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Panigrahy S, Nayar D. Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle. J Chem Phys 2024; 160:014901. [PMID: 38165098 DOI: 10.1063/5.0179238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024] Open
Abstract
Understanding the influence of a crowded intracellular environment on the structure and solvation of DNA functionalized gold nanoparticles (ss-DNA AuNP) is necessary for designing applications in nanomedicine. In this study, the effect of single (Gly, Ser, Lys) and mixture of amino acids (Gly+Ser, Gly+Lys, Ser+Lys) at crowded concentrations is examined on the structure of the ss-DNA AuNP using molecular dynamics simulations. Using the structural estimators such as pair correlation functions and ligand shell positional fluctuations, the solvation entropy is estimated. Combining the AuNP-solvent interaction energy with the solvation entropy estimates, the free energy of solvation of the AuNP in crowded solutions is computed. The solvation entropy favours the solvation free energy which becomes more favourable for larger effective size of AuNP in crowded solutions relative to that in water. The effective size of AuNP depends on the different propensity of the crowders to adsorb on Au surface, with the smallest crowder (Gly) having the highest propensity inducing the least effective AuNP size as compared to other single crowder solutions. In mixed crowded solutions of amino acids of variable size and chemistry, distinctive local adsorption of the crowders on the gold surface is observed that controls the additive or non-additive crowding effects which govern an increase (in Gly+Ser) or decrease (in Gly+Lys) in nanoparticle effective size respectively. The results shed light into the fundamental understanding of the influence of intracellular crowding on structure of ss-DNA AuNP and plausible employability of crowding as a tool to design programmable self-assembly of functionalized nanoparticles.
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Affiliation(s)
- Sibasankar Panigrahy
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Divya Nayar
- Department of Materials Science and Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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2
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Singh A, Maity A, Singh N. Structure and Dynamics of dsDNA in Cell-like Environments. ENTROPY (BASEL, SWITZERLAND) 2022; 24:1587. [PMID: 36359677 PMCID: PMC9689892 DOI: 10.3390/e24111587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 06/01/2023]
Abstract
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA's structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
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3
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Kim HJ, Wang W, Mallapragada SK, Vaknin D. The Effects of Temperature on the Assembly of Gold Nanoparticle by Interpolymer Complexation. J Phys Chem Lett 2021; 12:1461-1467. [PMID: 33528263 DOI: 10.1021/acs.jpclett.0c03749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Using synchrotron-based small-angle X-ray scattering techniques, we demonstrate that poly(ethylene glycol)-functionalized gold nanoparticles (PEG-AuNPs) are assembled into close-packed structures that include short-range order with face-centered cubic structure, where crystalline qualities are varied by controlling the electrolyte concentration, pH, and temperature of the suspensions. We show that interpolymer complexation with poly(acrylic acid) (PAA) is induced by lowering the pH level of the PEG-AuNPs suspensions, and furthermore, increasing the temperature of the suspension strengthens interparticle attraction, leading to improved supercrystal structures. Our results indicate that this strategy creates robust nanoparticle superlattices with high thermal stability. The effects of PAA and PEG chain lengths on the assemblies are also investigated, and their optimal conditions for creating improved superlattices are discussed.
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Affiliation(s)
- Hyeong Jin Kim
- Ames Laboratory and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Wenjie Wang
- Division of Materials Sciences and Engineering, Ames Laboratory, U.S. DOE, Ames, Iowa 50011, United States
| | - Surya K Mallapragada
- Ames Laboratory and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - David Vaknin
- Ames Laboratory and Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, United States
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4
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Cho SY, Han JH, Jang YJ, Kim SK, Lee YA. Binding Properties of Various Cationic Porphyrins to DNA in the Molecular Crowding Condition Induced by Poly(ethylene glycol). ACS OMEGA 2020; 5:10459-10465. [PMID: 32426603 PMCID: PMC7226857 DOI: 10.1021/acsomega.0c00471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/23/2020] [Indexed: 05/08/2023]
Abstract
The binding modes of various cationic porphyrins to DNA in an aqueous solution and under the molecular crowding condition induced by poly(ethylene glycol) (PEG) were compared by normal absorption, circular dichroism (CD), and linear dichroism (LD) spectroscopy techniques. Large negative CD and LD signals in the Soret absorption regions of the meta- and para-TMPyP [meso-tetrakis (n-N-methylpyridiniumyl) porphyrin (meta, n = 3) and (para, n = 4)] were apparent in the aqueous solution, indicating an intercalative-binding mode, while a positive CD spectrum and a less intense negative LD spectrum for the ortho-TMPyP (n = 2)-complexed DNA suggested a major-groove-binding mode. These binding modes are retained under a molecular crowding condition, suggesting that the PEG cluster cannot access the TMPyPs that are intercalated between the DNA base pairs or that bind at the major groove. The spectral properties of the ortho-, meta-, and para-trans-BMPyP [trans-bis(N-methylpyrodinium-n-yl)diphenyl porphyrin, n = 2,3,4]-bound DNA in an aqueous solution correspond to neither the intercalative-binding nor the groove-binding mode, which is in contrast with the TMPyP cases. The spectral properties under the molecular crowding condition are altered considerably for all of the three trans-BMPyPs compared to those in an aqueous solution, suggesting that the matted PEG cluster is in contact with the cationic trans-BMPyPs, causing a change in the polarity of the porphyrin environment. Consequently, trans-BMPyPs bind to the external side of the DNA.
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Affiliation(s)
- Su Yeon Cho
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Ji Hoon Han
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yoon Jung Jang
- College
of Basis Education, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
| | - Seog K. Kim
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
- ,
| | - Young-Ae Lee
- Department
of Chemistry, Yeungnam University, Gyeongsan, Gyeong-buk 38541, Republic of Korea
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5
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Hata Y, Sawada T, Serizawa T. Macromolecular crowding for materials-directed controlled self-assembly. J Mater Chem B 2018; 6:6344-6359. [PMID: 32254643 DOI: 10.1039/c8tb02201a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Macromolecular crowding refers to intracellular environments where various macromolecules, including proteins and nucleic acids, are present at high total concentrations. Its influence on biological processes has been investigated using a highly concentrated in vitro solution of water-soluble polymers as a model. Studies have revealed significant effects of macromolecular crowding on the thermodynamic equilibria and dynamics of biomolecular self-assembly in vivo. Recently, macromolecular crowding has attracted materials scientists, especially those in bio-related areas, as a tool to control molecular/colloidal self-assembly. Macromolecular crowding has been exploited to control the structure of supramolecular materials, assemble nanomaterials, and improve the performance of polymeric materials. Furthermore, nanostructured materials have been shown to be an interesting alternative to water-soluble polymers for creating crowded environments for controlled self-assembly. In this review article, we summarize recent progress in research on macromolecular crowding for controlled self-assembly in bio-related materials chemistry.
