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Fu P, Chen H, Ouyang L, Li L, Wang Y, Qian S, Cao Z, Wu K, Chao J, Zheng J. DNA Nanoribbon for Efficient Anti-miRNA Peptide Nucleic Acid Delivery and Synergistic Enhancement of Cancer Cell Apoptosis. Anal Chem 2022; 95:1811-1816. [PMID: 36542541 DOI: 10.1021/acs.analchem.2c04760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Antisense peptide nucleic acid (asPNA), an effective antisense drug, has been employed as a gene therapy agent and a useful tool in molecular biology. Gaining control over the delivery of asPNA to target tissues has been a major hindrance to its wide application in clinical practice. A simple and efficient DNA nanoribbon (DNR)-based drug delivery process has been designed in this study that releases the asPNA agent to inhibit oncogenic microRNAs (miRNAs). Furthermore, we demonstrated how the AS1411 aptamer that binds nucleolin on the cell membranes works as a control mechanism capable of identifying target cancer cells and enhancing the enrichment capacity of DNR. With the biodegradability of DNR, we can efficiently initiate the release of asPNA into the cytoplasm, particularly targeting the intended miR-21 and synergistically increasing programmed cell death 4 (PDCD4) expression to enhance cell apoptosis. We assume that this well-defined delivery mechanism will aid in designing antisense site-specific treatments for various diseases, including cancer.
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Affiliation(s)
- Pan Fu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Hao Chen
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Lilin Ouyang
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lin Li
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Yuhui Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Sihua Qian
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Zhanglei Cao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Kerong Wu
- Ningbo First Hospital, Ningbo, Zhejiang 315000, P. R. China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays and Jiangsu Key Laboratory for Biosensors, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
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2
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Affiliation(s)
- Jason S. Kahn
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
| | - Oleg Gang
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Department of Applied Physics and Applied Mathematics Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
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3
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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4
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Kahn JS, Gang O. Designer Nanomaterials through Programmable Assembly. Angew Chem Int Ed Engl 2021; 61:e202105678. [PMID: 34128306 DOI: 10.1002/anie.202105678] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 11/08/2022]
Abstract
Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.
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Affiliation(s)
- Jason S Kahn
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
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5
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Xin X, Wang L, Wang K, Dai L, Cao H, Li Z, Tian Y. Stepwise assembly of nanoclusters guided by DNA origami frames with high-throughput. Chem Commun (Camb) 2020; 56:4918-4921. [PMID: 32238995 DOI: 10.1039/d0cc00274g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We contrive two strategies to assemble well-defined nanoclusters with high-throughput guided by DNA origami frames either by (1) introducing a micro-sized surface to fabricate patchy particles for binding with DNA structures or (2) restricting the assembly process of free nanoparticles and DNA origami frames on the fixed sites. Both the strategies can omit the process of gel purification of the final products.
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Affiliation(s)
- Xiaodong Xin
- School of Materials Science and Engineering, Xiangtan University, Xiangtan, 411105, China.
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6
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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7
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Hu Q, Wang Q, Kong J, Li L, Zhang X. Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference. Biosens Bioelectron 2017; 101:1-6. [PMID: 29031128 DOI: 10.1016/j.bios.2017.09.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/10/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr4+-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable CuII deactivators can be reduced into the CuI activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.
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Affiliation(s)
- Qiong Hu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252000, PR China
| | - Xueji Zhang
- Chemistry Department, College of Arts and Sciences, University of South Florida, East Fowler Ave, Tampa, FL 33620-4202, United States.
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8
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Pedersen RO, Kong J, Achim C, LaBean TH. Comparative Incorporation of PNA into DNA Nanostructures. Molecules 2015; 20:17645-58. [PMID: 26404232 PMCID: PMC6331967 DOI: 10.3390/molecules200917645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/13/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022] Open
Abstract
DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.
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Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708-0354, USA.
| | - Jing Kong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Catalina Achim
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Thomas H LaBean
- Department of Materials Science and Engineering, North Carolina State University, 911 Partners Way, Raleigh, NC 27695-7907, USA.
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9
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Akiyama Y, Shikagawa H, Kanayama N, Takarada T, Maeda M. Modulation of Interparticle Distance in Discrete Gold Nanoparticle Dimers and Trimers by DNA Single-Base Pairing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3153-3161. [PMID: 25739374 DOI: 10.1002/smll.201500045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Self-assembled structures of metallic nanoparticles with dynamically changeable interparticle distance hold promise for the regulation of collective physical properties. This paper describes gold nanoparticle dimers and trimers that exhibit spontaneous and reversible changes in interparticle distance. To exploit this property, a gold nanoparticle is modified with precisely one long DNA strand and approximately five short DNA strands. The long DNA serves to align the nanoparticles on a template DNA via hybridization, while the short DNAs function to induce the interparticle distance changes. The obtained dimer and trimer are characterized with gel electrophoresis, dynamic light scattering measurements, and transmission electron microscopy (TEM). When the complementary short DNA is added to form the fully matched duplexes on the particle surface in the presence of MgCl2 , spontaneous reduction of the interparticle distance is observed with TEM and cryo-electron microscopy. By contrast, when the terminal-mismatched DNA is added, no structural change occurs under the same conditions. Therefore, the single base pairing/unpairing at the outermost surface of the nanoparticle impacts the interparticle distance. This unique feature could be applied to the regulation of structures and properties of various DNA-functionalized nanoparticle assemblies.
