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Fu R, Hou J, Wang Z, Xianyu Y. DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles. ACS NANO 2024; 18:14754-14763. [PMID: 38781600 DOI: 10.1021/acsnano.4c04265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
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2
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Sodomaco S, Gómez S, Giovannini T, Cappelli C. Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces. J Phys Chem A 2023; 127:10282-10294. [PMID: 37993110 DOI: 10.1021/acs.jpca.3c05560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.
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Affiliation(s)
- Sveva Sodomaco
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Tommaso Giovannini
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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3
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Ding Y, Liu J. Quantitative Comparison of Capture-SELEX, GO-SELEX, and Gold-SELEX for Enrichment of Aptamers. Anal Chem 2023; 95:14651-14658. [PMID: 37721984 DOI: 10.1021/acs.analchem.3c02477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Since 1990, numerous methods for aptamer selection have been developed, although a quantitative comparison of their sequence enrichment is lacking. In this study, we compared the enrichment factors of three library-immobilization SELEX methods (capture-SELEX, GO-SELEX, and gold-SELEX). We used a spiked library that contained multiple DNA aptamers with different affinities for adenosine. The aptamer separation efficiency was measured using qPCR, and all of the three methods showed a very low DNA release (<1%) in the presence of 100 μM adenosine. Among these, barely any DNA was released from the gold nanoparticles. Deep sequencing was used to compare the enrichment of three aptamers: Ade1301, Ade1304, and the classical aptamer. Enrichment up to 30 to 50-fold was observed only for the capture-SELEX method, whereas the other two methods showed enrichment factors below 1. By blocking the primer-binding regions of the library, GO-SELEX reached up to 14% enrichment. Finally, the enrichment of aptamers based on nonspecific release and target-induced release was discussed, and the advantages of capture-SELEX were rationalized. Taken together, these results indicate that capture-SELEX is a much more efficient method for enriching aptamers.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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4
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Rotondi SMC, Canepa P, Angeli E, Canepa M, Cavalleri O. DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23094557. [PMID: 37177760 PMCID: PMC10181596 DOI: 10.3390/s23094557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/15/2023]
Abstract
By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.
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Affiliation(s)
| | - Paolo Canepa
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Elena Angeli
- Dipartimento di Fisica, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Maurizio Canepa
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
- INFN, Sezione di Genova, Via Dodecaneso 33, 16146 Genova, Italy
| | - Ornella Cavalleri
- Dipartimento di Fisica and Optmatlab, Università di Genova, Via Dodecaneso 33, 16146 Genova, Italy
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5
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Sen A, Sester C, Poulsen H, Hodgkiss JM. Accounting for Interaction Kinetics between Gold Nanoparticles and Aptamers Enables High-Performance Colorimetric Sensors. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32813-32822. [PMID: 35833898 DOI: 10.1021/acsami.2c04747] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA aptamers have emerged as promising probes for challenging analytes that cannot be easily detected by conventional probes, including small-molecule targets. Among the different signal transduction approaches, gold nanoparticle (AuNP) aggregation assays have been widely used to generate a colorimetric response from aptamer-target interactions. This sensor design relies on the competition between the aptamer adsorbing to the AuNP surface versus interacting with the target, whereby target binding reduces the number of adsorbed aptamers that destabilizes AuNPs toward salt-induced aggregation, thereby inducing a color change. However, this thermodynamic framework overlooks the potential influence of interaction kinetics of different aptamer conformations with AuNP surfaces and with targets in solution or near surfaces. Here, we show that aptamers become more strongly adsorbed on AuNPs over time, and these trapped aptamers are less responsive toward the target analyte. By varying the sequence of addition in sensing assays, we demonstrate that these interaction kinetics have a significant effect on the sensor response and thereby produce an effective sensor for methamphetamine (meth) at biologically relevant levels in oral fluids. Along with underpinning new tools for assay development, this new knowledge also highlights the need for aptamer selection strategies that evolve aptamer sequences based on the functionality that they need to exhibit in an actual sensor.
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Affiliation(s)
- Anindita Sen
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6040, New Zealand
| | - Clément Sester
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6040, New Zealand
| | - Helen Poulsen
- Forensic Specialised Analytical Services (F-SAS), Institute of Environmental Science and Research (ESR), P.O. Box 50348, Wellington 5240, New Zealand
| | - Justin M Hodgkiss
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, Wellington 6012, New Zealand
- School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington 6040, New Zealand
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6
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Probing and modulating the interactions of the DNAzyme with DNA-functionalized nanoparticles. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Chen C, Ding PC, Li Z, Shi GQ, Sun Y, Kantorovich LN, Besenbacher F, Yu M. Super‐Robust Xanthine–Sodium Complexes on Au(111). Angew Chem Int Ed Engl 2022; 61:e202200064. [DOI: 10.1002/anie.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Chong Chen
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Chemistry and Chemical Engineering Suzhou University Suzhou 234000 China
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Pengcheng C. Ding
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Zhuo Li
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Guoqiang Q. Shi
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of Physics King's College London The Strand London WC2R 2LS UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Miao Yu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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8
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Chen C, Ding PC, Li Z, Shi GQ, Sun Y, Kantorovich LN, Besenbacher F, Yu M. Super‐Robust Xanthine–Sodium Complexes on Au(111). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chong Chen
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Chemistry and Chemical Engineering Suzhou University Suzhou 234000 China
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Pengcheng C. Ding
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Zhuo Li
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Guoqiang Q. Shi
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
| | - Ye Sun
- School of Instrumentation Science and Engineering Harbin Institute of Technology Harbin 150001 China
| | - Lev N. Kantorovich
- Department of Physics King's College London The Strand London WC2R 2LS UK
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO) and Deptment of Physics and Astronomy Aarhus University Aarhus 8000 Denmark
| | - Miao Yu
- School of Chemistry and Chemical Engineering Harbin Institute of Technology Harbin 150001 China
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9
