (XPS) core spectra of S2p, N1s, Mg1s, P2p and C1s. XPS results confirmed that indeed both DNA and by-products of LAMP attached to the surface. Listeria monocytogenes DNA served to study in-situ detection of amplified LAMP products on DNA-functionalized surfaces.
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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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6
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Castellanos A, Hernandez MG, Tomic-Canic M, Jozic I, Fernandez-Lima F. Multimodal, in Situ Imaging of Ex Vivo Human Skin Reveals Decrease of Cholesterol Sulfate in the Neoepithelium during Acute Wound Healing. Anal Chem 2019; 92:1386-1394. [PMID: 31789498 DOI: 10.1021/acs.analchem.9b04542] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Skin repair is a significant aspect of human health. While the makeup of healthy stratum corneum and epidermis is generally understood, the mobilization of molecular components during skin repair remains largely unknown. In the present work, we utilize multimodal, in situ, mass spectrometry, and immunofluorescence imaging for the characterization of newly formed epidermis, following an initial acute wound for the first 96 h of epithelization. In particular, TOF-SIMS and confirmatory MALDI FT-ICR MS (/MS) analysis permitted the mapping of several lipid classes, including phospholipids, neutral lipids, cholesterol, ceramides, and free fatty acids. Endogenous lipid species were localized in discrete epidermal skin layers, including the stratum corneum (SC), stratum granulosum (SG), stratum basale (SB), and dermis. Experiments revealed that healthy re-epithelializing skin is characterized by diminished cholesterol sulfate signal along the stratum corneum toward the migrating epithelial tongue. The spatial distribution and relative abundances of cholesterol sulfate are reported and correlated with the healing time. The multimodal imaging approach enabled in situ high-confidence chemical mapping based on accurate mass and fragmentation pattern of molecular components. The use of postanalysis immunofluorescence imaging from the same tissue confirmed the localization of endogenous lipid species and Filaggrin and Cav-1 proteins at high spatial resolution (approximately a few microns).
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Affiliation(s)
- Anthony Castellanos
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW Eighth Street, AHC4-233 , Miami , Florida 33199 , United States
| | - Mario Gomez Hernandez
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW Eighth Street, AHC4-233 , Miami , Florida 33199 , United States
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery , University of Miami Miller School of Medicine , 1600 NW 10th Avenue, RMSB 6056 , Miami , Florida 33136 , United States
| | - Ivan Jozic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery , University of Miami Miller School of Medicine , 1600 NW 10th Avenue, RMSB 6056 , Miami , Florida 33136 , United States
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry , Florida International University , 11200 SW Eighth Street, AHC4-233 , Miami , Florida 33199 , United States.,Biomolecular Sciences Institute , Florida International University , Miami , Florida 33199 , United States
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7
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Castellanos A, Ramirez CE, Michalkova V, Nouzova M, Noriega FG, Francisco FL. Three Dimensional Secondary Ion Mass Spectrometry Imaging (3D-SIMS) of Aedes aegypti ovarian follicles. JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY 2019; 34:874-883. [PMID: 31680712 PMCID: PMC6824543 DOI: 10.1039/c8ja00425k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The mobilization of nutrient reserves into the ovaries of Aedes aegypti mosquitoes after sugar-feeding plays a vital role in the female's reproductive maturation. In the present work, three-dimensional secondary ion mass spectrometry imaging (3D-SIMS) was used to generate ultrahigh spatial resolution (~1 μm) chemical maps and study the composition and spatial distribution of lipids at the single ovarian follicle level (~100 μm in size). 3D-Mass Spectrometry Imaging (3D-MSI) allowed the identification of cellular types in the follicle (oocyte, nurse and follicular cells) using endogenous markers, and revealed that most of the triacyglycerides (TGs) were compartmentalized in the oocyte region. By comparing follicles from water-fed and sugar-fed females (n=2), 3D-MSI-Time of Flight-SIMS showed that TGs were more abundant in ovarian follicles of sugar-fed females; despite relative sample reproducibility per feeding condition, more biological replicates will better support the trends observed. While the current 3D-MSI-TOF-SIMS does not permit MS/MS analysis of the lipid species, complementary LC-MS/MS analysis of the ovarian follicles aided tentative lipid assignments of the SIMS data. The combination of these MS approaches is giving us a first glimpse of the distribution of functionally relevant ovarian lipid molecules at the cellular level. These new tools can be used to investigate the roles of different lipids on follicle fitness and overall mosquito reproductive output.
