1
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Bag S, Ghosal S, Mukherjee M, Pramanik G, Bhowmik S. Quercetin Exhibits Preferential Binding Interaction by Selectively Targeting HRAS1 I-Motif DNA-Forming Promoter Sequences. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10157-10170. [PMID: 38700902 DOI: 10.1021/acs.langmuir.4c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
I-Motif (iM) DNA structures represent among the most significant noncanonical nucleic acid configurations. iM-forming DNA sequences are found in an array of vital genomic locations and are particularly frequent in the promoter islands of various oncogenes. Thus, iM DNA is a crucial candidate for anticancer medicines; therefore, binding interactions between iM DNA and small molecular ligands, such as flavonoids, are critically important. Extensive sets of spectroscopic strategies and thermodynamic analysis were utilized in the present investigation to find out the favorable interaction of quercetin (Que), a dietary flavonoid that has various health-promoting characteristics, including anticancer properties, with noncanonical iM DNA structure. Spectroscopic studies and thermal analysis revealed that Que interacts preferentially with HRAS1 iM DNA compared with VEGF, BCL2 iM, and duplex DNA. Que, therefore, emerged as a suitable natural-product-oriented antagonist for targeting HRAS1 iM DNA. The innovative spectroscopic as well as mechanical features of Que and its specific affinity for HRAS1 iM may be useful for therapeutic applications and provide crucial insights for the design of compounds with remarkable medicinal properties.
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Affiliation(s)
- Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
| | - Moupriya Mukherjee
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Goutam Pramanik
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata 700 106, India
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry 607402, India
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2
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Hirao G, Fukuzumi N, Ogawa A, Asahi T, Mizuo M, Zako T. Effect of DNA density immobilized on gold nanoparticles on nucleic acid detection. RSC Adv 2023; 13:30690-30695. [PMID: 37869395 PMCID: PMC10585452 DOI: 10.1039/d3ra06528f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Gold nanoparticles (AuNPs) have been utilized as colorimetric biosensors, where target molecule-induced AuNP aggregation can be recognized by a colour change from red to blue. Particularly, single-stranded DNA (ssDNA)-immobilized AuNPs (ssDNA-AuNPs) have been applied to genetic diagnosis due to their rapid and sequence-specific aggregation properties. However, the effect of the density of immobilized ssDNA have not been investigated yet. In this study, we developed a method to control the amount of immobilized ssDNA by use of ethylene glycol, which is expected to control the ice crystal spacing in a freezing-thawing ssDNA-AuNP synthesis method. We also investigated the effect of the DNA density on the sensitivity of the target ssDNA detection, and found that the detection sensitivity was improved at lower DNA densities. To discuss the reason for the improved detection sensitivity, we modified the ssDNA-AuNPs with alkane thiol for better dispersion stability against salt. The results suggest that the DNA density, rather than the dispersion stability, has a significant impact on detection sensitivity.
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Affiliation(s)
- Gen Hirao
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Nanami Fukuzumi
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Tsuyoshi Asahi
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
| | - Maeda Mizuo
- RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Tamotsu Zako
- Department of Chemistry and Biology, Graduate School of Science and Engineering, Ehime University 2-5 Bunkyo Matsuyama Ehime 790-8577 Japan
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3
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Kodikara S, Gyawali P, Gleeson JT, Jakli A, Sprunt S, Balci H. Stability of End-to-End Base Stacking Interactions in Highly Concentrated DNA Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4838-4846. [PMID: 36952670 PMCID: PMC10078606 DOI: 10.1021/acs.langmuir.3c00318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Positionally ordered bilayer liquid crystalline nanostructures formed by gapped DNA (GDNA) constructs provide a practical window into DNA-DNA interactions at physiologically relevant DNA concentrations; concentrations several orders of magnitude greater than those in commonly used biophysical assays. The bilayer structure of these states of matter is stabilized by end-to-end base stacking interactions; moreover, such interactions also promote in-plane positional ordering of duplexes that are separated from each other by less than twice the duplex diameter. The end-to-end stacked as well as in-plane ordered duplexes exhibit distinct signatures when studied via small-angle X-ray scattering (SAXS). This enables analysis of the thermal stability of both the end-to-end and side-by-side interactions. We performed synchrotron SAXS experiments over a temperature range of 5-65 °C on GDNA constructs that differ only by the terminal base-pairs at the blunt duplex ends, resulting in identical side-by-side interactions, while end-to-end base stacking interactions are varied. Our key finding is that bilayers formed by constructs with GC termination transition into the monolayer state at temperatures as much as 30 °C higher than for those with AT termination, while mixed (AT/GC) terminations have intermediate stability. By modeling the bilayer melting in terms of a temperature-dependent reduction in the average fraction of end-to-end paired duplexes, we estimate the stacking free energies in DNA solutions of physiologically relevant concentrations. The free-energies thereby determined are generally smaller than those reported in single-molecule studies, which might reflect the elevated DNA concentrations in our studies.