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Affiliation(s)
- Yoshitsugu Akiyama
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Hiroto Shikagawa
- 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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10
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Aiba Y, Honda Y, Komiyama M. Promotion of double-duplex invasion of peptide nucleic acids through conjugation with nuclear localization signal peptide. Chemistry 2015; 21:4021-6. [PMID: 25640012 DOI: 10.1002/chem.201406085] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Indexed: 11/10/2022]
Abstract
Pseudo-complementary peptide nucleic acid (pcPNA), as one of the most widely used synthetic DNA analogues, invades double-stranded DNA according to Watson-Crick rules to form invasion complexes. This unique mode of DNA recognition induces structural changes at the invasion site and can be used for a range of applications. In this paper, pcPNA is conjugated with a nuclear localization signal (NLS) peptide, and its invading activity is notably promoted both thermodynamically and kinetically. Thus, the double-duplex invasion complex is formed promptly at low pcPNA concentrations under high salt conditions, where the invasion otherwise never occurs. Furthermore, NLS-modified pcPNA is successfully employed for site-selective DNA scission, and the targeted DNA is selectively cleaved under conditions that are not conducive for DNA cutters using unmodified pcPNAs. This strategy of pcPNA modification is expected to be advantageous and promising for a range of in vitro and in vivo applications.
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Affiliation(s)
- Yuichiro Aiba
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577 (Japan); Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904 (Japan); Present address: Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041 (USA)
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11
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Ryu Y, Jin Z, Lee JJ, Noh SH, Shin TH, Jo SM, Choi J, Park H, Cheon J, Kim HS. Size-Controlled Construction of Magnetic Nanoparticle Clusters Using DNA-Binding Zinc Finger Protein. Angew Chem Int Ed Engl 2014; 54:923-6. [DOI: 10.1002/anie.201408593] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/13/2014] [Indexed: 12/25/2022]
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12
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Ryu Y, Jin Z, Lee JJ, Noh SH, Shin TH, Jo SM, Choi J, Park H, Cheon J, Kim HS. Size-Controlled Construction of Magnetic Nanoparticle Clusters Using DNA-Binding Zinc Finger Protein. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408593] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Shiraishi T, Deborggraeve S, Büscher P, Nielsen PE. Sensitive detection of nucleic acids by PNA hybridization directed co-localization of fluorescent beads. ARTIFICIAL DNA, PNA & XNA 2014; 2:60-66. [PMID: 21912728 DOI: 10.4161/adna.2.2.16562] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 06/20/2011] [Indexed: 11/19/2022]
Abstract
We have designed a pair of biotinylated peptide nucleic acid (PNA) probes targeting two sequences in 18S rRNA (from the parasite Trypanosoma brucei) at a distance of 191 nt (corresponding to maximum distance of ca. 60 nm) from each other. The PNA probes were individually bound to (strept)avidin-coated fluorescent beads, differing in size and color [green beads (1 µm) and red beads (5.9 µm)], thereby allowing distinct detection of each PNA probe by conventional fluorescence microscopy. These two PNA beads showed easily detectable co-localization when simultaneously hybridizing to a target nucleic acid. The assay detected the parasite 18S rRNA down to 1.6 fmol while there was no such co-localization visible with human 18S rRNA not containing the PNA targets. Furthermore, the assay showed positive detection with 1.6 ng of total RNA (corresponding to RNA from ca. 300 parasites). Upon further optimization this method may provide a new tool for a diagnosis of Human African Trypanosomiasis (HAT) and it may more generally have applications within diagnostics for (neglected) infectious diseases.
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Affiliation(s)
- Takehiko Shiraishi
- Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen N, Denmark
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14
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Sun D, Gang O. DNA-functionalized quantum dots: fabrication, structural, and physicochemical properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7038-7046. [PMID: 23706124 DOI: 10.1021/la4000186] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We have systematically investigated the effect of physicochemical conditions, such as pH, salt concentration, and DNA/nanoparticle ratio, on the chemical conjugation process and structural and optical stability of carboxyl-functionalized quantum dots (QDs) functionalized with amino-modified DNA. We reveal the relationship between aqueous conditions and the amount of DNA conjugated on QDs, colloidal stability, and yield of the final QD-DNA conjugates. By carefully adjusting the environmental variables we have successfully achieved up to 20 DNA strands conjugated per QD, and demonstrated how this number can be tuned. The fabricated QD-DNA conjugates are dispersed and optically stable in salted solutions for over a month. We have also evaluated the involved interparticle interactions to explain the solution behavior of QD-DNA conjugates. Our results provide a basic understanding of the physiochemical processes governing a nanoparticle-biomolecule conjugation and the structural stability of the formed conjugates. Such fabricated QD-DNA conjugates might be of great benefit for programmable assemblies of optically active nanomaterials and for emerging biosensing methods based on nanomaterials.