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Affiliation(s)
- Anthony Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Cesar E. Ramirez
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
| | - Marcela Nouzova
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Institute of Parasitology, Biology Centre CAS, Ceske, Budejovice, Czech Republic; and
| | - Fernando G. Noriega
- Department of Biological Sciences, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
| | - Fernández-Lima Francisco
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, 33199, United States
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, 33199, United States
- Corresponding author: Francisco A. Fernández-Lima, Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St AHC4-233, Miami, FL 33199, USA;
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8
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Zhang Z, Hou Z, Qiao C, Zhu C, Zhou K, Xu X, Li T, Xu J. Electrostatic and hydrophobic controlled self-assembly of PDMS-E grafted gelatin for self-cleaning application. Colloids Surf B Biointerfaces 2018; 171:647-655. [DOI: 10.1016/j.colsurfb.2018.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/16/2018] [Accepted: 08/06/2018] [Indexed: 12/29/2022]
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9
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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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Vellampatti S, Chandrasekaran G, Mitta SB, Lakshmanan VK, Park SH. Metallo-Curcumin-Conjugated DNA Complexes Induces Preferential Prostate Cancer Cells Cytotoxicity and Pause Growth of Bacterial Cells. Sci Rep 2018; 8:14929. [PMID: 30297802 PMCID: PMC6175843 DOI: 10.1038/s41598-018-33369-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
DNA nanotechnology can be used to create intricate DNA structures due to the ability to direct the molecular assembly of nanostructures through a bottom-up approach. Here, we propose nanocarriers composed of both synthetic and natural DNA for drug delivery. The topological, optical characteristics, and interaction studies of Cu2+/Ni2+/Zn2+-curcumin-conjugated DNA complexes were studied using atomic force microscopy (AFM), UV-vis spectroscopy, Fourier transform infrared and mass spectroscopy. The maximum release of metallo-curcumin conjugates from the DNA complexes, triggered by switching the pH, was found in an acidic medium. The bacterial growth curves of E. coli and B. subtilis displayed a prolonged lag phase when tested with the metallo-curcumin-conjugated DNA complexes. We also tested the in vitro cytotoxicity of the metallo-curcumin-conjugated DNA complexes to prostate cancer cells using an MTS assay, which indicated potent growth inhibition of the cells. Finally, we studied the cellular uptake of the complexes, revealing that DNA complexes with Cu2+/Ni2+-curcumin exhibited brighter fluorescence than those with Zn2+-curcumin.
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Affiliation(s)
- Srivithya Vellampatti
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon, 16419, Korea
| | | | - Sekhar Babu Mitta
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon, 16419, Korea
| | - Vinoth-Kumar Lakshmanan
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, 61469, Korea. .,Department of Biomedical Engineering, Sri Shakthi Institute of Engineering and Technology, Coimbatore, 641062, India.
| | - Sung Ha Park
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) and Department of Physics, Sungkyunkwan University, Suwon, 16419, Korea.
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11
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Chiang YJ, Lin YS, Lin HR, Liu CL. Specific dissociation of core-excited pyrimidine nucleobases. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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12
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Enhancement of Resistance to Protein Fouling of Poly(ether imide) Membrane by Surface Grafting with PEG under Organic Solvent-free Condition. CHINESE JOURNAL OF POLYMER SCIENCE 2018. [DOI: 10.1007/s10118-018-2144-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Volkov IL, Smirnova A, Makarova AA, Reveguk ZV, Ramazanov RR, Usachov DY, Adamchuk VK, Kononov AI. DNA with Ionic, Atomic, and Clustered Silver: An XPS Study. J Phys Chem B 2017; 121:2400-2406. [DOI: 10.1021/acs.jpcb.6b11218] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan L. Volkov
- Saint-Petersburg State University, 199034 St. Petersburg, Russia
| | | | - Anna A. Makarova
- Institut
für Festkörperphysik, Technische Universität Dresden, 01062 Dresden, Germany
| | | | | | | | - Vera K. Adamchuk
- Saint-Petersburg State University, 199034 St. Petersburg, Russia
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14
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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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15
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Li J, Zhu Z, Liu F, Zhu B, Ma Y, Yan J, Lin B, Ke G, Liu R, Zhou L, Tu S, Yang C. DNA-Mediated Morphological Control of Silver Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5449-5487. [PMID: 27551864 DOI: 10.1002/smll.201601338] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/16/2016] [Indexed: 06/06/2023]
Abstract
It is demonstrated that DNA can be used to control the synthesis of silver nanoplates with different morphologies using spherical silver seeds. UV-vis spectroscopy, transmission electron microscopy, scanning electron microscopy, X-ray photoelectron spectroscopy, and Raman spectroscopy are used to characterize the synthesized nanoparticles. Silver nanoprisms are encoded by poly C and poly G, while silver flower bouquets and silver nanodiscs are synthesized using poly A and poly T, respectively. The length of DNA is found to have little effect on the morphology of silver nanoparticles. Moreover, the synthesized silver nanoplates are found to have high surface enhanced Raman scattering enhancement ability, good antibacterial activity, and good biocompatibility. These discoveries will broaden the application of DNA in nanoscience and will provide a new platform to investigate the interaction between DNA sequences and silver nanoparticles.
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Affiliation(s)
- Jiuxing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Fang Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Bingqing Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Yanli Ma
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Jinmao Yan
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Bingqian Lin
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Guoliang Ke
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Rudi Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Leiji Zhou
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Song Tu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Engineering, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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16
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Selectivity of peptide bond dissociation on excitation of a core electron: Effects of a phenyl group. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Yakovleva MA, Gulin AA, Feldman TB, Bel’skich YC, Arbukhanova PM, Astaf’ev AA, Nadtochenko VA, Borzenok SA, Ostrovsky MA. Time-of-flight secondary ion mass spectrometry to assess spatial distribution of A2E and its oxidized forms within lipofuscin granules isolated from human retinal pigment epithelium. Anal Bioanal Chem 2016; 408:7521-8. [DOI: 10.1007/s00216-016-9854-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/24/2016] [Accepted: 08/01/2016] [Indexed: 11/25/2022]
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18
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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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19
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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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20
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Gulin A, Nadtochenko V, Astafiev A, Pogorelova V, Rtimi S, Pogorelov A. Correlating microscopy techniques and ToF-SIMS analysis of fully grown mammalian oocytes. Analyst 2016; 141:4121-9. [DOI: 10.1039/c6an00665e] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An innovative protocol for the 2D-molecular thin film analysis applying ToF-SIMS, SEM, AFM and optical microscopy imaging of fully grown mice oocytes is described.