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Zhang F, Liu J. Interactions of the Cocaine and Quinine Aptamer with Gold Nanoparticles under the Dilute Biosensor and Concentrated NMR Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11939-11947. [PMID: 34591480 DOI: 10.1021/acs.langmuir.1c02239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The cocaine aptamer was later found to bind quinine with an even higher affinity. In this work, we used a fluorescently labeled aptamer named MN4 to study its adsorption by gold nanoparticles (AuNPs), and the subsequent displacement by the nonlabeled aptamer and by quinine. Without washing, 14% of the preadsorbed MN4 strands were displaced by 4000-fold excess of free MN4, whereas no displacement was observed after washing, suggesting that washing removed weakly adsorbed aptamers. In a previous paper, rapid exchange was observed with NMR by directly mixing AuNPs and concentrated MN4, and our work has unified the dilute and concentrated aptamer conditions. The difference is attributable to the conformation of the adsorbed aptamer, where dilute aptamers are adsorbed in a collapsed state with a much higher affinity to AuNPs. In addition, the preadsorbed MN4 aptamer cannot be desorbed by adding quinine, indicating that direct desorption-based fluorescent sensors cannot be made. Finally, based on the similar color responses to both the aptamer and its nonbinding mutants, the label-free colorimetric detection method cannot be directly applied for the detection of quinine. This work indicated that different experimental conditions need to be carefully compared to have a unified understanding of aptamer/AuNP systems.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People's Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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10
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Behera RK, Sau A, Mishra L, Mondal S, Bera K, Kumar S, Basu S, Sarangi MK. Metal nanoparticle alters adenine induced charge transfer kinetics of vitamin K3 in magnetic field. Sci Rep 2020; 10:18454. [PMID: 33116189 PMCID: PMC7595215 DOI: 10.1038/s41598-020-75262-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 09/28/2020] [Indexed: 01/05/2023] Open
Abstract
In this article, we highlight the alterations in the photoinduced electron transfer (ET) and hydrogen atom transfer (HAT) pathways between an anti-tumor drug vitamin-K3 (MQ) and a nucleobase adenine (ADN) in the presence of gold (Au) and iron (Fe) nanoparticles (NPs). Inside the confined micellar media, with laser flash photolysis corroborated with an external magnetic field (MF), we have detected the transient geminate radicals of MQ and ADN, photo-generated through ET and HAT. We observe that the presence of AuNP on the MQ-ADN complex (AuMQ-ADN) assists HAT by limiting the ET channel, on the other hand, FeNP on the MQ-ADN complex (FeMQ-ADN) mostly favors a facile PET. We hypothesize that through selective interactions of the ADN molecules with AuNP and MQ molecules with FeNP, a preferential HAT and PET process is eased. The enhanced HAT and PET have been confirmed by the escape yields of radical intermediates by time-resolved transient absorption spectroscopy in the presence of MF.
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Affiliation(s)
| | - Abhishek Sau
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India.,Department of Molecular and Cellular Medicine, Texas A&M University, College Station, USA
| | - Leepsa Mishra
- Department of Physics, Indian Institute of Technology Patna, Patna, India
| | - Sankalan Mondal
- Department of Physics, Indian Institute of Technology Patna, Patna, India
| | - Kallol Bera
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India.,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Satish Kumar
- Department of Physics, Indian Institute of Technology Patna, Patna, India
| | - Samita Basu
- Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata, India
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11
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Zhang F, Huang PJJ, Liu J. Sensing Adenosine and ATP by Aptamers and Gold Nanoparticles: Opposite Trends of Color Change from Domination of Target Adsorption Instead of Aptamer Binding. ACS Sens 2020; 5:2885-2893. [PMID: 32847353 DOI: 10.1021/acssensors.0c01169] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The 27 mer DNA aptamer for adenosine and adenosine 5'-triphosphate (ATP) is a popular model system for designing biosensors. Various strategies have been reported for label-free colorimetric detection using gold nanoparticles (AuNPs). It is generally accepted that free aptamers can protect AuNPs against salt-induced aggregation, whereas target-bound aptamers cannot. However, these studies only considered the aptamer binding to its target, and the adsorption of the aptamer on AuNPs, but none considered the adsorption of target molecules by AuNPs. We herein report that the adsorption of adenosine destabilized citrate-capped AuNPs with an apparent Kd of just 7.7 μM adenosine, whereas that of ATP stabilized the AuNPs because of the negative charges from the triphosphate group. The adsorbed ATP inhibited the adsorption of DNA. Using the aptamer and a nonbinding mutant, ATP and guanosine 5'-triphosphate (GTP) had the same colorimetric response, and so did adenosine and guanosine, regardless of the DNA sequence, indicating that the color change mainly reflected the adsorption of the nucleosides and nucleotides instead of aptamer binding. The related literature examples using this aptamer were classified into three types and individually analyzed, where the reported color changes can all be explained by the adsorption of target analytes.
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Affiliation(s)
- Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, People’s Republic of China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo N2L 3G1, Ontario, Canada
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12
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Factors that control the gold nanoparticles' aggregation induced by adenine molecules: New insights through a combined experimental and theoretical study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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13
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A facile and sensitive colorimetric detection for RNase A activity based on target regulated protection effect on plasmonic gold nanoparticles aggregation. Sci China Chem 2020. [DOI: 10.1007/s11426-020-9702-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Satyavolu NSR, Loh KY, Tan LH, Lu Y. Discovery of and Insights into DNA "Codes" for Tunable Morphologies of Metal Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900975. [PMID: 31074939 PMCID: PMC6663601 DOI: 10.1002/smll.201900975] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/14/2019] [Indexed: 05/28/2023]
Abstract
The discovery and elucidation of genetic codes has profoundly changed not only biology but also many fields of science and engineering. The fundamental building blocks of life comprises of four simple deoxyribonucleotides and yet their combinations serve as the carrier of genetic information that encodes for proteins that can carry out many biological functions due to their unique functionalities. Inspired by nature, the functionalities of DNA molecules have been used as a capping ligand for controlling morphology of nanomaterials, and such a control is sequence dependent, which translates into distinct physical and chemical properties of resulting nanoparticles. Herein, an overview on the use of DNA as engineered codes for controlling the morphology of metal nanoparticles, such as gold, silver, and Pd-Au bimetallic nanoparticles is provided. Fundamental insights into rules governing DNA controlled growth mechanisms are also summarized, based on understanding of the affinity of the DNA nucleobases to various metals, the effect of combination of nucleobases, functional modification of DNA, the secondary structures of DNA, and the properties of the seed employed. The resulting physical and chemical properties of these DNA encoded nanomaterials are also reviewed, while perspectives into the future directions of DNA-mediated nanoparticle synthesis are provided.