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Affiliation(s)
- Yuuki Hata
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 2-12-1-H121 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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6
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Singh A, Singh N. DNA melting in the presence of molecular crowders. Phys Chem Chem Phys 2017; 19:19452-19460. [DOI: 10.1039/c7cp03624h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We study the opening of double stranded DNA (dsDNA) in the presence of molecular crowders using the Peyrard–Bishop–Dauxois (PBD) model.
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Affiliation(s)
- Amar Singh
- Department of Physics
- BITS Pilani
- Pilani Campus
- India
| | - Navin Singh
- Department of Physics
- BITS Pilani
- Pilani Campus
- India
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7
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Wang G, Akiyama Y, Shiraishi S, Kanayama N, Takarada T, Maeda M. Cross-Linking versus Non-Cross-Linking Aggregation of Gold Nanoparticles Induced by DNA Hybridization: A Comparison of the Rapidity of Solution Color Change. Bioconjug Chem 2016; 28:270-277. [DOI: 10.1021/acs.bioconjchem.6b00410] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Guoqing Wang
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoshitsugu Akiyama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shota Shiraishi
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Kanayama
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tohru Takarada
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mizuo Maeda
- Bioengineering
Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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8
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Zinchenko A. DNA conformational behavior and compaction in biomimetic systems: Toward better understanding of DNA packaging in cell. Adv Colloid Interface Sci 2016; 232:70-79. [PMID: 26976700 DOI: 10.1016/j.cis.2016.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/05/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
In a living cell, long genomic DNA is strongly compacted and exists in the environment characterized by a dense macromolecular crowding, high concentrations of mono- and divalent cations, and confinement of ca. 10μm size surrounded by a phospholipid membrane. Experimental modelling of such complex biological system is challenging but important to understand spatiotemporal dynamics and functions of the DNA in cell. The accumulated knowledge about DNA condensation/compaction in conditions resembling those in the real cell can be eventually used to design and construct partly functional "artificial cells" having potential applications in drug delivery systems, gene therapy, and production of synthetic cells. In this review, I would like to overview the past progress in our understanding of the DNA conformational behavior and, in particular, DNA condensation/compaction phenomenon and its relation to the DNA biological activity. This understanding was gained by designing relevant experimental models mimicking DNA behavior in the environment of living cell. Starting with a brief summary of classic experimental systems to study DNA condensation/compaction, in later parts, I highlight recent experimental methodologies to address the effects of macromolecular crowding and nanoscale and microscale confinements on DNA conformation dynamics. All the studies are discussed in the light of their relevance to DNA behavior in living cells, and future prospects of the field are outlined.
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9
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Chapman CD, Gorczyca S, Robertson-Anderson RM. Crowding induces complex ergodic diffusion and dynamic elongation of large DNA molecules. Biophys J 2016; 108:1220-8. [PMID: 25762333 DOI: 10.1016/j.bpj.2015.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 01/15/2023] Open
Abstract
Despite the ubiquity of molecular crowding in living cells, the effects of crowding on the dynamics of genome-sized DNA are poorly understood. Here, we track single, fluorescent-labeled large DNA molecules (11, 115 kbp) diffusing in dextran solutions that mimic intracellular crowding conditions (0-40%), and determine the effects of crowding on both DNA mobility and conformation. Both DNAs exhibit ergodic Brownian motion and comparable mobility reduction in all conditions; however, crowder size (10 vs. 500 kDa) plays a critical role in the underlying diffusive mechanisms and dependence on crowder concentration. Surprisingly, in 10-kDa dextran, crowder influence saturates at ∼20% with an ∼5× drop in DNA diffusion, in stark contrast to exponentially retarded mobility, coupled to weak anomalous subdiffusion, with increasing concentration of 500-kDa dextran. Both DNAs elongate into lower-entropy states (compared to random coil conformations) when crowded, with elongation states that are gamma distributed and fluctuate in time. However, the broadness of the distribution of states and the time-dependence and length scale of elongation length fluctuations depend on both DNA and crowder size with concentration having surprisingly little impact. Results collectively show that mobility reduction and coil elongation of large crowded DNAs are due to a complex interplay between entropic effects and crowder mobility. Although elongation and initial mobility retardation are driven by depletion interactions, subdiffusive dynamics, and the drastic exponential slowing of DNA, up to ∼300×, arise from the reduced mobility of larger crowders. Our results elucidate the highly important and widely debated effects of cellular crowding on genome-sized DNA.
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Affiliation(s)
- Cole D Chapman
- Department of Physics, University of California San Diego, La Jolla, California
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10
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Li H, Wang Z, Li N, He X, Liang H. Denaturation and renaturation behaviors of short DNA in a confined space. J Chem Phys 2014; 141:044911. [DOI: 10.1063/1.4891219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Huaping Li
- Department of Polymer Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, School of Science, Tianjin University, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Zilu Wang
- Department of Polymer Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, School of Science, Tianjin University, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Ningning Li
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Xuehao He
- Department of Chemistry, School of Science, Tianjin University, and Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Haojun Liang
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei 230026, China
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11
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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12
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Tan SJ, Kahn JS, Derrien TL, Campolongo MJ, Zhao M, Smilgies DM, Luo D. Crystallization of DNA-Capped Gold Nanoparticles in High-Concentration, Divalent Salt Environments. Angew Chem Int Ed Engl 2013; 53:1316-9. [DOI: 10.1002/anie.201307113] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 11/05/2013] [Indexed: 11/08/2022]
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13
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Tan SJ, Kahn JS, Derrien TL, Campolongo MJ, Zhao M, Smilgies DM, Luo D. Crystallization of DNA-Capped Gold Nanoparticles in High-Concentration, Divalent Salt Environments. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Tateishi-Karimta H, Sugimoto N. Control of stability and structure of nucleic acids using cosolutes. Methods 2013; 67:151-8. [PMID: 24270066 DOI: 10.1016/j.ymeth.2013.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/29/2013] [Accepted: 11/12/2013] [Indexed: 12/25/2022] Open
Abstract
The stabilities, structures, and functions of nucleic acids are responsive to surrounding conditions. Living cells contain biomolecules, including nucleic acids, proteins, polysaccharides, and other soluble and insoluble low-molecular weight components, that occupy a significant fraction of the cellular volume (up to 40%), resulting in a highly crowded intracellular environment. We have proven that conditions that mimic features of this intra-cellular environment alter the physical properties affect the stability, structure, and function of nucleic acids. The ability to control structure of nucleic acids by mimicking intra-cellular conditions will be useful in nanotechnology applications of nucleic acids. This paper describes methods that can be used to analyze quantitatively the intra-cellular environment effects caused by cosolutes on nucleic acid structures and to regulate properties of nucleic acids using cosolutes.