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Affiliation(s)
- Alexander Gulin
- N. N. Semenov Institute of Chemical Physics
- Russian Academy of Sciences
- 119991 Moscow
- Russia
- Moscow State University
| | - Victor Nadtochenko
- N. N. Semenov Institute of Chemical Physics
- Russian Academy of Sciences
- 119991 Moscow
- Russia
- Moscow State University
| | - Artyom Astafiev
- N. N. Semenov Institute of Chemical Physics
- Russian Academy of Sciences
- 119991 Moscow
- Russia
| | | | - Sami Rtimi
- Ecole Polytechnique Fédeérale de Lausanne
- Institute of chemical sciences and engineering (ISIC)
- Lausanne
- VD
- Switzerland
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21
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Cao HH, Nakatsuka N, Serino AC, Liao WS, Cheunkar S, Yang H, Weiss PS, Andrews AM. Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters. ACS NANO 2015; 9:11439-54. [PMID: 26426585 DOI: 10.1021/acsnano.5b05546] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nucleotide arrays require controlled surface densities and minimal nucleotide-substrate interactions to enable highly specific and efficient recognition by corresponding targets. We investigated chemical lift-off lithography with hydroxyl- and oligo(ethylene glycol)-terminated alkanethiol self-assembled monolayers as a means to produce substrates optimized for tethered DNA insertion into post-lift-off regions. Residual alkanethiols in the patterned regions after lift-off lithography enabled the formation of patterned DNA monolayers that favored hybridization with target DNA. Nucleotide densities were tunable by altering surface chemistries and alkanethiol ratios prior to lift-off. Lithography-induced conformational changes in oligo(ethylene glycol)-terminated monolayers hindered nucleotide insertion but could be used to advantage via mixed monolayers or double-lift-off lithography. Compared to thiolated DNA self-assembly alone or with alkanethiol backfilling, preparation of functional nucleotide arrays by chemical lift-off lithography enables superior hybridization efficiency and tunability.
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Affiliation(s)
- Huan H Cao
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Nako Nakatsuka
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Andrew C Serino
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Wei-Ssu Liao
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Sarawut Cheunkar
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Hongyan Yang
- Department of Psychiatry and Biobehavioral Health, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Materials Science and Engineering, University of California, Los Angeles , Los Angeles, California 90095, United States
| | - Anne M Andrews
- California NanoSystems Institute, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles , Los Angeles, California 90095, United States
- Department of Psychiatry and Biobehavioral Health, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles , Los Angeles, California 90095, United States
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22
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Gajos K, Petrou P, Budkowski A, Awsiuk K, Bernasik A, Misiakos K, Rysz J, Raptis I, Kakabakos S. Imaging and spectroscopic comparison of multi-step methods to form DNA arrays based on the biotin-streptavidin system. Analyst 2015; 140:1127-39. [PMID: 25535629 DOI: 10.1039/c4an00929k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Three multi-step multi-molecular approaches using the biotin-streptavidin system to contact-print DNA arrays on SiO2 surfaces modified with (3-glycidoxypropyl)trimethoxysilane are examined after each deposition/reaction step by atomic force microscopy, X-ray photoelectron spectroscopy and time of flight secondary ion mass spectrometry. Surface modification involves the spotting of preformed conjugates of biotinylated oligonucleotides with streptavidin onto surfaces coated with biotinylated bovine serum albumin b-BSA (approach I) or the spotting of biotinylated oligonucleotides onto a streptavidin coating, the latter prepared through a reaction with immobilized b-BSA (approach II) or direct adsorption (approach III). AFM micrographs, quantified by autocorrelation and height histogram parameters (e.g. roughness), reveal uniform coverage after each modification step with distinct nanostructures after the reaction of biotinylated BSA with streptavidin or of a streptavidin conjugate with biotinylated oligonucleotides. XPS relates the immobilization of biomolecules with covalent binding to the epoxy-silanized surface. Protein coverage, estimated from photoelectron attenuation, shows that regarding streptavidin the highest and the lowest immobilization efficiency is achieved by following approaches I and III, respectively, as confirmed by TOF-SIMS microanalysis. The size of the DNA spot reflects the contact radius of the printed droplet and increases with protein coverage (and roughness) prior to the spotting, as epoxy-silanized surfaces are hardly hydrophilic. Representative TOF-SIMS images show sub-millimeter spots: uniform for approach I, doughnut-like (with a small non-zero minimum) for approach II, both with coffee-rings or peak-shaped for approach III. Spot features, originating from pinned contact lines and DNA surface binding and revealed by complementary molecular distributions (all material, DNA, streptavidin, BSA, epoxy, SiO2), indicate two modes of droplet evaporation depending on the details of each applied approach.