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Affiliation(s)
- Nitya Sai Reddy Satyavolu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kang Yong Loh
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Li Huey Tan
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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15
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Wang X, Wang X, Bai X, Yan L, Liu T, Wang M, Song Y, Hu G, Gu Z, Miao Q, Chen C. Nanoparticle Ligand Exchange and Its Effects at the Nanoparticle-Cell Membrane Interface. NANO LETTERS 2019; 19:8-18. [PMID: 30335394 DOI: 10.1021/acs.nanolett.8b02638] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The nanoparticle (nano)-cell membrane interface is one of the most important interactions determining the fate of nanoparticles (NPs), which can stimulate a series of biological events, allowing theranostic and other biomedical applications. So far, there remains a lack of knowledge about the mechanisms governing the nanoparticle-cell membrane interface, especially the impact of ligand exchange, in which molecules on the nanosurface become replaced with components of the cell membrane, resulting in unique interfacial phenomena. Herein, we describe a family of gold nanoparticles (AuNPs) of the same core size (∼13 nm core), modified with 12 different kinds of surface ligands, and the effects of their exchangeable ligands on both nanoparticle-supported lipid bilayers (SLBs) and nanoparticle-natural cell membrane interfaces. The ligands are categorized according to their molecular weight, charge, and bonding modes (physisorption or chemisorption). Importantly, we found that, depending on the adsorption affinity and size of ligand molecules, physisorbed ligands on the surface of NPs can be exchanged with lipid molecules. At a ligand exchange-dominated interface, the AuNPs typically aggregated into an ordered monolayer in the lipid bilayers, subsequently affecting cell membrane integrity, NP uptake efficiency, and the NP endocytosis pathways. These findings advance our understanding of the underlying mechanisms of the biological effects of nanoparticles from a new point of view and will aid in the design of novel, safe, and effective nanomaterials for biomedicine.
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Affiliation(s)
- Xinyi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS Center for Excellence in Nanoscience , National Center for Nanoscienceand Technology of China, and University of Chinese Academy of Sciences , Beijing 100190 , China
- College of Sciences , Shenyang Agricultural University , Shenyang 110161 , China
- College of Environment , Liaoning University , Shenyang 110036 , China
| | - Xiaofeng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences (CAS), and University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xuan Bai
- The State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics , Chinese Academy of Sciences, and University of Chinese Academy of Sciences , Beijing 100190 , China
| | - Liang Yan
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences (CAS), and University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Tao Liu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS Center for Excellence in Nanoscience , National Center for Nanoscienceand Technology of China, and University of Chinese Academy of Sciences , Beijing 100190 , China
| | - Mingzhe Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS Center for Excellence in Nanoscience , National Center for Nanoscienceand Technology of China, and University of Chinese Academy of Sciences , Beijing 100190 , China
| | - Youtao Song
- College of Environment , Liaoning University , Shenyang 110036 , China
| | - Guoqing Hu
- The State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics , Chinese Academy of Sciences, and University of Chinese Academy of Sciences , Beijing 100190 , China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics , Chinese Academy of Sciences (CAS), and University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Qing Miao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS Center for Excellence in Nanoscience , National Center for Nanoscienceand Technology of China, and University of Chinese Academy of Sciences , Beijing 100190 , China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, & CAS Center for Excellence in Nanoscience , National Center for Nanoscienceand Technology of China, and University of Chinese Academy of Sciences , Beijing 100190 , China
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16
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Rosa M, Di Felice R, Corni S. Adsorption Mechanisms of Nucleobases on the Hydrated Au(111) Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14749-14756. [PMID: 29723478 DOI: 10.1021/acs.langmuir.8b00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The solution environment is of fundamental importance in the adsorption of molecules on surfaces, a process that is strongly affected by the capability of the adsorbate to disrupt the hydration layer above the surface. Here we disclose how the presence of interface water influences the adsorption mechanism of DNA nucleobases on a gold surface. By means of metadynamics simulations, we describe the distinctive features of a complex free-energy landscape for each base, which manifests activation barriers for the adsorption process. We characterize the different pathways that allow each nucleobase to overcome the barriers and be adsorbed on the surface, discussing how they influence the kinetics of adsorption of single-stranded DNA oligomers with homogeneous sequences. Our findings offer a rationale as to why experimental data on the adsorption of single-stranded homo-oligonucleotides do not straightforwardly follow the thermodynamics affinity rank.
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Affiliation(s)
| | - Rosa Di Felice
- Center S3 , CNR Institute of Nanoscience , 41125 Modena , Italy
- Department of Physics and Astronomy , University of Southern California , Los Angeles , California 90089 , United States
| | - Stefano Corni
- Center S3 , CNR Institute of Nanoscience , 41125 Modena , Italy
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17
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Jaworska A, Jablonska A, Wilanowski T, Palys B, Sek S, Kudelski A. Influence of amine and thiol modifications at the 3' ends of single stranded DNA molecules on their adsorption on gold surface and the efficiency of their hybridization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:31-39. [PMID: 29857258 DOI: 10.1016/j.saa.2018.05.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 05/22/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Adsorption of molecules of DNA (deoxyribonucleic acid) or modified DNA on gold surfaces is often the first step in construction of many various biosensors, including biosensors for detection of DNA with a particular sequence. In this work we study the influence of amine and thiol modifications at the 3' ends of single stranded DNA (ssDNA) molecules on their adsorption on the surface of gold substrates and on the efficiency of hybridization of immobilized DNA with the complementary single stranded DNA. The characterization of formed layers has been carried out using infrared spectroscopy and atomic force microscopy. As model single stranded DNA we used DNA containing 20 adenine bases, whereas the complementary DNA contained 20 thymine bases. We found that the bands in polarization modulation-infrared reflection-adsorption spectroscopy (PM-IRRAS) spectra of layers formed from thiol-modified DNA are significantly narrower and sharper, indicating their higher regularity in the orientation of DNA on gold surface when using thiol linker. Also, hybridization of the layer of thiol-modified DNA containing 20 adenine bases with the respective DNA containing thymine bases leads to formation of much more organized structures than in the case of unmodified DNA or DNA with the amine linker. We conclude that the thiol-modified ssDNA is more promising for the preparation of biosensors, in comparison with the amine-modified or unmodified ssDNA. We have also found that the above-mentioned modifications at the 3' end of ssDNA significantly influence the IR spectrum (and hence the structure) of polycrystalline films formed from such compounds, even though adsorbed fragments contain less than 5% of the DNA chain. This effect should be taken into account when comparing IR spectra of various polycrystalline films formed from modified and unmodified DNA.