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Affiliation(s)
- Sineth
G. Kodikara
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Prabesh Gyawali
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - James T. Gleeson
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
| | - Antal Jakli
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Samuel Sprunt
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
- Advanced
Materials and Liquid Crystals Institute, Kent State University, Kent, Ohio 44242, United States
| | - Hamza Balci
- Department
of Physics, Kent State University, Kent, Ohio 44242, United States
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4
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He Z, Chen Q, Ding S, Wang G, Takarada T, Maeda M. Suppressed DNA base pair stacking assembly of gold nanoparticles in an alcoholic solvent for enhanced ochratoxin A detection in Baijiu. Analyst 2023; 148:1291-1299. [PMID: 36846974 DOI: 10.1039/d3an00016h] [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: 02/15/2023]
Abstract
The currently established DNA nanoprobes for the detection of mycotoxin from beverages have been limited by complicated sample pretreatment and uncontrollable nanoparticle flocculation in complex systems. We develop a rapid colorimetric approach for ochratoxin A (OTA) detection in Baijiu in a sample-in/"yes" or "no" answer-out fashion through target-modulated base pair stacking assembly of DNA-functionalized gold nanoparticles (DNA-AuNPs). The colorimetric signification of OTA relies on the competition of OTA with the AuNP surface-grafted DNA in binding with an OTA-targeted aptamer. The specific recognition of OTA by the aptamer prevents DNA duplex formation on the AuNP surface, thereby inhibiting the base pair stacking assembly of the DNA-AuNPs and giving rise to a "turn-on" color. By further suppressing DNA hybridization using a bulged loop design and an alcohol solution, the DNA-AuNPs exhibit an improved reproducibility for OTA sensing while maintaining excellent susceptivity to OTA. A detection limit of 88 nM was achieved along with high specificity towards OTA, which is lower than the maximum tolerated level of OTA in foodstuffs defined by countries worldwide. The entire reaction time, avoiding sample pretreatment, is less than 17 min. The DNA-AuNPs with anti-interference features and sensitive "turn-on" performance promise convenient on-site detection of mycotoxin from daily beverages.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Qianyuan Chen
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Shansen Ding
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Tohru Takarada
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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5
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Hori K, Yoshimoto S, Yoshino T, Zako T, Hirao G, Fujita S, Nakamura C, Yamagishi A, Kamiya N. Recent advances in research on biointerfaces: From cell surfaces to artificial interfaces. J Biosci Bioeng 2022; 133:195-207. [PMID: 34998688 DOI: 10.1016/j.jbiosc.2021.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/16/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Biointerfaces are regions where biomolecules, cells, and organic materials are exposed to environmental media or come in contact with other biomaterials, cells, and inorganic/organic materials. In this review article, six research topics on biointerfaces are described to show examples of state-of-art research approaches. First, biointerface design of nanoparticles for molecular detection is described. Functionalized gold nanoparticles can be used for sensitive detection of various target molecules, including chemical compounds and biomolecules, such as DNA, proteins, cells, and viruses. Second, the interaction between bacterial cell surfaces and material surfaces, including the introduction of advances in analytical methods and theoretical calculations, are explained as well as their applications to bioprocesses. Third, bioconjugation technologies for localizing functional proteins at biointerfaces are introduced, in particular, by focusing the potential of enzymes as a catalytic tool for designing different types of bioconjugates that function at biointerfaces. Forth topics is focusing on lipid-protein interaction in cell membranes as natural biointerfaces. Examples of membrane lipid engineering are introduced, and it is mentioned how their compositional profiles affect membrane protein functions. Fifth topic is the physical method for molecular delivery across the biointerface being developed currently, such as highly efficient nanoinjection, electroporation, and nanoneedle devices, in which the key is how to perforate the cell membrane. Final topic is the chemical design of lipid- or polymer-based RNA delivery carriers and their behavior on the cell interface, which are currently attracting attention as RNA vaccine technologies targeting COVID-19. Finally, future directions of biointerface studies are presented.