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Affiliation(s)
- Katarzyna Gajos
- M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland.
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23
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Lin YS, Lin HR, Liu WL, Lee YT, Tseng CM, Ni CK, Liu CL, Tsai CC, Chen JL, Hu WP. Measurement and prediction of the NEXAFS spectra of pyrimidine and purine and the dissociation following the core excitation. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.07.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Gomes PJ, Ferraria AM, Botelho do Rego AM, Hoffmann SV, Ribeiro PA, Raposo M. Energy Thresholds of DNA Damage Induced by UV Radiation: An XPS Study. J Phys Chem B 2015; 119:5404-11. [DOI: 10.1021/acs.jpcb.5b01439] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- P. J. Gomes
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - A. M. Ferraria
- Centro
de Química-Física Molecular and IN, Instituto Superior
Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - A. M. Botelho do Rego
- Centro
de Química-Física Molecular and IN, Instituto Superior
Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - S. V. Hoffmann
- ISA,
Department of Physics and Astronomy, Aarhus University, Ny Munkegade
120, Building 1520, DK-8000 Aarhus C, Denmark
| | - P. A. Ribeiro
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - M. Raposo
- CEFITEC,
Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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25
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Mavrogiannopoulou E, Petrou PS, Koukouvinos G, Yannoukakos D, Siafaka-Kapadai A, Fornal K, Awsiuk K, Budkowski A, Kakabakos SE. Improved DNA microarray detection sensitivity through immobilization of preformed in solution streptavidin/biotinylated oligonucleotide conjugates. Colloids Surf B Biointerfaces 2015; 128:464-472. [PMID: 25805150 DOI: 10.1016/j.colsurfb.2015.02.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
A novel immobilization approach involving binding of preformed streptavidin/biotinylated oligonucleotide conjugates onto surfaces coated with biotinylated bovine serum albumin is presented. Microarrays prepared according to the proposed method were compared, in terms of detection sensitivity and specificity, with other immobilization schemes employing coupling of biotinylated oligonucleotides onto directly adsorbed surface streptavidin, or sequential coupling of streptavidin and biotinylated oligonucleotides onto a layer of adsorbed biotinylated bovine serum albumin. A comparison was performed employing biotinylated oligonucleotides corresponding to wild- and mutant-type sequences of seven single point mutations of the BRCA1 gene. With respect to the other immobilization protocols, the proposed oligonucleotide immobilization approach offered the highest hybridization signals (at least 5 times higher) and permitted more elaborative washings, thus providing considerably higher discrimination between complimentary and non-complementary DNA sequences for all mutations tested. In addition, the hybridization kinetics were significantly enhanced compared to two other immobilization protocols, permitting PCR sample analysis in less than 40 min. Thus, the proposed oligonucleotide immobilization approach offered improved detection sensitivity and discrimination ability along with considerably reduced analysis time, and it is expected to find wide application in DNA mutation detection.
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Affiliation(s)
- E Mavrogiannopoulou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - P S Petrou
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - G Koukouvinos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - D Yannoukakos
- Molecular Diagnostics Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece
| | - A Siafaka-Kapadai
- Biochemistry Lab, Department of Chemistry, University of Athens, GR-15771 Panepistimiopolis, Athens, Greece
| | - K Fornal
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - K Awsiuk
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - A Budkowski
- M. Smoluchowski Institute of Physics, Jagiellonian University, Reymonta 4, 30-059 Kraków, Poland
| | - S E Kakabakos
- Immunoassay/Immunosensors Lab, Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR "Demokritos", GR-15310 Aghia Paraskevi, Greece.
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26
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Annadhasan M, Kasthuri J, Rajendiran N. Green synthesis of gold nanoparticles under sunlight irradiation and their colorimetric detection of Ni2+ and Co2+ ions. RSC Adv 2015. [DOI: 10.1039/c4ra14034f] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel, green, one-pot and energy efficient route has been developed for the synthesis of gold nanoparticles by natural sunlight irradiation, and they were utilized effectively for the colorimetric detection of Ni2+ and Co2+ ions.
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Affiliation(s)
- M. Annadhasan
- Department of Polymer Science
- University of Madras
- Guindy campus
- Chennai
- India-600 025
| | - J. Kasthuri
- Department of Chemistry
- Quaid-E-Millath Government College for Women (Autonomous)
- Chennai
- India-600 002
| | - N. Rajendiran
- Department of Polymer Science
- University of Madras
- Guindy campus
- Chennai
- India-600 025
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27
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Park JW, Shumaker-Parry JS. Structural Study of Citrate Layers on Gold Nanoparticles: Role of Intermolecular Interactions in Stabilizing Nanoparticles. J Am Chem Soc 2014; 136:1907-21. [DOI: 10.1021/ja4097384] [Citation(s) in RCA: 439] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jong-Won Park
- Department of Chemistry, University of Utah, 1400 East 315 South
RM 2020, Salt Lake City, Utah 84112, United States
| | - Jennifer S. Shumaker-Parry
- Department of Chemistry, University of Utah, 1400 East 315 South
RM 2020, Salt Lake City, Utah 84112, United States
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28
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Fang S, Dong X, Zhang Y, Kang M, Liu S, Yan F, He L, Feng X, Wang P, Zhang Z. One-step synthesis of porous cuprous oxide microspheres on reduced graphene oxide for selective detection of mercury ions. NEW J CHEM 2014. [DOI: 10.1039/c4nj01347f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A facile one-step synthesis of Cu2OMS–rGO nanocomposites used as a sensitive layer for selective detection of mercury ions was reported.