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Affiliation(s)
- Aleksandra Jaworska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland.
| | - Anna Jablonska
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Tomasz Wilanowski
- Laboratory of Signal Transduction, Department of Cell Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Barbara Palys
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Slawomir Sek
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland
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18
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Farrokhpour H, Abedi S, Jouypazadeh H. Directional affinity of a spherical Gold nanoparticle for the adsorption of DNA bases. Colloids Surf B Biointerfaces 2018; 173:493-503. [PMID: 30336411 DOI: 10.1016/j.colsurfb.2018.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/10/2018] [Accepted: 10/01/2018] [Indexed: 11/19/2022]
Abstract
In this work, the adsorption activities of different facets of a spherical gold nanoparticle (Au(111), Au(100) and Au(110)) for adenine (ADE) and cytosine (CYT) in two different environments including gas phase and in the presence of solvent (water) have been investigated, separately. It has been found that the adsorption energy (Ead) and geometry of the DNA bases depend strongly on the kind of nanoparticle facet. The Au (110) facet showed the highest adsorption affinity for the ADE and CYT in both gas phase and water compared to Au(111) and Au(100) facets. Comparison of the Eads of bases calculated in the gas phase with those obtained in the presence of water showed that the electrostatic field of solvent decreases the Eads of bases, especially, for the Au (110) facet. The adsorption geometry of the CYT showed strong dependency on the kind of nanoparticle facet compared to ADE. Also, it has been shown that the direction and amount of charge transfer (CT) between the molecule and nanoparticle strongly depends on the kind of nanoparticle facet and environment. The CT is from the Au (111) facet to the ADE while the CT direction is reversed when the ADE is adsorbed on the Au (110) and Au (100) facets in the gas phase. The CT is from the CYT to three facets in the gas phase while its direction for the ADE and CYT adsorbed on Au (100) facet is reversed. The atoms in molecules (AIM) analysis has been employed to determine the bond paths (BPs) and bond critical points (BCPs) between the bases and facets. The infrared (IR) spectra of the bases adsorbed on the selected facets were calculated and compared with each other and with the spectra of the isolated bases. It was found that the symmetric and unsymmetric stretching of the NH of NH2 group, C-H stretching of the rings and CO stretching of bases can be used for the discrimination of the selected facets.
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Affiliation(s)
- Hossein Farrokhpour
- Department of chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Soraya Abedi
- Department of chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Hamidreza Jouypazadeh
- Department of chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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19
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Han J, Li Y, Zhan L, Xue J, Sun J, Xiong C, Nie Z. A novel mass spectrometry method based on competitive non-covalent interaction for the detection of biomarkers. Chem Commun (Camb) 2018; 54:10726-10729. [PMID: 30187034 DOI: 10.1039/c8cc06100a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report a novel biosensor platform based on competitive non-covalent interaction between ssDNA and a mass tag towards AuNPs, which detects PSA biomarkers sensitively, observed using MALDI MS. A detection limit of 57 pg mL-1 has been achieved, showing an improvement of two orders of magnitude compared to the traditional spectroscopic method.
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Affiliation(s)
- Jing Han
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
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20
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Carnevale KJF, Strouse GF. Intracellular DNA Cargo Release from a Gold Nanoparticle Modulated by the Nature of the Surface Coupling Functionality. Bioconjug Chem 2018; 29:3429-3440. [DOI: 10.1021/acs.bioconjchem.8b00575] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kate J. F. Carnevale
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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21
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Campos R, Kékedy-Nagy L, She Z, Sodhi R, Kraatz HB, Ferapontova EE. Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA 10 Tags. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8472-8479. [PMID: 29936843 DOI: 10.1021/acs.langmuir.8b01412] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA10 tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA10-tagged DNA duplex approached 361 s-1 at a ca. half-monolayer DNA surface coverage ΓDNA (with a linear regression limit of 670 s-1 at ΓDNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA5* tethering (6-fold for the C6-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA10 binding to the Au surface via the purine N, whereas dA5* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA10 tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.
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Affiliation(s)
- Rui Campos
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
| | - Zhe She
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
| | - Rana Sodhi
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, 1095 Military Trail , University of Toronto Scarborough , Toronto , Ontario M1C 1A4 , Canada
- Department of Chemical Engineering and Applied Chemistry , University of Toronto , 200 College Street , Toronto , Ontario M5S 3E5 , Canada
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Science and Technology , Aarhus University , Gustav Wieds Vej 14 , 8000 Aarhus C , Denmark
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22
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Harroun SG. The Controversial Orientation of Adenine on Gold and Silver. Chemphyschem 2018; 19:1003-1015. [DOI: 10.1002/cphc.201701223] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/07/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Scott G. Harroun
- Department of Chemistry; Université de Montréal; Montréal Québec H3C 3J7 Canada
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23
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Acres RG, Cheng X, Beranová K, Bercha S, Skála T, Matolín V, Xu Y, Prince KC, Tsud N. An experimental and theoretical study of adenine adsorption on Au(111). Phys Chem Chem Phys 2018; 20:4688-4698. [DOI: 10.1039/c7cp08102b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The parallel and upright adenine phases on Au(111) were studied by photoelectron and absorption spectroscopies in combination with density functional theory calculations.
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Affiliation(s)
| | - Xun Cheng
- Cain Department of Chemical Engineering
- Louisiana State University
- Baton Rouge
- USA
| | - Klára Beranová
- Elettra-Sincrotrone Trieste S.C.p.A
- Basovizza
- Italy
- Charles University
- Faculty of Mathematics and Physics
| | - Sofiia Bercha
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Tomáš Skála
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Vladimír Matolín
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
| | - Ye Xu
- Cain Department of Chemical Engineering
- Louisiana State University
- Baton Rouge
- USA
| | | | - Nataliya Tsud
- Charles University
- Faculty of Mathematics and Physics
- Department of Surface and Plasma Science
- 18000 Prague 8
- Czech Republic
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24
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Zhou Y, Huang Z, Yang R, Liu J. Selection and Screening of DNA Aptamers for Inorganic Nanomaterials. Chemistry 2017; 24:2525-2532. [PMID: 29205597 DOI: 10.1002/chem.201704600] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 11/10/2022]
Abstract
Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈1014 random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.