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Affiliation(s)
- Dazhi Sun
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
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15
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Yamazaki T, Aiba Y, Yasuda K, Sakai Y, Yamanaka Y, Kuzuya A, Ohya Y, Komiyama M. Clear-cut observation of PNA invasion using nanomechanical DNA origami devices. Chem Commun (Camb) 2013; 48:11361-3. [PMID: 23073563 DOI: 10.1039/c2cc36358e] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Invasive binding event of PNA into DNA duplex was clearly observed both by atomic force microscope (AFM) imaging and electrophoretic mobility shift assay (EMSA) with the aid of nanomechanical DNA origami devices as 'single-molecule' visual probes, showing their potential as universal platform for the analysis of PNA invasion.
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Affiliation(s)
- Takahiro Yamazaki
- RCAST, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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16
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Ackermann D, Famulok M. Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology. Nucleic Acids Res 2013; 41:4729-39. [PMID: 23444144 PMCID: PMC3632119 DOI: 10.1093/nar/gkt121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The structural reorganization of nanoscale DNA architectures is a fundamental aspect in dynamic DNA nanotechnology. Commonly, DNA nanoarchitectures are reorganized by means of toehold-expanded DNA sequences in a strand exchange process. Here we describe an unprecedented, toehold-free switching process that relies on pseudo-complementary peptide nucleic acid (pcPNA) by using a mechanism that involves double-strand invasion. The usefulness of this approach is demonstrated by application of these peptide nucleic acids (PNAs) as switches in a DNA rotaxane architecture. The monomers required for generating the pcPNA were obtained by an improved synthesis strategy and were incorporated into a PNA actuator sequence as well as into a short DNA strand that subsequently was integrated into the rotaxane architecture. Alternate addition of a DNA and PNA actuator sequence allowed the multiple reversible switching between a mobile rotaxane macrocycle and a stationary pseudorotaxane state. The switching occurs in an isothermal process at room temperature and is nearly quantitative in each switching step. pcPNAs can potentially be combined with light- and toehold-based switches, thus broadening the toolbox of orthogonal switching approaches for DNA architectures that open up new avenues in dynamic DNA nanotechnology.
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Affiliation(s)
- Damian Ackermann
- Chemical Biology and Medicinal Chemistry Unit, LIMES Institute, c/o Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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17
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Sun D, Stadler AL, Gurevich M, Palma E, Stach E, van der Lelie D, Gang O. Heterogeneous nanoclusters assembled by PNA-templated double-stranded DNA. NANOSCALE 2012; 4:6722-6725. [PMID: 23026861 DOI: 10.1039/c2nr31908j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Heterogeneous nanoclusters with trimeric and core-shell architectures containing nanoparticles of different size and composition have been fabricated via site-specific PNA-"invasion" of DNA double helix. This novel strategy facilitates the incorporation of double-stranded DNA into the nanoparticle assembly design.
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Affiliation(s)
- Dazhi Sun
- Center for Functional Nanomaterials, Brookhaven National Laboratory Upton, NY 11973, USA
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18
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Bonifazi D, Carloni LE, Corvaglia V, Delforge A. Peptide nucleic acids in materials science. ARTIFICIAL DNA, PNA & XNA 2012; 3:112-22. [PMID: 22925824 PMCID: PMC3581510 DOI: 10.4161/adna.21941] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights the recent methods to prepare PNA-based materials through a combination of self-assembly and self-organization processes. The use of these methods allows easy and versatile preparation of structured hybrid materials showing specific recognition properties and unique physicochemical properties at the nano- and micro-scale levels displaying potential applications in several directions, ranging from sensors and microarrays to nanostructured devices for biochips.
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Affiliation(s)
- Davide Bonifazi
- Namur Research College, Department of Chemistry, University of Namur, Namur, Belgium.
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19
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Aiba Y, Honda Y, Han Y, Komiyama M. Introduction of multiphosphonate ligand to peptide nucleic acid for metal ion conjugation. ARTIFICIAL DNA, PNA & XNA 2012; 3:73-9. [PMID: 22772037 PMCID: PMC3429533 DOI: 10.4161/adna.20727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Peptide nucleic acid (PNA) is one of the most widely used synthetic DNA analogs. Conjugation of functional molecules to PNA is very effective to further widen its potential applications. For this purpose, here we report the synthesis of several ligand monomers and introduced them to PNA. These ligand-modified PNAs attract cerium ion and are useful for site-selective DNA hydrolysis. It should be noted that these ligands on PNA are also effective even under the conditions of invasion complex.
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Affiliation(s)
- Yuichiro Aiba
- Research Center for Advanced Science and Technology; The University of Tokyo, Tokyo, Japan
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