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Affiliation(s)
- Shaoming Fang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Resoration, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Xiaodong Dong
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Yuanchang Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Mengmeng Kang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Shunli Liu
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Fufeng Yan
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Linghao He
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Xiaozhong Feng
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Peiyuan Wang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
| | - Zhihong Zhang
- Henan Provincial Key Laboratory of Surface and Interface Science, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
- Henan Collaborative Innovation Center of Environmental Pollution Control and Ecological Resoration, Zhengzhou University of Light Industry
- Zhengzhou 450001, P. R. China
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29
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Mahmoud KA, Zourob M. Fe3O4/Au nanoparticles/lignin modified microspheres as effectual surface enhanced Raman scattering (SERS) substrates for highly selective and sensitive detection of 2,4,6-trinitrotoluene (TNT). Analyst 2013; 138:2712-9. [PMID: 23515305 DOI: 10.1039/c3an00261f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new lignin modified hybrid microsphere, comprising poly(styrene-co-acrylic acid) core and magnetite (Fe3O4)/Au nanoparticle (NP) shell, was proposed here for the selective and highly sensitive detection and removal of 2,4,6-trinitrotoluene (TNT) explosives based on surface enhanced Raman scattering (SERS) and electrochemical detection methods. The presence of lignin and the highly packed layer of Fe3O4/AuNPs as a magnetic collector and metal enhancer for SERS signals allowed for the detection of TNT below 1 pM.
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Affiliation(s)
- Khaled A Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Qatar Foundation, P.O. Box 5825, Doha, Qatar.
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30
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Pekcevik IC, Poon LCH, Wang MCP, Gates BD. Tunable loading of single-stranded DNA on gold nanorods through the displacement of polyvinylpyrrolidone. Anal Chem 2013; 85:9960-7. [PMID: 24016255 DOI: 10.1021/ac4027737] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A quantitative and tunable loading of single-stranded (ss-DNA) molecules onto gold nanorods was achieved through a new method of surfactant exchange. This new method involves the exchange of cetyltrimethylammonium bromide surfactants for an intermediate stabilizing layer of polyvinylpyrrolidone and sodium dodecylsulfate. The intermediate layer of surfactants on the anisotropic gold particles was easily displaced by thiolated ss-DNA, forming a tunable density of single-stranded DNA molecules on the surfaces of the gold nanorods. The success of this ligand exchange process was monitored in part through the combination of extinction, X-ray photoelectron, and infrared absorption spectroscopies. The number of ss-DNA molecules per nanorod for nanorods with a high density of ss-DNA molecules was quantified through a combination of fluorescence measurements and elemental analysis, and the functionality of the nanorods capped with dense monolayers of DNA was assessed using a hybridization assay. Core-satellite assemblies were successfully prepared from spherical particles containing a probe DNA molecule and a nanorod core capped with complementary ss-DNA molecules. The methods demonstrated herein for quantitatively fine tuning and maximizing, or otherwise optimizing, the loading of ss-DNA in monolayers on gold nanorods could be a useful methodology for decorating gold nanoparticles with multiple types of biofunctional molecules.
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Affiliation(s)
- Idah C Pekcevik
- Department of Chemistry and 4D LABS, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6 Canada
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31
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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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Graham DJ, Castner DG. Image and Spectral Processing for ToF-SIMS Analysis of Biological Materials. Mass Spectrom (Tokyo) 2013; 2:S0014. [PMID: 24349933 DOI: 10.5702/massspectrometry.s0014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/23/2012] [Indexed: 12/14/2022] Open
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) instruments can rapidly produce large complex data sets. Within each spectrum, there can be hundreds of peaks. A typical 256×256 pixel image contains 65,536 spectra. If this is extended to a 3D image, the number of spectra in a given data set can reach the millions. The challenge becomes how to process these large data sets while taking into account the changes and differences between all the peaks in the spectra. This is particularly challenging for biological materials that all contain the same types of proteins and lipids, just in varying concentrations and spatial distributions. This data analysis challenge is further complicated by the limitations in the ion yield of higher mass, more chemically specific species, and potentially by the processing power of typical computers. Herein we briefly discuss analysis methodologies including univariate analysis, multivariate analysis (MVA) methods, and some of the limitations of ToF-SIMS analysis of biological materials.