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Affiliation(s)
- Yibo Zhou
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Ronghua Yang
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China
| | - Juewen Liu
- School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha, 410114, P. R. China.,Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
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25
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Wang R, Zhou X, Liedberg B, Zhu X, Memon AG, Shi H. Screening Criteria for Qualified Antibiotic Targets in Unmodified Gold Nanoparticles-Based Aptasensing. ACS APPLIED MATERIALS & INTERFACES 2017; 9:35492-35497. [PMID: 28956590 DOI: 10.1021/acsami.7b12796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In designing unmodified gold nanoparticles-based aptasensing (uGA) assays for antibiotics, we find that some antibiotics can adsorb directly on gold nanoparticles (GNP) regardless of the presence of aptamers, which have been long overlooked in the past. Some adsorptions, however, would strongly disturb the charge distribution on the GNP surface, break up the static colloidal profile, and thus generate false positive colorimetric signals. To identify antibiotics qualified for uGA assays, we established two rational screening criteria for antibiotic targets relying on their oil-water partition coefficients (log P values) and net physiological charges: log P > 0 and charge ≤0. A good agreement of the GNP color change was obtained between the two criteria-based predictions and the actual tests using six representative antibiotics. The proposed criteria help to shed light on GNP-target interactions, which is significant for developing novel GNP-based colorimetric assays with high reliability.
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Affiliation(s)
- Ruoyu Wang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Bo Liedberg
- School of Materials Science and Engineering, Nanyang Technological University , 639798 Singapore
| | - Xiyu Zhu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Abdul Ghaffar Memon
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University , Beijing 100084, China
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26
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Farrokhpour H, Jouypazadeh H. Description of adenine and cytosine on Au(111) nano surface using different DFT functionals (PW91PW91, wB97XD, M06-2X, M06-L and CAM-B3LYP) in the framework of ONIOM scheme: Non-periodic calculations. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Harroun SG, Zhang Y, Chen TH, Ku CR, Chang HT. Biomarkers of cigarette smoking and DNA methylating agents: Raman, SERS and DFT study of 3-methyladenine and 7-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 176:1-7. [PMID: 28061366 DOI: 10.1016/j.saa.2016.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/02/2016] [Accepted: 12/13/2016] [Indexed: 05/09/2023]
Abstract
3-Methyladenine and 7-methyladenine are biomarkers of DNA damage from exposure to methylating agents. For example, the concentration of 3-methyladenine increases significantly in the urine of cigarette smokers. Surface-enhanced Raman spectroscopy (SERS) has shown much potential for detection of biomolecules, including DNA. Much work has been dedicated to the canonical nucleobases, with comparatively fewer investigations of modified DNA and modified DNA nucleobases. Herein, Raman spectroscopy and SERS are used to examine the adsorption orientations of 3-methyladenine and 7-methyladenine on Ag nanoparticles. Density functional theory (DFT) calculations at the B3LYP level are used to support the conclusions via simulated spectra of the nucleobases and of Ag+/nucleobase complexes. The results herein show that 7-methyladenine adsorbs upright via its N3 and N9 atoms side, similarly to adenine. 3-Methyladenine adsorbs in a very tilted or flat orientation on the Ag nanoparticles. These findings will be useful for future SERS or other nanoparticle-based bioanalytical assays for detection of these methyladenines or other modified nucleobases.
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Affiliation(s)
- Scott G Harroun
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Yaoting Zhang
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Tzu-Heng Chen
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Ching-Rong Ku
- De Lin Institute of Technology, 1, Lane 380, Qingyun Road, Tucheng District, New Taipei City 23654, Taiwan
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan; Department of Chemistry, Chung Yuan Christian University, Chungli District, Taoyuan City 32023, Taiwan.
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28
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Hossain T, Mahmudunnabi G, Masud MK, Islam MN, Ooi L, Konstantinov K, Hossain MSA, Martinac B, Alici G, Nguyen NT, Shiddiky MJA. Electrochemical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 94:63-73. [PMID: 28259051 DOI: 10.1016/j.bios.2017.02.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Golam Mahmudunnabi
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Mostafa Kamal Masud
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia; Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Md Nazmul Islam
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Konstantin Konstantinov
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Gursel Alici
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia.
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29
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Zhu Q, Li T, Ma Y, Wang Z, Huang J, Liu R, Gu Y. Colorimetric detection of cholic acid based on an aptamer adsorbed gold nanoprobe. RSC Adv 2017. [DOI: 10.1039/c7ra00255f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Au NPs modified with aptamers of different densities will grow into varied nanostructures with colours changing from blue to red.
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Affiliation(s)
- Qiuyun Zhu
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Tingting Li
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Yi Ma
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Zhaohui Wang
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Jinxin Huang
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Ruonan Liu
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
| | - Yueqing Gu
- Department of Biomedical Engineering
- School of Engineering
- China Pharmaceutical University
- Nanjing 210009
- China
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30
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Carnerero JM, Sánchez-Coronilla A, Martín EI, Jimenez-Ruiz A, Prado-Gotor R. Quantification of nucleobases/gold nanoparticles interactions: energetics of the interactions through apparent binding constants determination. Phys Chem Chem Phys 2017; 19:22121-22128. [DOI: 10.1039/c7cp03692b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction between AuNPs and adenine/thymine molecules is quantified by absorption spectroscopy and deconvolution methods; results are confirmed by DFT calculations.