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Affiliation(s)
- Hisae Tateishi-Karimta
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan; Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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15
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Xiang Y, Deng K, Xia H, Yao C, Chen Q, Zhang L, Liu Z, Fu W. Isothermal detection of multiple point mutations by a surface plasmon resonance biosensor with Au nanoparticles enhanced surface-anchored rolling circle amplification. Biosens Bioelectron 2013; 49:442-9. [DOI: 10.1016/j.bios.2013.04.044] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 04/23/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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16
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Ghosh R, Deka J, Chattopadhyay A, Paul A. Conformation aspect in the α-amylase induced agglomeration of citrate-stabilized gold nanoparticles. RSC Adv 2013. [DOI: 10.1039/c3ra43623c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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17
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Khimji I, Shin J, Liu J. DNA duplex stabilization in crowded polyanion solutions. Chem Commun (Camb) 2013; 49:1306-8. [DOI: 10.1039/c2cc38627e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Zhang X, Huang PJJ, Servos MR, Liu J. Effects of polyethylene glycol on DNA adsorption and hybridization on gold nanoparticles and graphene oxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14330-14337. [PMID: 22989102 DOI: 10.1021/la302799s] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Understanding the interface between DNA and nanomaterials is crucial for rational design and optimization of biosensors and drug delivery systems. For detection and delivery into cells, where high concentrations of cellular proteins are present, another layer of complexity is added. In this context, we employ polyethylene glycol (PEG) as a model polymer to mimic the excluded volume effect of cellular proteins and to test its effects on DNA adsorption and hybridization on gold nanoparticles (AuNPs) and graphene oxide (GO), both of which show great promise for designing intracellular biosensors and drug delivery systems. We show that PEG 20000 (e.g., 4%) accelerates DNA hybridization to DNA-functionalized AuNPs by 50-100%, but this enhanced hybridization kinetics has not been observed with free DNA. Therefore, this rate enhancement is attributed to the surface blocking effect by PEG instead of the macromolecular crowding effect. On the other hand, DNA adsorption on citrate-capped AuNP surfaces is impeded even in the presence of a trace level (i.e., parts per billion) of PEG, confirming PEG competes with DNA for surface binding sites. Additional insights have been obtained by studying the adsorption of a thiolated DNA and a peptide nucleic acid. In these cases, the steric effects of PEG to impede adsorption are observed. Similar observations have also been made with GO. Therefore, PEG may be used as an effective blocking agent for both hydrophilic AuNP and for GO that also contains hydrophobic domains.
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Affiliation(s)
- Xu Zhang
- Department of Chemistry and Waterloo Institute for Nanotechnology, University Of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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19
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Mandal M, Bandyopadhyay A. Engineering of DNA templated tri-functional nano-chain of Fecore–Aushell and a preliminary study for cancer cell labeling and treatment. J Adv Res 2012. [DOI: 10.1016/j.jare.2012.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Miyoshi D, Fujimoto T, Sugimoto N. Molecular Crowding and Hydration Regulating of G-Quadruplex Formation. Top Curr Chem (Cham) 2012; 330:87-110. [DOI: 10.1007/128_2012_335] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Menhaj AB, Smith BD, Liu J. Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents. Chem Sci 2012. [DOI: 10.1039/c2sc20565c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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22
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Zaki A, Dave N, Liu J. Amplifying the Macromolecular Crowding Effect Using Nanoparticles. J Am Chem Soc 2011; 134:35-8. [DOI: 10.1021/ja207661z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ahmed Zaki
- Department
of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1,
Canada
| | - Neeshma Dave
- 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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23
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Liu Y, Kermanpour F, Liu HL, Hu Y, Shang YZ, Sandler SI, Jiang JW. Molecular thermodynamic model for DNA melting in ionic and crowded solutions. J Phys Chem B 2011; 114:9905-11. [PMID: 20666530 DOI: 10.1021/jp104121q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A molecular thermodynamic model is developed to predict DNA melting in ionic and crowded solutions. Each pair of nucleotides in the double-stranded DNA and each nucleotide in the single-stranded DNA are respectively represented by two types of charged Lennard-Jones spheres. The predicted melting curves and melting temperatures T(m) of the model capture the general feature of DNA melting and match fairly well with the available simulation and experimental results. It is found that the melting curve is steeper and T(m) is higher for DNA with a longer chain. With increasing the fraction of the complementary cytosine-guanine (CG) base pairs, T(m) increases almost linearly as a consequence of the stronger hydrogen bonding of the CG base pair than that of adenine-thymine (AT) base pair. At a greater ionic concentration, T(m) is higher due to the shielding effect of counterions on DNA strands. It is observed that T(m) increases in the presence of crowder because the crowder molecules occupy a substantial amount of system volume and suppress the entropy increase for DNA melting. At a given concentration, a larger crowder exhibits a greater suppression for DNA melting and hence a higher T(m). At the same packing fraction, however, a smaller crowder leads to a higher T(m).