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Affiliation(s)
- Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan.
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Tamotsu Zako
- Faculty of Science, Ehime University, 2-5 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Gen Hirao
- Faculty of Science, Ehime University, 2-5 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Satoshi Fujita
- Photo BIO-OIL, National Institute of Advanced Industrial Science and Technology, Suita, Osaka 565-0871, Japan; Department of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Chikashi Nakamura
- DAILAB, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan; Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ayana Yamagishi
- DAILAB, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan; Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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6
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Grupa U, Liebl K, Zacharias M. Orientation Dependence of DNA Blunt-End Stacking Studied by Free-Energy Simulations. J Phys Chem B 2021; 125:13850-13857. [PMID: 34928161 DOI: 10.1021/acs.jpcb.1c07829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA blunt ends can associate mediated by stacking interactions between the terminal base pairs that form blunt ends. The blunt end association plays a role in DNA repair and recombination processes and can also be of importance for the design of DNA-based nano-materials. Its function depends on the sequence and on the geometric arrangement that leads to stable interaction. For a stacked state, the relative orientation (twisting) of the base pairs is important. Molecular dynamics and advanced sampling simulations were used to calculate free energy change associated with twist changes of the stacked blunt-end base pairs. The calculations reproduce blunt stacking arrangements found in crystal structures of DNA oligonucleotides as free energy minima. To elucidate the physical origin of the stabilization of certain angular arrangements, the interactions between backbone atoms in the blunt-end stack were switched off in additional free energy calculations. It allows us to decipher the contributions to stacking stabilization due to the nucleobases and the backbone and to analyze the sequence dependence of the angular stacking preferences. Good qualitative agreement was also found for the comparison with quantum mechanical calculations. The results may help in the design of novel DNA-based materials.
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Affiliation(s)
- Ulrich Grupa
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Korbinian Liebl
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies and Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
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7
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Chang R, Quimada Mondarte EA, Palai D, Sekine T, Kashiwazaki A, Murakami D, Tanaka M, Hayashi T. Protein- and Cell-Resistance of Zwitterionic Peptide-Based Self-Assembled Monolayers: Anti-Biofouling Tests and Surface Force Analysis. Front Chem 2021; 9:748017. [PMID: 34692644 PMCID: PMC8527039 DOI: 10.3389/fchem.2021.748017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/15/2021] [Indexed: 11/13/2022] Open
Abstract
Peptide-based self-assembled monolayers (peptide-SAMs) with specific zwitterionic amino acid sequences express an anti-biofouling property. In this work, we performed protein adsorption and cell adhesion tests using peptide-SAMs with repeating units of various zwitterionic pairs of amino acids (EK, DK, ER, and DR). The SAMs with the repeating units of EK and DK (EK and DK SAMs) manifested excellent bioinertness, whereas the SAMs with the repeating units of ER and DR (ER and DR SAMs) adhered proteins and cells. We also performed surface force measurements using atomic force microscopy to elucidate the mechanism underlying the difference in the anti-biofouling property. Our measurements revealed that water-induced repulsion with a range of about 8 nm acts between EK SAMs (immobilized on both probe and substrate) and DK SAMs, whereas such repulsion was not observed for ER and DR SAMs. The strength of the repulsion exhibited a clear correlation with the protein- and cell-resistance of the SAMs, indicating that the interfacial water in the vicinity of EK and DK SAMs is considered as a physical barrier to deter protein and cells from their adsorption or adhesion. The range of the repulsion observed for EK and DK SAMs is longer than 8 nm, indicating that the hydrogen bonding state of the interfacial water with a thickness of 4 nm is modified by EK and DK SAMs, resulting in the expression of the anti-biofouling property.