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Affiliation(s)
- J. M. Carnerero
- Departamento de Química Física
- Facultad de Química
- Universidad de Sevilla
- Seville
- Spain
| | - A. Sánchez-Coronilla
- Departamento de Química Física
- Facultad de Química
- Universidad de Sevilla
- Seville
- Spain
| | - E. I. Martín
- Departamento de Ingeniería Química
- Facultad de Química
- Universidad de Sevilla
- Seville
- Spain
| | - A. Jimenez-Ruiz
- Departamento de Química Física
- Facultad de Química
- Universidad de Sevilla
- Seville
- Spain
| | - R. Prado-Gotor
- Departamento de Química Física
- Facultad de Química
- Universidad de Sevilla
- Seville
- Spain
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31
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Carnerero JM, Jimenez‐Ruiz A, Castillo PM, Prado‐Gotor R. Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research. Chemphyschem 2016; 18:17-33. [DOI: 10.1002/cphc.201601077] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Jose M. Carnerero
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Aila Jimenez‐Ruiz
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Paula M. Castillo
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
| | - Rafael Prado‐Gotor
- Physical Chemistry. Faculty of Chemistry University of Seville C/Profesor Garcia Gonzalez, s/n 41012 Seville Spain
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32
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Farkhari N, Abbasian S, Moshaii A, Nikkhah M. Mechanism of adsorption of single and double stranded DNA on gold and silver nanoparticles: Investigating some important parameters in bio-sensing applications. Colloids Surf B Biointerfaces 2016; 148:657-664. [PMID: 27697740 DOI: 10.1016/j.colsurfb.2016.09.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 08/24/2016] [Accepted: 09/18/2016] [Indexed: 11/29/2022]
Abstract
The mechanism of adsorption of single and double stranded DNAs on colloidal gold and silver nanoparticles has been studied by measuring the resistance of the nanoparticles, surrounded by various oligonucleotides, against salt induced aggregation. It is shown that both single and double stranded DNAs can be adsorbed on the metal nanoparticles and the adsorption strength is determined by the interaction between various bases of DNA and the nanoparticles. By changing the salt concentration, the difference between adsorption of various DNA strands on the nanoparticles can be specified. The results indicate that a key parameter in success of a sensing assay of DNA hybridization is the salt concentration which should be greater than a minimum threshold depending on the nanoparticles characteristics. We have also investigated the interaction mechanism between various DNA bases with the metal nanoparticles. For both gold and silver nanoparticles, adenine has the highest and thymine has the lowest attachment to the nanoparticles. From surface enhanced Raman spectroscopy (SERS) data of various bases in the presence of gold nanoparticles, the probable interaction points in the bases with the nanoparticles have been determined, which are mainly the nitrogen sites of these oligonucleotides.
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Affiliation(s)
- Nahid Farkhari
- Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Sara Abbasian
- Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran; School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Ahmad Moshaii
- Department of Physics, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran; School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran.
| | - Maryam Nikkhah
- Department of Nanobiotechnology, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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33
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Christian MS, Otero-de-la-Roza A, Johnson ER. Surface Adsorption from the Exchange-Hole Dipole Moment Dispersion Model. J Chem Theory Comput 2016; 12:3305-15. [PMID: 27253340 DOI: 10.1021/acs.jctc.6b00222] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accurate calculation of intermolecular interaction energies with density functional theory requires methods that include a treatment of long-range, nonlocal dispersion correlation. In this work, we explore the ability of the exchange-hole dipole moment (XDM) dispersion correction to model molecular surface adsorption. Adsorption energies are calculated for six small aromatic molecules (benzene, furan, pyridine, thiophene, thiophenol, and benzenediamine) and the four DNA nucleobases (adenine, thymine, guanine, and cytosine) on the (111) surfaces of the three coinage metals (copper, silver, and gold). For benzene, where the experimental reference data is most precise, the mean absolute error in the computed absorption energies is 0.04 eV. For the other aromatic molecules, the computed binding energies are found to be within 0.09 eV of the available reference data, on average, which is well below the expected experimental uncertainties for temperature-programmed desorption measurements. Unlike other dispersion-corrected functionals, adequate performance does not require changes to the canonical XDM implementation, and the good performance of XDM is explained in terms of the behavior of the exchange hole. Additionally, the base functional employed (B86bPBE) is also optimal for molecular studies, making B86bPBE-XDM an excellent candidate for studying chemistry on material surfaces. Finally, the noncovalent interaction (NCI) plot technique is shown to detect adsorption effects in real space on the order of tenths of an eV.
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Affiliation(s)
- Matthew S Christian
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alberto Otero-de-la-Roza
- Department of Chemistry, University of British Columbia, Okanagan , 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University , 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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34
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Nguyen VT, Lee BH, Kim SH, Gu MB. Aptamer-aptamer linkage based aptasensor for highly enhanced detection of small molecules. Biotechnol J 2016; 11:843-9. [PMID: 27221154 DOI: 10.1002/biot.201500433] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/14/2016] [Accepted: 05/04/2016] [Indexed: 11/08/2022]
Abstract
The multi-target colorimetric aptasensors can be easily fabricated by using two different aptamer sequences. However, there have been no research reports about improvement or enhancing of colorimetric signals based on the aggregation properties of AuNPs. Herein, we report a simple and efficient method to control and enhance the function of the multi-target aptasensor using an aptamer-aptamer linkage method. The aptasensor was developed for highly sensitive multiple-target detection of small molecules. The extension of aptamer DNA sequences using this method resulted in the enhanced analytical sensitivity of this aptasensor in sensing applications for two small molecule targets. Furthermore, the mechanism of the interaction between DNA aptamer and AuNPs was studied by measuring the zeta potential to explain the enhancement of the sensitivity of this multi-target aptasensor. The limit of detection of this multi-target aptasensor was found to be 1 nM and 37 nM for kanamycin (KAN) and chlortetracycline (CHLOR), respectively. It is 25-fold lower than in the previous report using an AuNP-based sensor for defining the limit of detection (LOD) of KAN and five times lower than the LOD for CHLOR. This aptasensor has great potential in the simultaneous detection of a wide range of KAN and CHLOR concentrations.
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Affiliation(s)
- Van-Thuan Nguyen
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Bang Hyun Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Sang Hoon Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea
| | - Man Bock Gu
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seongbuk-Gu, Seoul, Rep. of Korea.