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Affiliation(s)
- Daniel J Graham
- National ESCA and Surface Analysis Center for Biomedical Problems
| | - David G Castner
- National ESCA and Surface Analysis Center for Biomedical Problems ; Chemical Engineering University of Washington
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Rao AN, Vandencasteele N, Gamble LJ, Grainger DW. High-resolution epifluorescence and time-of-flight secondary ion mass spectrometry chemical imaging comparisons of single DNA microarray spots. Anal Chem 2012; 84:10628-36. [PMID: 23150996 DOI: 10.1021/ac3019334] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA microarray assay performance is commonly compromised by spot-spot probe and signal variations as well as heterogeneity within printed microspots. Accurate metrics for captured DNA target signal rely upon uniform spot distribution of both probe and target DNA to yield reliable hybridized signal. While often presumed, this is neither easily achieved nor often proven experimentally. High-resolution imaging techniques were used to determine spot heterogeneity in identical DNA array microspots comprising varied ratios of unlabeled and dye-labeled DNA probes contact-printed onto commercial arraying surfaces. Epifluorescence imaging data for individual array microspots were correlated with time-of-flight secondary ion mass spectrometry (TOF-SIMS) chemical state imaging of the same spots. Epifluorescence imaging intensity distinguished varying DNA density distributed both within a given spot and from spot to spot. TOF-SIMS chemical analysis confirmed these heterogeneous printed DNA distributions by tracking bound Cy3 dye, DNA base, and phosphate specific ion fragments often correlating to fluorescence patterns within identical spots. TOF-SIMS ion fragments originating from probe DNA and Cy3 dye are enriched in microspot centers, correlating with high fluorescence intensity regions. Both TOF-SIMS and epifluorescence support Marangoni flow effects on spot drying, with high-density DNA-Cy3 located in spot centers and nonhomogeneous DNA distribution within printed spots. Microspot image dimensional analysis results for DNA droplet spreading show differing DNA densities across printed spots. The study directly supports different DNA probe chemical and spatial microenvironments within spots that yield spot-spot signal variations known to affect DNA target hybridization efficiencies and kinetics. These variations critically affect probe-target duplex formation and DNA array signal generation.
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Affiliation(s)
- Archana N Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84112-5820, USA
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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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35
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Robinson MA, Graham DJ, Castner DG. ToF-SIMS depth profiling of cells: z-correction, 3D imaging, and sputter rate of individual NIH/3T3 fibroblasts. Anal Chem 2012; 84:4880-5. [PMID: 22530745 DOI: 10.1021/ac300480g] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proper display of three-dimensional time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging data of complex, nonflat samples requires a correction of the data in the z-direction. Inaccuracies in displaying three-dimensional ToF-SIMS data arise from projecting data from a nonflat surface onto a 2D image plane, as well as possible variations in the sputter rate of the sample being probed. The current study builds on previous studies by creating software written in Matlab, the ZCorrectorGUI (available at http://mvsa.nb.uw.edu/), to apply the z-correction to entire 3D data sets. Three-dimensional image data sets were acquired from NIH/3T3 fibroblasts by collecting ToF-SIMS images, using a dual beam approach (25 keV Bi(3)(+) for analysis cycles and 20 keV C(60)(2+) for sputter cycles). The entire data cube was then corrected by using the new ZCorrectorGUI software, producing accurate chemical information from single cells in 3D. For the first time, a three-dimensional corrected view of a lipid-rich subcellular region, possibly the nuclear membrane, is presented. Additionally, the key assumption of a constant sputter rate throughout the data acquisition was tested by using ToF-SIMS and atomic force microscopy (AFM) analysis of the same cells. For the dried NIH/3T3 fibroblasts examined in this study, the sputter rate was found to not change appreciably in x, y, or z, and the cellular material was sputtered at a rate of approximately 10 nm per 1.25 × 10(13) ions C(60)(2+)/cm(2).
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Affiliation(s)
- Michael A Robinson
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, Washington 98195-1750, United States
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36
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Frisz JF, Choi JS, Wilson RL, Harley BAC, Kraft ML. Identifying differentiation stage of individual primary hematopoietic cells from mouse bone marrow by multivariate analysis of TOF-secondary ion mass spectrometry data. Anal Chem 2012; 84:4307-13. [PMID: 22507202 DOI: 10.1021/ac203329j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ability to self-renew and differentiate into multiple types of blood and immune cells renders hematopoietic stem and progenitor cells (HSPCs) valuable for clinical treatment of hematopoietic pathologies and as models of stem cell differentiation for tissue engineering applications. To study directed hematopoietic stem cell (HSC) differentiation and identify the conditions that recreate the native bone marrow environment, combinatorial biomaterials that exhibit lateral variations in chemical and mechanical properties are employed. New experimental approaches are needed to facilitate correlating cell differentiation stage with location in the culture system. We demonstrate that multivariate analysis of time-of-flight secondary ion mass spectrometry (TOF-SIMS) data can be used to identify the differentiation state of individual hematopoietic cells (HCs) isolated from mouse bone marrow. Here, we identify primary HCs from three distinct stages of B cell lymphopoiesis at the single cell level: HSPCs, common lymphoid progenitors, and mature B cells. The differentiation state of individual HCs in a test set could be identified with a partial least-squares discriminant analysis (PLS-DA) model that was constructed with calibration spectra from HCs of known differentiation status. The lowest error of identification was obtained when the intrapopulation spectral variation between the cells in the calibration and test sets was minimized. This approach complements the traditional methods that are used to identify HC differentiation stage. Further, the ability to gather mass spectrometry data from single HSCs cultured on graded biomaterial substrates may provide significant new insight into how HSPCs respond to extrinsic cues as well as the molecular changes that occur during cell differentiation.