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Affiliation(s)
- Ryongsok Chang
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Evan Angelo Quimada Mondarte
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Debabrata Palai
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Taito Sekine
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Aki Kashiwazaki
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan
| | - Daiki Murakami
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan
| | - Masaru Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, Japan.,Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Fukuoka, Japan
| | - Tomohiro Hayashi
- Department of Material Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, Yokohama, Japan.,JST-PRESTO, Saitama, Japan.,The Institute for Solid State Physics, the University of Tokyo, Chiba, Japan
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8
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Cheng L, Wang L, He Z, Sun X, Li Y, Wang G, Tian Y, Takarada T, Maeda M, Liang X. Plasmon switching of gold nanoparticles through thermo-responsive terminal breathing of surface-grafted DNA in hydrated ionic liquids. Analyst 2021; 146:4154-4160. [PMID: 33977966 DOI: 10.1039/d1an00548k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly performed in ionic liquids (ILs) as a unique solvent promises distinct functions and applications in sensors, therapeutics, and optoelectronic devices due to the rich interactions between nanoparticle building blocks and ILs. However, the general consideration that common nanoparticles are readily destabilized by counterions in an IL has largely prevented researchers from investigating controlled nanoparticle assembly in IL-based systems. This study explores the assembling behaviour of double-stranded (ds) DNA-functionalized gold nanoparticles (dsDNA-AuNPs) in hydrated ionic liquids. The DNA base pair stacking assembly of dsDNA-AuNPs occurs at a low IL concentration (<5%). However, a moderate ionic liquid concentration (5-40%) can de-hybridize dsDNA and leaves single-stranded (ss) DNA stabilizing the AuNPs. In concentrated ionic liquids (>40%), interestingly, the higher ionic strength leads to the assembly of DNA-AuNPs. The triphasic assembly trend is also generally observed regardless of the type of IL. By down-regulation of DNA's melting temperature with the IL, the assembly of DNA-AuNPs affords robust response to a lower temperature range, promising applications in plasmonic devices and range-tunable temperature sensors.
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Affiliation(s)
- Lu Cheng
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Luyang Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Zhiyu He
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Xun Sun
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Yujin Li
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China. and Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Yongshuai Tian
- Qingdao Hightop Biotech Co., Ltd, 369 Hedong Road, High-Tech Industrial Development Zone, Qingdao 266111, China
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China. and Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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9
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Affiliation(s)
- Tomohiro Hayashi
- Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- JST-PRESTO (Materials Informatics), 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
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10
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Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes. Proc Natl Acad Sci U S A 2021; 118:2019996118. [PMID: 33731478 DOI: 10.1073/pnas.2019996118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline behavior. End-to-end interactions between concentrated, ultrashort DNA duplexes-driving the self-assembly of aggregates that organize into liquid crystal phases-and the incorporation of flexible single-stranded "gaps" in otherwise fully paired duplexes-producing clear evidence of an elementary lamellar (smectic-A) phase in DNA solutions-are two exciting developments that have opened avenues for discovery. Here, we report on a wider investigation of the nature and temperature dependence of smectic ordering in concentrated solutions of various "gapped" DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48-base pair duplex segments bridged by a single-stranded sequence of 2 to 20 thymine bases. Two distinct smectic layer structures are observed for DNA concentration in the range [Formula: see text] mg/mL. One exhibits an interlayer periodicity comparable with two-duplex lengths ("bilayer" structure), and the other has a period similar to a single-duplex length ("monolayer" structure). The bilayer structure is observed for gap length ≳10 bases and melts into the cholesteric phase at a temperature between 30 °C and 35 °C. The monolayer structure predominates for gap length ≲10 bases and persists to [Formula: see text]C. We discuss models for the two layer structures and mechanisms for their stability. We also report results for asymmetric gapped constructs and for constructs with terminal overhangs, which further support the model layer structures.