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Affiliation(s)
- Y Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117576, Singapore
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24
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Cavalieri F, Ng SL, Mazzuca C, Jia Z, Bulmus V, Davis TP, Caruso F. Thin multilayer films and microcapsules containing DNA quadruplex motifs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:101-111. [PMID: 21105053 DOI: 10.1002/smll.201001246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The assembly of multifunctional nanostructures bearing G-quadruplex motifs broadens the prospects of using G-quadruplexes as therapeutic carriers. Herein, we report the synthesis and characterization of an oligodeoxyguanosine, G15-mer polymer conjugate. We demonstrate that G15-mer oligonucleotides grafted to a polymer chain preserve the ability to self-assemble into ordered structures. The G-quadruplex-polymer conjugates were assembled onto a surface via hybridization with 30-mer cytosine strands, C30-mer, using a layer-by-layer approach to form microcapsules. A mechanism for the sequential assembly of the multilayer films and microcapsules is presented. We further investigate the photophysical behavior of porphyrin TMPyP4 bound to multilayer-coated particles. This study shows that the multilayer films bear residual and functional quadruplex moieties that can be used to effectively bind therapeutic agents.
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Affiliation(s)
- Francesca Cavalieri
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, 00173 Rome, Italy
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Park S, Hamad-Schifferli K. Nanoscale interfaces to biology. Curr Opin Chem Biol 2010; 14:616-22. [PMID: 20674473 PMCID: PMC2953582 DOI: 10.1016/j.cbpa.2010.06.186] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/25/2010] [Accepted: 06/28/2010] [Indexed: 11/27/2022]
Abstract
Nanotechnology has held great promise for revolutionizing biology. The biological behavior of nanomaterials depends primarily on how they interface to biomolecules and their surroundings. Unfortunately, interface issues like non-specific adsorption are still the biggest obstacles to the success of nanobiotechnology and nanomedicine, and have held back widespread practical use of nanotechnology in biology. Not only does the biological interface of nanoparticles (NPs) need to be understood and controlled, but also NPs must be treated as biological entities rather than inorganic ones. Furthermore, one can adopt an engineering perspective of the NP-biological interface, realizing that it has unique, exploitable properties.
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Affiliation(s)
- Sunho Park
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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26
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Nanoparticle diffraction gratings for DNA detection on photopatterned glass substrates. Biointerphases 2010; 3:FD23-9. [PMID: 20408697 DOI: 10.1116/1.2994689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
An ex situ nanoparticle DNA detection assay utilizing DNA-modified nanoparticles attached to DNA monolayer gratings on glass substrates is developed. The assay utilizes the simultaneous hybridization of a single stranded DNA (ssDNA) target molecule to both an amine-modified DNA oligonucleotide attached to an amine-reactive glass surface and a thiol-modified DNA oligonucleotide attached to a 13 nm gold nanoparticle. Surface plasmon resonance imaging measurements are used to characterize the two sequential hybridization adsorption processes employed in the assay, and fluorescence microscopy is used to characterize the formation of DNA monolayer gratings via the photopatterning of the amine-reactive glass slides. First order diffraction measurements utilizing incoherent collimated white light source and a 10 nm bandpass filter centered at 600 nm provided quantitative measurements of target ssDNA down to a concentration of 10 pM. Fourth order diffraction measurements employing a HeNe laser and avalanche photodiode were used to detect target ssDNA adsorption from 10 microl of a solution with a concentration as low as 10 fM, corresponding to 60,000 target DNA molecules. This simple yet sensitive grating-based nanoparticle DNA detection assay should be directly applicable for genetic screening, mRNA expression assays, and microRNA profiling.
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Niikura K, Nagakawa K, Ohtake N, Suzuki T, Matsuo Y, Sawa H, Ijiro K. Gold Nanoparticle Arrangement on Viral Particles through Carbohydrate Recognition: A Non-Cross-Linking Approach to Optical Virus Detection. Bioconjug Chem 2009; 20:1848-52. [DOI: 10.1021/bc900255x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Kenichi Niikura
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Keita Nagakawa
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Noriko Ohtake
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Tadaki Suzuki
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Yasutaka Matsuo
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
| | - Kuniharu Ijiro
- Graduate School of Science and Research Institute for Electronic Science, Hokkaido University, N21W10, Sapporo 001-0021, Japan, Research Center for Zoonosis Control and Global COE program, Hokkaido University, N20W10, Sapporo 001-0020, Japan
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Sakai H, Sato A, Takeoka S, Tsuchida E. Mechanism of Flocculate Formation of Highly Concentrated Phospholipid Vesicles Suspended in a Series of Water-Soluble Biopolymers. Biomacromolecules 2009; 10:2344-50. [DOI: 10.1021/bm900455e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiromi Sakai
- Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, and Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 169-8555, Japan
| | - Atsushi Sato
- Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, and Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 169-8555, Japan
| | - Shinji Takeoka
- Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, and Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 169-8555, Japan
| | - Eishun Tsuchida
- Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, and Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, Tokyo 169-8555, Japan
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Fent GM, Casteel SW, Kim DY, Kannan R, Katti K, Chanda N, Katti K. Biodistribution of maltose and gum arabic hybrid gold nanoparticles after intravenous injection in juvenile swine. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2009; 5:128-35. [DOI: 10.1016/j.nano.2009.01.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Yokoyama K, Cho H, Cullen SP, Kowalik M, Briglio NM, Hoops HJ, Zhao Z, Carpenter MA. Microscopic investigation of reversible nanoscale surface size dependent protein conjugation. Int J Mol Sci 2009; 10:2348-2366. [PMID: 19564953 PMCID: PMC2695281 DOI: 10.3390/ijms10052348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 05/14/2009] [Accepted: 05/18/2009] [Indexed: 11/16/2022] Open
Abstract
Aβ(1-40) coated 20 nm gold colloidal nanoparticles exhibit a reversible color change as pH is externally altered between pH 4 and 10. This reversible process may contain important information on the initial reversible step reported for the fibrillogenesis of Aβ (a hallmark of Alzheimer's disease). We examined this reversible color change by microscopic investigations. AFM images on graphite surfaces revealed the morphology of Aβ aggregates with gold colloids. TEM images clearly demonstrate the correspondence between spectroscopic features and conformational changes of the gold colloid.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mails:
(H.C.);
(S.P.C.);
(M.K.);
(N.M.B.)
| | - Hyunah Cho
- Department of Chemistry, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mails:
(H.C.);
(S.P.C.);
(M.K.);
(N.M.B.)
| | - Sean P. Cullen
- Department of Chemistry, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mails:
(H.C.);
(S.P.C.);
(M.K.);
(N.M.B.)
| | - Matthew Kowalik
- Department of Chemistry, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mails:
(H.C.);
(S.P.C.);
(M.K.);
(N.M.B.)
| | - Nicole M. Briglio
- Department of Chemistry, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mails:
(H.C.);
(S.P.C.);
(M.K.);
(N.M.B.)
| | - Harold J. Hoops
- Department of Biology, The State University of New York at Geneseo, 1 College Circle, Geneseo, NY 14454, USA; E-Mail:
(H.J.H.)
| | - Zhouying Zhao
- College of Nanoscale Science and Engineering, University of Albany-SUNY, 255 Fuller Road, Albany, NY 12203, USA; E-Mails:
(Z.-Y.Z.);
(M.A.C.)
| | - Michael A. Carpenter
- College of Nanoscale Science and Engineering, University of Albany-SUNY, 255 Fuller Road, Albany, NY 12203, USA; E-Mails:
(Z.-Y.Z.);
(M.A.C.)