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Affiliation(s)
- Jessica F Frisz
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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37
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Crozals GD, Farre C, Hantier G, Léonard D, Marquette CA, Mandon CA, Marmuse L, Louis C, Toulmé JJ, Billotey C, Janier M, Chaix C. Oligonucleotide solid-phase synthesis on fluorescent nanoparticles grafted on controlled pore glass. RSC Adv 2012. [DOI: 10.1039/c2ra22077f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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38
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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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39
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Anderton CR, Vaezian B, Lou K, Frisz JF, Kraft ML. Identification of a lipid-related peak set to enhance the interpretation of TOF-SIMS data from model and cellular membranes. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3806] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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40
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Hua W, Gao B, Li S, Agren H, Luo Y. Refinement of DNA structures through near-edge X-ray absorption fine structure analysis: applications on guanine and cytosine nucleobases, nucleosides, and nucleotides. J Phys Chem B 2011; 114:13214-22. [PMID: 20873844 DOI: 10.1021/jp1034745] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work we highlight the potential of NEXAFS—near-edge X-ray absorption fine structure—analysis to perform refinements of hydrogen-bond structure in DNA. For this purpose we have carried out first-principle calculations of the N1s NEXAFS spectra of the guanine and cytosine nucleobases and their tautomers, nucleosides, and nucleotides in the gas phase, as well as for five crystal structures of guanine, cytosine, or guanosine. The spectra all clearly show imine (π1*) and amine (π2*) nitrogen absorption bands with a characteristic energy difference (Δ). Among all of the intramolecule covalent connections, the tautomerism of hydrogens makes the largest influence, around ±0.4−0.5 eV change of Δ, to the spectra due to a switch of single−double bonds. Deoxyribose and ribose sugars can cause at most 0.2 eV narrowing of Δ, while the phosphate groups have nearly negligible effects on the spectra. Two kinds of intermolecule interactions are analyzed, the hydrogen bonds and the stacking effect, by comparing “compressed” and “expanded” models or by comparing models including or excluding the nearest stacking molecules. The shortening of hydrogen-bond length by 0.2−0.3 Å can result in the reduction of Δ by 0.2−0.8 eV. This is because the hydrogen bonds make the electrons more delocalized, and the amine and imine nitrogens become less distinguishable. Moreover, the hydrogen bond has a different ability to influence the spectra of different crystals, with guanine crystals as the largest (change by 0.8 eV) and the guanosine crystal as the smallest (change by 0.2 eV). The stacking has negligible effects on the spectra in all studied systems. A comparison of guanosine to guanine crystals shows that the sugars in the crystal could create “blocks” in the π-and hydrogen bonds network of bases and thus makes the imine and amine nitrogens more distinguishable with a larger Δ. Our theoretical calculations offer a good match with experimental findings and explain earlier discrepancies in the NEXAFS analysis.
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Affiliation(s)
- Weijie Hua
- Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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41
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Wong AKY, Sodhi RNS, Krull UJ. Bin+ cluster ion sources for investigation of a covalently immobilized mixed film composed of oligonucleotides and poly(2-hydroxyethyl methacrylate) brushes. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Cun D, Jensen DK, Maltesen MJ, Bunker M, Whiteside P, Scurr D, Foged C, Nielsen HM. High loading efficiency and sustained release of siRNA encapsulated in PLGA nanoparticles: Quality by design optimization and characterization. Eur J Pharm Biopharm 2011; 77:26-35. [DOI: 10.1016/j.ejpb.2010.11.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/01/2010] [Accepted: 11/11/2010] [Indexed: 11/24/2022]
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43
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Kummer K, Vyalikh DV, Gavrila G, Preobrajenski AB, Kick A, Bönsch M, Mertig M, Molodtsov SL. Electronic structure of genomic DNA: a photoemission and X-ray absorption study. J Phys Chem B 2010; 114:9645-52. [PMID: 20608694 DOI: 10.1021/jp1013237] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electronic structure of genomic DNA has been comprehensively characterized by synchrotron-based X-ray absorption and X-ray photoelectron spectroscopy. Both unoccupied and occupied states close to the Fermi level have been unveiled and attributed to particular sites within the DNA structure. A semiconductor-like electronic structure with a band gap of approximately 2.6 eV has been found at which the pi and pi* orbitals of the nucleobase stack make major contributions to the highest occupied and lowest unoccupied molecular orbitals, respectively, in agreement with previous theoretical predictions.
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Affiliation(s)
- Kurt Kummer
- Institut für Festkörperphysik, Technische Universität Dresden, 01062 Dresden, Germany
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44
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Brison J, Benoit DSW, Muramoto S, Robinson M, Stayton PS, Castner DG. ToF-SIMS imaging and depth profiling of HeLa cells treated with bromodeoxyuridine. SURF INTERFACE ANAL 2010; 43:354-357. [PMID: 22058579 DOI: 10.1002/sia.3415] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Time of flight secondary ion mass spectrometry 2D images and molecular depth profiles of human HeLa cells treated with bromodeoxyuridine (BrdU) were acquired in the dual beam mode (Bi(3) (+) analysis beam, C(60) (+) etching beam). Several preparation protocols were investigated and were compared to a simple wash-and-dry method. The feasibility of using C(60) to clean the samples prior to imaging with Bi was also investigated quantitatively by calibrating full depth profiles of the cells using atomic force microscopy. BrdU was used as a marker for the cell nucleus, facilitating identification and localization of sub-cellular features during depth profiling. Results show that C(60) can be used to remove the surface contamination and to access different layers within the cells for 2D imaging. For a 1 nA, 10 keV C(60) (+) beam incident at 45° and rastered over a 500 × 500 μm(2) area, ~1 nm of biological material was sputtered every second. Our results show that HeLa cells were completely removed after etching with 1.3×10(15) C(60) (+) ions per cm(2), giving an average etching rate of 3.9 nm for every 10(13) C(60) per cm(2) at 10 keV and 45° incidence.