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11
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He Z, Wang G, Liang X, Takarada T, Maeda M. DNA Base Pair Stacking Assembly of Anisotropic Nanoparticles for Biosensing and Ordered Assembly. ANAL SCI 2020; 37:415-423. [PMID: 33071270 DOI: 10.2116/analsci.20scr02] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Anisotropic gold nanoparticles have attracted great interest due to their unique physicochemical properties derived from the shape anisotropy. Manipulation of their interfacial interactions, and thereby the assembling behaviors are often requisite in their applications ranging from optical sensing and diagnosis to self-assembly. Recently, the control of interfacial force based on base pair stacking of DNA terminals have offered a new avenue to surface engineering of nanostructures. In this review, we focus on the DNA base stacking-induced assembly of anisotropic gold nanoparticles, such as nanorods and nanotriangles. The fundamental aspects of anisotropic gold nanoparticles are provided, including the mechanism of the anisotropic growth, the properties arising from the anisotropic shape, and the construction of DNA-grafted anisotropic gold nanoparticles. Then, the advanced applications of their functional assemblies in biosensing and ordered assembly are summarized, followed by a comparison with gold nanospheres. Finally, conclusions and the direction of outlooks are given including future challenges and opportunities in this field.
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Affiliation(s)
- Zhiyu He
- College of Food Science and Engineering, Ocean University of China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China.,Bioengineering Laboratory, RIKEN Cluster for Pioneering Research.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao)
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao)
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
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12
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Diao W, Wang G, Wang L, Zhang L, Ding S, Takarada T, Maeda M, Liang X. Opposite Effects of Flexible Single-Stranded DNA Regions and Rigid Loops in DNAzyme on Colloidal Nanoparticle Stability for “Turn-On” Plasmonic Detection of Lead Ions. ACS APPLIED BIO MATERIALS 2020; 3:7003-7010. [DOI: 10.1021/acsabm.0c00873] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Wenhui Diao
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Guoqing Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Luyang Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Lan Zhang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Shansen Ding
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Tohru Takarada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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13
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Kwaria RJ, Mondarte EAQ, Tahara H, Chang R, Hayashi T. Data-Driven Prediction of Protein Adsorption on Self-Assembled Monolayers toward Material Screening and Design. ACS Biomater Sci Eng 2020; 6:4949-4956. [DOI: 10.1021/acsbiomaterials.0c01008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Rudolf Jason Kwaria
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Evan Angelo Quimada Mondarte
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Hiroyuki Tahara
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Ryongsok Chang
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8502, Japan
- Japan Science and Technology Agency-Precursory Research for Embryonic Science and Technology (JST-PRESTO), 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
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14
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Wang L, Wang G, Shi Y, Zhang L, An R, Takarada T, Maeda M, Liang X. Accelerated non-crosslinking assembly of DNA-functionalized nanoparticles in alcoholic solvents: for application in the identification of clear liquors. Analyst 2020; 145:3229-3235. [PMID: 32191236 DOI: 10.1039/d0an00029a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Colorimetric detection of various target molecules in aqueous solutions based on the non-crosslinking assembly of DNA-functionalized Au nanoparticles (DNA-AuNPs) has been well established in recent years. The extension of DNA-AuNPs to other solvents remains much less explored, despite the practical importance of detection in non-aqueous solutions, such as those containing an organic ingredient that is required or not removable in many contexts. However, the general consideration that DNA is easily denatured and precipitated in organic solvents has been hampering the use of DNA-AuNPs in low polar solvents. Herein, we report a more rapid non-crosslinking assembly of double-stranded (ds) DNA-AuNPs in alcoholic solvents than in aqueous solvents. When the concentration of ethanol in the disperse medium is increased from 0% to 20% (v/v), the rate of non-crosslinking assembly is distinctly increased by a factor of 5-6, whereas the rate is sharply decreased when the ethanol concentration is further increased to 40%. This biphasic kinetics trend could be attributed to the competitive balance between the enhanced intermolecular attraction between dsDNAs and the increased propensity for melting of dsDNA. Rapid naked-eye identification of clear liquors that are encoded by oligonucleotide additives has also been demonstrated by using the alcoholic non-crosslinking assembly of dsDNA-AuNPs as a proof-of-concept.