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31
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Yokoyama K, Briglio NM, Sri Hartati D, Tsang SMW, Maccormac JE, Welchons DR. Nanoscale size dependence in the conjugation of amyloid beta and ovalbumin proteins on the surface of gold colloidal particles. NANOTECHNOLOGY 2008; 19:375101. [PMID: 21832538 DOI: 10.1088/0957-4484/19/37/375101] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Absorption spectroscopy was utilized to investigate the conjugation of amyloid β protein solution (Aβ(1-40)) and chicken egg albumin (ovalbumin) with various sizes of gold colloidal nanoparticles for various pHs, ranging from pH 2 to pH 10. The pH value that indicates the colour change, pH(o), exhibited colloidal size dependence for both Aβ(1-40) and ovalbumin coated particles. In particular, Aβ(1-40) coated gold colloidal particles exhibited non-continuous size dependence peaking at 40 and 80 nm, implying that their corresponding cage-like structures provide efficient net charge cancellation at these core sizes. Remarkably, only the pH(o) value for ovalbumin coated 80 nm gold colloid was pH>7, and a specific cage-like structure is speculated to have a positive net charge facing outward when ovalbumin self-assembles over this particular gold colloid. The previously reported reversible colour change between pH 4 and 10 took place only with Aβ(1-40) coated 20 nm gold colloids; this was also explored with ovalbumin coated gold colloids. Interestingly, gold colloidal nanoparticles showed a quasi-reversible colour change when they were coated with ovalbumin for all test sizes. The ovalbumin coated gold colloid was found to maintain reversible properties longer than Aβ(1-40) coated gold colloid.
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He F, Shen Q, Jiang H, Zhou J, Cheng J, Guo D, Li Q, Wang X, Fu D, Chen B. Rapid identification and high sensitive detection of cancer cells on the gold nanoparticle interface by combined contact angle and electrochemical measurements. Talanta 2008; 77:1009-14. [PMID: 19064083 DOI: 10.1016/j.talanta.2008.07.063] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Revised: 07/24/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
In this study, we have proposed a novel strategy for the rapid identification and high sensitive detection of different kinds of cancer cells by means of electrochemical and contact angle measurements. A simple, unlabeled method based on the functionalized Au nanoparticles (GNPs) modified interface has been utilized to distinguish the different cancer cells, including lung cancer cells, liver cancer cells, drug sensitive leukemia K562/B.W cells and drug resistant leukemia K562/ADM cells. The relevant results indicate that under optimal conditions, this method can provide the quantitative determination of cancer cells, with a detection limit of approximately 10(3)cells mL(-1). Our observations demonstrate that the difference in the hydrophilic properties for target cellular surfaces and in the uptake efficiency of the anticancer drug daunorubicin for different cancer cells could be readily chosen as the elements of cancer identification and sensitive detection. This raises the possibility to advance the promising clinic diagnosis and monitoring of tumors with the aim of successful chemotherapy of human cancers.
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Affiliation(s)
- Fang He
- State Key Laboratory of Bioelectronics, Chien-Shiung Wu Laboratory, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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McCullagh M, Prytkova T, Tonzani S, Winter ND, Schatz GC. Modeling Self-Assembly Processes Driven by Nonbonded Interactions in Soft Materials. J Phys Chem B 2008; 112:10388-98. [DOI: 10.1021/jp803192u] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Tatiana Prytkova
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Stefano Tonzani
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Nicolas D. Winter
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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Zhang J, Badugu R, Lakowicz JR. Fluorescence Quenching of CdTe Nanocrystals by Bound Gold Nanoparticles in Aqueous Solution. PLASMONICS (NORWELL, MASS.) 2008; 3:3-11. [PMID: 19890452 PMCID: PMC2772157 DOI: 10.1007/s11468-007-9047-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Water-soluble gold nanoparticles with an average diameter of 5 nm were prepared with carboxylic acid terminated thiol ligands. These ligands contain zero to eight methylene moieties. CdTe nanocrystals with an average diameter of 5 nm were synthesized with aminoethanethiol capping. These nanocrystals displayed characteristic absorption and emission spectra of quantum dots. The amine terminated CdTe nanocrystals and carboxylic-acid-terminated gold nanoparticles were conjugated in aqueous solution at pH 5.0 by electrostatic interaction, and the conjugation was monitored with fluorescence spectroscopy. The CdTe nanocrystals were significantly quenched upon binding with gold nanoparticles. The quenching efficiency was affected by both the concentration of gold nanoparticles in the complex and the length of spacer between the CdTe nanocrystal and Au nanoparticle. The observed quenching was explained using Förster resonance energy transfer (FRET) mechanism, and the Förster distance was estimated to be 3.8 nm between the donor-acceptor pair.
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Affiliation(s)
- Jian Zhang
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, MD 21201, USA
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35
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Miyoshi D, Sugimoto N. Molecular crowding effects on structure and stability of DNA. Biochimie 2008; 90:1040-51. [PMID: 18331845 DOI: 10.1016/j.biochi.2008.02.009] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 02/08/2008] [Indexed: 10/22/2022]
Abstract
Living cells contain a variety of biomolecules including nucleic acids, proteins, polysaccharides, and metabolites as well as other soluble and insoluble components. These biomolecules occupy a significant fraction (20-40%) of the cellular volume. The total concentration of biomolecules reaches 400gL(-1), leading to a crowded intracellular environment referred to as molecular crowding. Therefore, an understanding of the effects of molecular crowding conditions on biomolecules is important to broad research fields such as biochemical, medical, and pharmaceutical sciences. In this review, we describe molecular conditions in the cytoplasm and nucleus, which are totally different from in vitro conditions, and then show the biochemical and biophysical consequences of molecular crowding. Finally, we discuss the effect of molecular crowding on the structure, stability, and function of nucleic acids and the significance of molecular crowding in biotechnology and nanotechnology.