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35
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Sun J, Curry D, Yuan Q, Zhang X, Liang H. Highly Hybridizable Spherical Nucleic Acids by Tandem Glutathione Treatment and Polythymine Spacing. ACS APPLIED MATERIALS & INTERFACES 2016; 8:12504-12513. [PMID: 27128167 DOI: 10.1021/acsami.6b00717] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Gold nanoparticle (AuNP)-templated spherical nucleic acids (SNAs) have been demonstrated as an important functional material in bionanotechnology. Fabrication of SNAs having high hybridization capacity to their complementary sequences is critical to ensure their applicability in areas such as antisense gene therapy and cellular sensing. The traditional salt-aging procedure is effective but tedious, requiring 1-3 days to complete. The rapid low-pH assisted protocol is efficient, but causes concerns related to nonspecific DNA adsorption to the AuNP core. To address these issues, we systematically compared the SNAs prepared by these two methods (salt-aging method and low-pH protocol). In terms of the number of complementary DNA that each SNA can bind and the average binding affinity of each thiolated DNA probe to its complementary strand, both methods yielded comparable hybridizability, although higher loading capacity was witnessed with SNAs made using the low-pH method. Additionally, it was found that nonspecific DNA binding could be eliminated almost completely by a simple glutathione (GSH) treatment of SNAs. Compared to conventional methods using toxic mercapto-hexanol or alkanethiols to remove nonspecific DNA adsorption, GSH is mild, cost-effective, and technically easy to use. In addition, GSH-passivated SNAs minimize the toxicity concerns related to AuNP-induced GSH depletion and therefore offer a more biocompatible alternative to previously reported SNAs. Moreover, rational design of probe sequences through inclusion of a polythymine spacer into the DNA sequences resulted in enhanced DNA loading capacity and stability against salt-induced aggregation. This work provides not only efficient and simple technical solutions to the issue of nonspecific DNA adsorption, but also new insights into the hybridizability of SNAs.
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Affiliation(s)
- Jing Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Dennis Curry
- Verschuren Centre for Sustainability in Energy and the Environment, Cape Breton University , 1250 Grand Lake Road, Sydney, Nova Scotia B1P 6L2, Canada
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
| | - Xu Zhang
- Verschuren Centre for Sustainability in Energy and the Environment, Cape Breton University , 1250 Grand Lake Road, Sydney, Nova Scotia B1P 6L2, Canada
| | - Hao Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing 100029, People's Republic of China
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36
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Wu Y, Lai RY. A reagentless DNA-based electrochemical silver(I) sensor for real time detection of Ag(I) - the effect of probe sequence and orientation on sensor response. Biotechnol J 2016; 11:788-96. [PMID: 26901685 DOI: 10.1002/biot.201500428] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/11/2015] [Accepted: 02/16/2016] [Indexed: 11/09/2022]
Abstract
Ag(I) is known to interact with cytosine (C) via the formation C-Ag(I)-C complexes. The authors have utilized this concept to design six electrochemical Ag(I) sensors using C-rich DNA probes. Alternating current voltammetry and cyclic voltammetry were used to analyze the sensors. The results show that the dual-probe sensors that require the use of both 5'- and 3'-thiolated DNA probes are not suitable for this application, the differences in probe orientation impedes formation of C-Ag(I)-C complexes. Sensors fabricated with DNA probes containing both thymine (T) and C, independent of the location of the alkanethiol linker, do not response to Ag(I) either; T-T mismatches destabilize the duplex even in the presence of Ag(I). However, sensors fabricated with DNA probes containing both adenine (A) and C are ideal for this application, owing to the formation of C-Ag(I)-C complexes, as well as other lesser known interactions between A and Ag(I). Both sensors are sensitive, specific and selective enough to be used in 50% human saliva. They can also be used to detect silver sulfadiazine, a commonly prescribed antimicrobial drug. With further optimization, this sensing strategy may offer a promising approach for detection of Ag(I) in environmental and clinical samples.
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Affiliation(s)
- Yao Wu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Rebecca Y Lai
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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37
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Mamián-López MB, Corio P, Temperini MLA. Cooperative hydrogen-bonding of the adenine–thymine pair as a strategy for lowering the limit of detection of thymine by surface-enhanced Raman spectroscopy. Analyst 2016; 141:3428-36. [DOI: 10.1039/c6an00222f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of cooperative hydrogen bonds between the thymine–adenine pair was used to indirectly determine thymine by SERS, improving the limit of detection values up to two orders of magnitude.
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Affiliation(s)
- Mónica B. Mamián-López
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- CEP 05508-000
- Brazil
| | - Paola Corio
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- CEP 05508-000
- Brazil
| | - Marcia L. A. Temperini
- Department of Fundamental Chemistry
- Institute of Chemistry
- University of São Paulo
- CEP 05508-000
- Brazil
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38
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Haghighi FH, Hadadzadeh H, Farrokhpour H. Investigation of the in situ generation of oxide-free copper nanoparticles using pulsed-laser ablation of bulk copper in aqueous solutions of DNA bases. RSC Adv 2016. [DOI: 10.1039/c6ra22038j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The pulsed-laser ablation method was used as a facile and green approach to prepare oxide-free copper nanoparticles, and was performed by laser ablation of a copper target in aqueous solutions of the DNA bases.
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Affiliation(s)
- Farid Hajareh Haghighi
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
- Department of Molecular Biotechnology
| | - Hassan Hadadzadeh
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | - Hossein Farrokhpour
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
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39
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Meunier A, Triffaux E, Bizzotto D, Buess-Herman C, Doneux T. In Situ Fluorescence Microscopy Study of the Interfacial Inhomogeneity of DNA Mixed Self-Assembled Monolayers at Gold Electrodes. ChemElectroChem 2015. [DOI: 10.1002/celc.201402273] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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40
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Borse S, Joshi S, Khan A. Enhanced in vitro cytotoxicity and cellular uptake of DNA bases functionalized gold nanoparticles in HeLa cell lines. RSC Adv 2015. [DOI: 10.1039/c4ra15356a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
DNA base functionalized AuNPs are internalized to a greater extent with high cellular uptake and enhanced cytotoxicity in HeLa cells.