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Affiliation(s)
- Luyang Wang
- College of Food Science and Engineering, Ocean University of China, 5 Yushan Road, Qingdao 266003, China.
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15
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Sato K, Hosokawa K, Maeda M. Characterizing the non-crosslinked aggregation of DNA-modified gold nanoparticles: effects of DNA length and terminal base pair. Analyst 2020; 144:5580-5588. [PMID: 31418003 DOI: 10.1039/c9an00822e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We previously reported that fully complementary DNA duplexes formed on gold nanoparticle (GNP) surfaces aggregate at high salt concentrations. We previously reported that DNA-functionalized gold nanoparticles (GNPs) aggregate by hybridization with fully complementary DNA at high salt concentrations. Although this behavior has been applied to some precise naked-eye colorimetric analyses of DNA-related molecules, the aggregation mechanism is still unclear and comprehensive studies are needed. In this paper, we reveal the key factors that influence GNP aggregation. The effects of temperature, electrolyte concentration, probe length, and particle size, which control the stabilities of double-stranded DNAs and GNPs, were investigated. Larger GNPs aggregated more easily, and GNP aggregates were easily formed with ∼15-mer-long probes, while longer probes prevented aggregation, perhaps by preventing the formation of rigid double-stranded DNA layers, compared to shorter probes. Furthermore, GNPs with purine bases at their 5' ends aggregated more easily than those with these bases at their 3' ends. This phenomenon is different from that based on the melting-temperature trend calculated using the nearest-neighbor method.
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Affiliation(s)
- Kae Sato
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo, Tokyo 112-8681, Japan.
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Chang CC, Chen CP, Wu TH, Yang CH, Lin CW, Chen CY. Gold Nanoparticle-Based Colorimetric Strategies for Chemical and Biological Sensing Applications. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E861. [PMID: 31174348 PMCID: PMC6631916 DOI: 10.3390/nano9060861] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/31/2019] [Accepted: 06/03/2019] [Indexed: 12/18/2022]
Abstract
Gold nanoparticles are popularly used in biological and chemical sensors and their applications owing to their fascinating chemical, optical, and catalytic properties. Particularly, the use of gold nanoparticles is widespread in colorimetric assays because of their simple, cost-effective fabrication, and ease of use. More importantly, the gold nanoparticle sensor response is a visual change in color, which allows easy interpretation of results. Therefore, many studies of gold nanoparticle-based colorimetric methods have been reported, and some review articles published over the past years. Most reviews focus exclusively on a single gold nanoparticle-based colorimetric technique for one analyte of interest. In this review, we focus on the current developments in different colorimetric assay designs for the sensing of various chemical and biological samples. We summarize and classify the sensing strategies and mechanism analyses of gold nanoparticle-based detection. Additionally, typical examples of recently developed gold nanoparticle-based colorimetric methods and their applications in the detection of various analytes are presented and discussed comprehensively.
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Affiliation(s)
- Chia-Chen Chang
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 310, Taiwan.
| | - Chie-Pein Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei 104, Taiwan.
| | - Tzu-Heng Wu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan.
| | - Ching-Hsu Yang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan.
| | - Chii-Wann Lin
- Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu 310, Taiwan.
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 106, Taiwan.
- Department of Biomedical Engineering, National Taiwan University, Taipei 106, Taiwan.
| | - Chen-Yu Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei 104, Taiwan.
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