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Affiliation(s)
- Jeremy Brison
- National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Seattle, WA 98195
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45
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Dietrich PM, Horlacher T, Gross T, Wirth T, Castelli R, Shard AG, Alexander M, Seeberger PH, Unger WES. Surface analytical characterization of carbohydrate microarrays. SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Pris AD, Ostrowski SG, Garaas SD. Simultaneous optimization of monolayer formation factors, including temperature, to significantly improve nucleic acid hybridization efficiency on gold substrates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:5655-5660. [PMID: 20345116 DOI: 10.1021/la903699f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Past literature investigations have optimized various single factors used in the formation of thiolated, single stranded DNA (ss-DNA) monolayers on gold. In this study a more comprehensive approach is taken, where a design of experiment (DOE) is employed to simultaneously optimize all of the factors involved in construction of the capture monolayer used in a fluorescence-based hybridization assay. Statistical analysis of the fluorescent intensities resulting from the DOE provides empirical evidence for the importance and the optimal levels of traditional and novel factors included in this investigation. We report on the statistical importance of a novel factor, temperature of the system during monolayer formation of the capture molecule and lateral spacer molecule, and how proper usage of this temperature factor increased the hybridization signal 50%. An initial theory of how the physical factor of heat is mechanistically supplementing the function of the lateral spacer molecule is provided.
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Affiliation(s)
- Andrew D Pris
- General Electric-Global Research Center, One Research Circle, Niskayuna, New York 12309, USA.
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47
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Zhou JC, Wang X, Xue M, Xu Z, Hamasaki T, Yang Y, Wang K, Dunn B. Characterization of gold nanoparticle binding to microtubule filaments. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2010. [DOI: 10.1016/j.msec.2009.08.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Patra A, Ralston J, Sedev R, Zhou J. Design of pyrimidine-based photoresponsive surfaces and light-regulated wettability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:11486-11494. [PMID: 19702251 DOI: 10.1021/la901309b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Photoresponsive surfaces were prepared by attaching pyrimidine-terminated molecules to flat gold substrates (as thiol self-assembled monolayers) or by dip-coating quartz surfaces. Both types of films underwent photodimerization (two pyrimidine rings react with one another and form a cyclobutane type dimer through the C5=C6 double bond) when irradiated with light of 280 nm wavelength. The reverse reaction was carried out by irradiating the dimerized surface with light of 240 nm wavelength. The photoinduced chemical changes are accompanied by a change in the physical properties of the surface (e.g., wettability and acidity), and are highly dependent on the structure of the photoactive molecules. The surface dimerization reaction follows a pseudo-first order reaction. The rate constant is determined by the structure of the pyrimidine headgroup. In self-assembled monolayers, uracil derivatives dimerize faster than thymine derivatives due to a reduced steric repulsion near the reaction center. In dip-coated films, however, uracil derivatives appear to be less ordered and, correspondingly, the efficiency of the reaction is lower. The reaction rate is also very sensitive to the ordering within the layer, which can be manipulated through the structure of the tail. In SAMs, faster dimerization occurs with molecules containing flexible chains. In dip-coated films, the presence of a polar group at the chain terminus favors dimerization.
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Affiliation(s)
- Anuttam Patra
- Ian Wark Research Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
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49
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Liu ZC, Zhang X, He NY, Lu ZH, Chen ZC. Probing DNA hybridization efficiency and single base mismatch by X-ray photoelectron spectroscopy. Colloids Surf B Biointerfaces 2009; 71:238-42. [PMID: 19282155 DOI: 10.1016/j.colsurfb.2009.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 02/10/2009] [Accepted: 02/11/2009] [Indexed: 10/21/2022]
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50
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Zubavichus Y, Shaporenko A, Korolkov V, Grunze M, Zharnikov M. X-ray absorption spectroscopy of the nucleotide bases at the carbon, nitrogen, and oxygen K-edges. J Phys Chem B 2008; 112:13711-6. [PMID: 18842017 DOI: 10.1021/jp802453u] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Near-edge X-ray absorption fine structure spectra of three pyrimidine (viz., cytosine, uracil, and thymine) and two purine (viz., adenine and guanine) nucleobases, which are the key constituents of DNA and RNA, were measured at the C, N, and O K-edges using the self-absorption-free partial electron yield mode. The nucleobase samples were prepared as highly pure native polycrystalline powder films. The spectra are analyzed in terms of the electronic structure of the nucleobases. Subtle chemical effects related to the molecular structures of these heterocyclic compounds with extended pi-electron systems are considered and discussed.
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Affiliation(s)
- Yan Zubavichus
- Angewandte Physikalische Chemie, University of Heidelberg, Heidelberg, Germany.
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