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Affiliation(s)
- Shubhangi Borse
- Department of Chemistry
- Savitribai Phule Pune University
- Pune-411007
- India
| | - Satyawati Joshi
- Department of Chemistry
- Savitribai Phule Pune University
- Pune-411007
- India
| | - Ayesha Khan
- Department of Chemistry
- Savitribai Phule Pune University
- Pune-411007
- India
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41
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Ternary DNA chip based on a novel thymine spacer group chemistry. Colloids Surf B Biointerfaces 2015; 125:270-6. [DOI: 10.1016/j.colsurfb.2014.10.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 10/24/2014] [Accepted: 10/30/2014] [Indexed: 11/24/2022]
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42
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Distinct Adsorbed States of DNA and RNA Bases Investigated by Flocculation-Assisted Surface Enhanced Raman Scattering. E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY 2015. [DOI: 10.1380/ejssnt.2015.223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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Hung SY, Shih YC, Tseng WL. Tween 20-stabilized gold nanoparticles combined with adenosine triphosphate-BODIPY conjugates for the fluorescence detection of adenosine with more than 1000-fold selectivity. Anal Chim Acta 2014; 857:64-70. [PMID: 25604821 DOI: 10.1016/j.aca.2014.11.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/26/2014] [Accepted: 11/30/2014] [Indexed: 01/27/2023]
Abstract
This study describes the development of a simple, enzyme-free, label-free, sensitive, and selective system for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles (Tween 20-AuNPs) as an efficient fluorescence quencher for boron dipyrromethene-conjugated adenosine 5'-triphosphate (BODIPY-ATP) and as a recognition element for adenosine. BODIPY-ATP can interact with Tween 20-AuNPs through the coordination between the adenine group of BODIPY-ATP and Au atoms on the NP surface, thereby causing the fluorescence quenching of BODIPY-ATP through the nanometal surface energy transfer (NSET) effect. When adenosine attaches to the NP surface, the attached adenosine exhibits additional electrostatic attraction to BODIPY-ATP. As a result, the presence of adenosine enhances the efficiency of AuNPs in fluorescence quenching of BODIPY-ATP. The AuNP-induced fluorescence quenching of BODIPY-ATP progressively increased with an increase in the concentration of adenosine; the detection limit at a signal-to-noise ratio of 3 for adenosine was determined to be 60nM. The selectivity of the proposed system was more than 1000-fold for adenosine over any adenosine analogs and other nucleotides. The proposed system combined with a phenylboronic acid-containing column was successfully applied to the determination of adenosine in urine.
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Affiliation(s)
- Szu-Ying Hung
- Department of Chemistry, National Sun Yat-sen University, Taiwan
| | - Ya-Chen Shih
- Department of Chemistry, National Sun Yat-sen University, Taiwan
| | - Wei-Lung Tseng
- Department of Chemistry, National Sun Yat-sen University, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Taiwan; Center for Nanoscience and Nanotechnology, National Sun Yat-sen University, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Taiwan.
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44
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Sina AAI, Carrascosa LG, Palanisamy R, Rauf S, Shiddiky MJA, Trau M. Methylsorb: A Simple Method for Quantifying DNA Methylation Using DNA–Gold Affinity Interactions. Anal Chem 2014; 86:10179-85. [DOI: 10.1021/ac502214z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Abu Ali Ibn Sina
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Laura G. Carrascosa
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Ramkumar Palanisamy
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Sakandar Rauf
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Muhammad J. A. Shiddiky
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland QLD
4072, Australia
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45
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Rosa M, Corni S, Di Felice R. Enthalpy–Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface. J Chem Theory Comput 2014; 10:1707-16. [DOI: 10.1021/ct401117g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marta Rosa
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- Department
of Physics, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Stefano Corni
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Rosa Di Felice
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
- Department
of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
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46
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Koo KM, Ibn Sina AA, Carrascosa LG, Shiddiky MJA, Trau M. eMethylsorb: rapid quantification of DNA methylation in cancer cells on screen-printed gold electrodes. Analyst 2014; 139:6178-84. [DOI: 10.1039/c4an01641f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A simple, sensitive and inexpensive electrochemical method has been reported to detect regional DNA methylation by using differential adsorption affinity of DNA bases to gold.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Abu Ali Ibn Sina
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Laura G. Carrascosa
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Muhammad J. A. Shiddiky
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- , Australia
- School of Chemistry and Molecular Biosciences
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47
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Heo JH, Cho HH, Lee JH. Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing. Analyst 2014; 139:5936-44. [DOI: 10.1039/c4an01271b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.
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Affiliation(s)
- Jun Hyuk Heo
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Hui Hun Cho
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
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48
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Semyonov SA, Rudoy VM. The study of the possibility of gold hydrosol stabilization with nonthiolated homooligonucleotides with different lengths and sequences. COLLOID JOURNAL 2013. [DOI: 10.1134/s1061933x13050141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Rosa M, Corni S, Di Felice R. Interaction of Nucleic Acid Bases with the Au(111) Surface. J Chem Theory Comput 2013; 9:4552-61. [PMID: 26589170 DOI: 10.1021/ct4002416] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The fate of an individual DNA molecule when it is deposited on a hard inorganic surface in a "dry" environment is unknown, while it is a crucial determinant for nanotechnology applications of nucleic acids. In the absence of experimental approaches that are able to unravel the three-dimensional atomic structure of the target system, here we tackle the first step toward a computational solution of the problem. By using first-principles quantum mechanical calculations of the four nucleobases on the Au(111) surface, we present results for the geometries, energetics, and electronic structure, in view of developing a force field that will enable classical simulations of DNA on Au(111) to investigate the structural modifications of the duplex in these non-native conditions. We fully characterize each system at the individual level. We find that van der Waals interactions are crucial for a correct description of the geometry and energetics. However, the mechanism of adsorption is well beyond pure dispersion interactions. Indeed, we find charge sharing between the substrate and the adsorbate, the formation of hybrid orbitals, and even bonding orbitals. Yet, this molecule-surface association is qualitatively distinct from the thiol adsorption mechanism: we discuss such differences and also the relation to the adsorption mechanism of pure aromatic molecules.
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Affiliation(s)
- Marta Rosa
- Center S3, CNR Institute of Nanoscience , Via Campi 213/A, 41125 Modena, Italy.,Department of Physics, University of Modena and Reggio Emilia , 41125 Modena, Italy
| | - Stefano Corni
- Center S3, CNR Institute of Nanoscience , Via Campi 213/A, 41125 Modena, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience , Via Campi 213/A, 41125 Modena, Italy
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50
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Yang X, Li J, Pei H, Li D, Zhao Y, Gao J, Lu J, Shi J, Fan C, Huang Q. Pattern recognition analysis of proteins using DNA-decorated catalytic gold nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2844-9. [PMID: 23447503 DOI: 10.1002/smll.201202772] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 12/28/2012] [Indexed: 05/23/2023]
Abstract
A label-free protein analysis strategy is based on patterns of gold nanoparticle (AuNP) growth. AuNPs pretreated with different oligonucleotides are challenged with various proteins. After Au reduction, the colorimetric patterns are processed with linear discriminant analysis. This method discriminates different proteins, or one protein of different concentrations, in mixed samples or even serum and urine.
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Affiliation(s)
- Xiafeng Yang
- College of Life Sciences, Sichuan University, Chengdu 610064, China; Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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