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Affiliation(s)
- Daisuke Miyoshi
- Frontier Institute for Biomolecular Engineering Research , Konan University, Kobe 658-8501, Japan.
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36
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Chen SH, Wu VCH, Chuang YC, Lin CS. Using oligonucleotide-functionalized Au nanoparticles to rapidly detect foodborne pathogens on a piezoelectric biosensor. J Microbiol Methods 2008; 73:7-17. [PMID: 18279983 DOI: 10.1016/j.mimet.2008.01.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 01/03/2008] [Accepted: 01/09/2008] [Indexed: 11/19/2022]
Abstract
A circulating-flow piezoelectric biosensor, based on an Au nanoparticle amplification and verification method, was used for real-time detection of a foodborne pathogen, Escherichia coli O157:H7. A synthesized thiolated probe (Probe 1; 30-mer) specific to E. coli O157:H7 eaeA gene was immobilized onto the piezoelectric biosensor surface. Hybridization was induced by exposing the immobilized probe to the E. coli O157:H7 eaeA gene fragment (104-bp) amplified by PCR, resulting in a mass change and a consequent frequency shift of the piezoelectric biosensor. A second thiolated probe (Probe 2), complementary to the target sequence, was conjugated to the Au nanoparticles and used as a "mass enhancer" and "sequence verifier" to amplify the frequency change of the piezoelectric biosensor. The PCR products amplified from concentrations of 1.2 x 10(2) CFU/ml of E. coli O157:H7 were detectable by the piezoelectric biosensor. A linear correlation was found when the E. coli O157:H7 detected from 10(2) to 10(6) CFU/ml. The piezoelectric biosensor was able to detect targets from real food samples.
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Affiliation(s)
- Sz-Hau Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30005, Taiwan
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Triplett DA, Fichthorn KA. Monte Carlo simulation of two-dimensional hard rectangles: confinement effects. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:011707. [PMID: 18351866 DOI: 10.1103/physreve.77.011707] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 09/24/2007] [Indexed: 05/26/2023]
Abstract
We use orientational-bias Monte Carlo simulations to examine the phase behavior of two-dimensional hard rectangles in the bulk and under confinement by hard walls. For all of the rod aspect ratios and area fractions studied, we find that confinement increases the degree of nematic ordering over the bulk, as confined rods tend to align their long axes parallel to the confining walls. The extent of nematic ordering increases as the separation between the confining walls decreases. If the aspect ratio of the rectangles is sufficiently large, they exhibit nematic ordering in both the bulk and under confinement, where the nematic director is set by the walls. Rods with a small aspect ratio are isotropic in the bulk and exhibit weak tetratic tendencies for sufficiently high densities. From studies of density profiles, angular distributions, and orientational correlation functions for confined, low-aspect-ratio rods, it is apparent that they align their long axes parallel to the wall in the near-wall region, where layering occurs for sufficiently high rod densities. However, confined rods with low aspect ratios still exhibit weak tetratic (isotropic) tendencies near the center of the confined region for all but the smallest wall separations. We note that although our studies probe the ordering of hard rectangles, the entropic tendencies that we observe here will be present for rods with energetic interactions. Thus, these studies serve as a general starting point for understanding and controlling the assembly of rods in two-dimensional confining geometries.
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Affiliation(s)
- Derek A Triplett
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Wark AW, Lee HJ, Qavi AJ, Corn RM. Nanoparticle-enhanced diffraction gratings for ultrasensitive surface plasmon biosensing. Anal Chem 2007; 79:6697-701. [PMID: 17676761 DOI: 10.1021/ac071062b] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrasensitive surface bioaffinity sensors are created by the adsorption of gold nanoparticles onto gold diffraction gratings. An enhanced diffraction obtained in a surface plasmon resonance geometry is observed due to the optical coupling of the planar surface plasmons in the grating to the localized surface plasmons in the gold nanoparticles. As a first example, these nanoparticle grating biosensors are employed to detect unmodified DNA at a concentration of 10 fM.
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Affiliation(s)
- Alastair W Wark
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
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Park SY, Lee JS, Georganopoulou D, Mirkin CA, Schatz GC. Structures of DNA-linked nanoparticle aggregates. J Phys Chem B 2007; 110:12673-81. [PMID: 16800601 DOI: 10.1021/jp062212+] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The room-temperature structure of DNA-linked gold nanoparticle aggregates is investigated using a combination of experiment and theory. The experiments involve extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30 base-pair DNA. The theoretical studies use calculated spectra for models of the aggregate structures to determine which structure matches the observations. These models include diffusion-limited cluster-cluster aggregation (DLCA), reaction-limited cluster-cluster aggregation (RLCA), and compact (nonfractal) cluster aggregation. The diameter of the nanoparticles used in the experiments is larger than has been considered previously, and this provides greater sensitivity of spectra to aggregate structure. We show that the best match between experiment and theory occurs for the RLCA fractal structures. This indicates that DNA hybridization takes place under irreversible conditions in the room-temperature aggregation. Some possible structural variations which might influence the result are considered, including the edge-to-edge distance between nanoparticles, variation in the diameter of the nanoparticles, underlying lattice structures of on-lattice compact clusters, and positional disorders in the lattice structures. We find that these variations do not change the conclusion that the room-temperature structure of the aggregates is fractal. We also examine the variation in extinction at 260 nm as temperature is increased, showing that the decrease in extinction at temperatures below the melting temperature is related to a morphological change from fractal toward compact structures.
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Affiliation(s)
- Sung Yong Park
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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40
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Lee J, Javed T, Skeini T, Govorov AO, Bryant GW, Kotov NA. Bioconjugated Ag nanoparticles and CdTe nanowires: metamaterials with field-enhanced light absorption. Angew Chem Int Ed Engl 2007; 45:4819-23. [PMID: 16802399 DOI: 10.1002/anie.200600356] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaebeom Lee
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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Abstract
This article provides an overview of the use of theory and computation to describe the structural, thermodynamic, mechanical, and optical properties of nanoscale materials. Nanoscience provides important opportunities for theory and computation to lead in the discovery process because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial to understanding what is being measured. However, there are important challenges to using theory as well, as the systems of interest are usually too large, and the time scales too long, for a purely atomistic level theory to be useful. At the same time, continuum theories that are appropriate for describing larger-scale (micrometer) phenomena are often not accurate for describing the nanoscale. Despite these challenges, there has been important progress in a number of areas, and there are exciting opportunities that we can look forward to as the capabilities of computational facilities continue to expand. Some specific applications that are discussed in this paper include: self-assembly of supramolecular structures, the thermal properties of nanoscale molecular systems (DNA melting and nanoscale water meniscus formation), the mechanical properties of carbon nanotubes and diamond crystals, and the optical properties of silver and gold nanoparticles.
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Affiliation(s)
- George C Schatz
- Department of Chemistry, Northwestern University, Evanston, IL 60208-3113, USA.
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42
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Li J, Wang X, Wang C, Chen B, Dai Y, Zhang R, Song M, Lv G, Fu D. The Enhancement Effect of Gold Nanoparticles in Drug Delivery and as Biomarkers of Drug-Resistant Cancer Cells. ChemMedChem 2007; 2:374-8. [PMID: 17206735 DOI: 10.1002/cmdc.200600264] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The enhancement effect of 3-mercaptopropionic acid capped gold nanoparticles (NPs) in drug delivery and as biomarkers of drug-resistant cancer cells has been demonstrated through fluorescence microscopy and electrochemical studies. The results of cell viability experiments and confocal fluorescence microscopy studies illustrate that these functionalized Au NPs could play an important role in efficient drug delivery and biomarking of drug-resistant leukemia K562/ADM cells. This could be explored as a novel strategy to inhibit multidrug resistance in targeted tumor cells and as a sensitive method for the early diagnosis of certain cancers. Our observations also indicate that the interaction between the functionalized Au NPs and biologically active molecules on the surface of leukemia cells may contribute the observed enhancement in cellular drug uptake.
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Affiliation(s)
- Jingyuan Li
- State Key Lab of Bioelectronics (Chien-Shiung WU Laboratory), Southeast University, Nanjing, PR China
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43
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Lukatsky DB, Frenkel D. Surface and bulk dissolution properties, and selectivity of DNA-linked nanoparticle assemblies. J Chem Phys 2007; 122:214904. [PMID: 15974787 DOI: 10.1063/1.1906210] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using a simple mean-field model, we analyze the surface and bulk dissolution properties of DNA-linked nanoparticle assemblies. We find that the dissolution temperature and the sharpness of the dissolution profiles increase with the grafting density of the single-stranded DNA "probes" on the surface of colloids. The surface grafting density is controlled by the linker occupation number, in analogy with quantum particles obeying fractional statistics. The dissolution temperature increases logarithmically with the salt concentration. This is in agreement with the experimental findings [R. Jin, G. Wu, Z. Li, C. A. Mirkin, and G. C. Schatz, J. Am. Chem. Soc. 125, 1643 (2003)]. By exploiting the unique phase behavior of DNA-coated colloids, it should be possible to detect multiple "targets" in a single experiment by essentially mapping the DNA base-pair sequence onto the phase behavior of DNA-linked nanoparticle solution.
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Affiliation(s)
- D B Lukatsky
- FOM Institute for Atomic and Molecular Physics [AMOLF], Kruislaan 407, 1098 SJ Amsterdam, The Netherlands
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Matsui J, Goji S, Murashima T, Miyoshi D, Komai S, Shigeyasu A, Kushida T, Miyazawa T, Yamada T, Tamaki K, Sugimoto N. Molecular Imprinting under Molecular Crowding Conditions: An Aid to the Synthesis of a High-Capacity Polymeric Sorbent for Triazine Herbicides. Anal Chem 2007; 79:1749-57. [PMID: 17297982 DOI: 10.1021/ac060441m] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Molecular crowding, an important feature of the molecular environments in biological cells, was applied to the synthesis of antibody-mimic polymers selective for a group of biologically active compounds, the triazine herbicides. Synthesis of these polymers was conducted using molecular imprinting under molecular crowding conditions, whereby atrazine (a template molecule) was complexed with methacrylic acid (a functional monomer) in the presence of a macromolecular crowding agent (either poly(methyl methacrylate) (PMMA) or polystyrene (PS)) followed by cross-linking with ethylene glycol dimethacrylate. After removal of atrazine from the polymer matrix, the retention properties and selectivity of the resultant polymers were assessed by chromatographic tests. The addition of a crowding-inducing agent resulted in polymers with superior retention properties and excellent selectivity for triazine herbicides, as compared to polymers prepared without addition of a crowding-inducing agent. An imprinted polymer prepared in the presence of PS as a crowding agent exhibited a retention factor for atrazine an order of magnitude larger than that of an imprinted polymer prepared in the absence of a crowding agent. NMR results suggest that the crowding agent is capable of promoting hydrogen bond formation between atrazine and methacrylic acid, which could account for the effect of crowding on molecular imprinting.
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45
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Lee J, Javed T, Skeini T, Govorov AO, Bryant GW, Kotov NA. Bioconjugated Ag Nanoparticles and CdTe Nanowires: Metamaterials with Field-Enhanced Light Absorption. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600356] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Li Y, Wark AW, Lee HJ, Corn RM. Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions. Anal Chem 2006; 78:3158-64. [PMID: 16643008 PMCID: PMC2504468 DOI: 10.1021/ac0600151] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A sensitive method for the analysis of single nucleotide polymorphisms (SNPs) in genomic DNA that utilizes nanoparticle-enhanced surface plasmon resonance imaging (SPRI) measurements of surface enzymatic ligation reactions on DNA microarrays is demonstrated. SNP identification was achieved by using sequence-specific surface reactions of the enzyme Taq DNA ligase, and the presence of ligation products on the DNA microarray elements was detected using SPRI through the hybridization adsorption of complementary oligonucleotides attached to gold nanoparticles. The use of gold nanoparticles increases the sensitivity of the SPRI so that single bases in oligonucleotides can be successfully identified at a concentration of 1 pM. This sensitivity is amply sufficient for performing multiplexed SNP genotyping by using multiple PCR amplicons and should also allow for the direct detection and identification of SNP sequences from 1 pM unamplified genomic DNA samples with this array-based and label-free SPRI methodology. As a first example of SNP genotyping, three different human genomic DNA samples were screened for a possible point mutation in the BRCA1 gene that is associated with breast cancer.
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Affiliation(s)
- Yuan Li
- University of California-Irvine, Irvine, California 92697, USA
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Akamatsu K, Kimura M, Shibata Y, Nakano SI, Miyoshi D, Nawafune H, Sugimoto N. A DNA duplex with extremely enhanced thermal stability based on controlled immobilization on gold nanoparticles. NANO LETTERS 2006; 6:491-5. [PMID: 16522049 DOI: 10.1021/nl0524748] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The effect of DNA loadings on the thermal stability of DNA duplex immobilized on gold nanoparticles has been investigated. The modestly loaded duplexes on the gold nanoparticles showed enhanced thermal stability, as compared to that of the free duplex (without gold nanoparticles). However, the highly loaded duplex showed stability similar to that of free duplex. The stability could be controlled over a wide temperature range simply by varying the salt concentration (over 50 degrees C). Additionally, the gold nanoparticles with modestly loaded oligonucleotides could be used as nanoprobes for effective and fast strand exchange reactions, based on the increased thermal stability of the immobilized duplex. These results indicate that the interaction between the duplex and the nanoparticle surface plays an important role in determining the stability of the duplex.
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Affiliation(s)
- Kensuke Akamatsu
- Frontier Institute for Biomolecular Engineering Research, FIBER, Department of Chemistry, Faculty of Science and Engineering, and Graduate School of Science, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan.
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48
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Dillenback LM, Goodrich GP, Keating CD. Temperature-programmed assembly of DNA:Au nanoparticle bioconjugates. NANO LETTERS 2006; 6:16-23. [PMID: 16402780 DOI: 10.1021/nl0508873] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Temperature has been used to control the order of assembly events in a solution containing three types of particles to be linked by two different sets of complementary DNA. At higher temperatures, only the duplexes having higher thermal stability were able to form. By starting at a high temperature and then cooling the sample, these more stable sequences hybridized first, followed by the less stable sequences at lower temperatures. Because of the use of thiolated DNA on Au particles, some loss and exchange of the DNA strands occurred at elevated temperatures. However, since cooperativity favors the "correct" assemblies, Au-S bond lability did not appreciably impact the order of the assembly process. Temperature programming combines the selectivity of DNA-directed assembly with the ability to control the order in which several complementary strands hybridize in a common solution and could contribute to the synthesis of more complex nanostructured materials.
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Affiliation(s)
- Lisa M Dillenback
- Department of Chemistry, The Pennsylvania State University, University Park, 16802, USA
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Rochelet-Dequaire M, Limoges B, Brossier P. Subfemtomolar electrochemical detection of target DNA by catalytic enlargement of the hybridized gold nanoparticle labels. Analyst 2006; 131:923-9. [PMID: 17028726 DOI: 10.1039/b603963d] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
After showing the failure of conventional gold-enhancement procedures to amplify the gold nanoparticle-based electrochemical transduction of DNA hybridization in polystyrene microwells, a new efficient protocol was developed and evaluated for the sensitive quantification of a 35 base-pair human cytomegalovirus nucleic acid target (tDNA). In this assay, the hybridization of the target adsorbed on the bottom of microwells with an oligonucleotide-modified Au nanoparticle detection probe (pDNA-Au) was monitored by the anodic stripping detection of the chemically oxidized gold label at a screen-printed microband electrode (SPMBE). Thanks to the combination of the sensitive Au(III) determination at a SPMBE with the large amount of Au(III) released from each pDNA-Au, picomolar detection limits of tDNA can be achieved. Further enhancement of the hybridization signal based on the autocatalytic reductive deposition of ionic gold (Au(III)) on the surface of the gold nanoparticle labels anchored on the hybrids was first envisaged by incubating the commonly used mixture of Au(III) and hydroxylamine (NH(2)OH). However, due to a considerable nonspecific current response of poor reproducibility it was not possible to significantly improve the analytical performances of the method under these conditions. Complementary transmission electronic microscopy experiments indicated the loss of most of the grown gold labels during the post-enlargement rinsing step. To circumvent this drawback, a polymeric solute containing polyethyleneglycol and sodium chloride was introduced in the growth media to act as an aggregating agent during the catalytic process and thus retain the enlarged labels on the bottom of the microwell. This strategy, which led to an efficient increase of the hybridization response, allowed detection of tDNA concentrations as low as 600 aM (i.e., 10(4) lower than without amplification), and thus offers great promise for ultrasensitive detection of other hybridization events.
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Affiliation(s)
- Murielle Rochelet-Dequaire
- Laboratoire de Microbiologie Médicale et Moléculaire, Facultés de Médecine et de Pharmacie, 7 Boulevard Jeanne d'Arc, Dijon 21000, France.
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Long MS, Keating CD. Nanoparticle Conjugation Increases Protein Partitioning in Aqueous Two-Phase Systems. Anal Chem 2005; 78:379-86. [PMID: 16408917 DOI: 10.1021/ac051882t] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the effect of bioconjugation to colloidal Au nanoparticles on protein partitioning in poly(ethylene glycol) (PEG)/dextran aqueous two-phase systems (ATPS). Horseradish peroxidase (HRP) was conjugated to colloidal Au nanoparticles by direct adsorption. Although HRP alone had very little phase preference, HRP/Au nanoparticle conjugates typically partitioned to the PEG-rich phase, up to a factor of 150:1 for conjugates of 15-nm colloidal Au. Other protein/Au nanoparticle conjugates exhibited partitioning of greater than 2000:1 to the dextran-rich phase, as compared with approximately 5:1 for the free protein. The degree of partitioning was dependent on polymer concentration and molecular weight, nanoparticle diameter, and in some instances, nanoparticle concentration in the ATPS. The substantial improvements in protein partitioning achievable by conjugation to Au nanoparticles appear to result largely from increased surface area of the conjugates and require neither chemical modification of the proteins or polymers with affinity ligands, increased polymer concentrations, nor addition of high concentrations of salts. Adsorption to colloidal particles thus provides an attractive route for increased partitioning of enzymes and other proteins in ATPS. Furthermore, these results point to ATPS partitioning as a powerful means of purification for biomolecule/nanoparticle conjugates, which are increasingly used in diagnostics and materials applications.
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Affiliation(s)
- M Scott Long
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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