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Mollarasouli F, Badilli U, Bakirhan NK, Ozkan SA, Ozkan Y. Advanced DNA nanomachines: Strategies and bioapplications. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2020.102290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Najahi-Missaoui W, Arnold RD, Cummings BS. Safe Nanoparticles: Are We There Yet? Int J Mol Sci 2020; 22:ijms22010385. [PMID: 33396561 PMCID: PMC7794803 DOI: 10.3390/ijms22010385] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/24/2020] [Accepted: 12/27/2020] [Indexed: 12/14/2022] Open
Abstract
The field of nanotechnology has grown over the last two decades and made the transition from the benchtop to applied technologies. Nanoscale-sized particles, or nanoparticles, have emerged as promising tools with broad applications in drug delivery, diagnostics, cosmetics and several other biological and non-biological areas. These advances lead to questions about nanoparticle safety. Despite considerable efforts to understand the toxicity and safety of these nanoparticles, many of these questions are not yet fully answered. Nevertheless, these efforts have identified several approaches to minimize and prevent nanoparticle toxicity to promote safer nanotechnology. This review summarizes our current knowledge on nanoparticles, their toxic effects, their interactions with mammalian cells and finally current approaches to minimizing their toxicity.
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Affiliation(s)
- Wided Najahi-Missaoui
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA;
- Correspondence: ; Tel.: +1-706-542-6552; Fax: +70-6542-5358
| | - Robert D. Arnold
- Department of Drug Discovery & Development, Harrison School of Pharmacy, Auburn University, Auburn, AL 36849, USA;
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
| | - Brian S. Cummings
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA;
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA 30602, USA
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Wu Z, Zhang L. Photoregulation between small DNAs and reversible photochromic molecules. Biomater Sci 2019; 7:4944-4962. [PMID: 31650136 DOI: 10.1039/c9bm01305a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oligonucleotides are widely used biological materials in the fields of biomedicine, nanotechnology, and materials science. Due to the demands for the photoregulation of DNA activities, scientists are placing more and more research interest in the interactions between reversible photochromic molecules and DNAs. Photochromic molecules can work as switches for regulating the DNAs' behavior under light irradiation; meanwhile, DNAs also exert influence over the photochromic molecules. The photochromic molecules can be attached to DNAs either by covalent bonds or by noncovalent forces, which results in different regulative functions. Azobenzenes, spiropyrans, diarylethenes, and stilbene-like compounds are important photochromic molecules working as photoswitches. By summarizing their interactions with oligonucleotides, this review intends to facilitate the relevant research on oligonucleotides/photochromic molecules in the biological and medicinal fields and in materials science.
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Affiliation(s)
- Zhongtao Wu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
| | - Lei Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, No. 53 Zhengzhou Rd, Qingdao, 266042, PR China.
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Hansen-Bruhn M, Nielsen LDF, Gothelf KV. Rapid Detection of Drugs in Human Plasma Using a Small-Molecule-Linked Hybridization Chain Reaction. ACS Sens 2018; 3:1706-1711. [PMID: 30105911 DOI: 10.1021/acssensors.8b00439] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Rapid detection and quantification of pharmaceutical drugs directly in human plasma is of major importance for the development of relevant point-of-care testing devices. Here, we report a method for detection and quantification of small molecules in human plasma. An assay employing a small molecule-linked hybridization chain reaction (HCR) has been devised for the detection of the pharmaceutically relevant drugs digoxin (Dig) and methotrexate (MTX). Double modification by small molecule ligands on the initiator strand act as sites to control the rate of the HCR. Upon protein binding to the modified initiator strand, the HCR is greatly inhibited. If the protein is preincubated with a sample containing the small molecule analyte, the protein binding site is occupied by the analyte and the initiator strand will initiate the HCR. This enables efficient detection and quantification of small-molecule analytes in nanomolar concentration even in 50% human plasma within 4 min. Thus, the rapidity and simplicity of this assay has potential for point-of-care testing.
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Affiliation(s)
- Malthe Hansen-Bruhn
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Line D. F. Nielsen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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Abstract
The field of nanotechnology has grown exponentially during the last few decades, due in part to the use of nanoparticles in many manufacturing processes, as well as their potential as clinical agents for treatment of diseases and for drug delivery. This has created several new avenues by which humans can be exposed to nanoparticles. Unfortunately, investigations assessing the toxicological impacts of nanoparticles (i.e. nanotoxicity), as well as their possible risks to human health and the environment, have not kept pace with the rapid rise in their use. This has created a gap-in-knowledge and a substantial need for more research. Studies are needed to help complete our understanding of the mechanisms of toxicity of nanoparticles, as well as the mechanisms mediating their distribution and accumulation in cells and tissues and their elimination from the body. This review summarizes our knowledge on nanoparticles, including their various applications, routes of exposure, their potential toxicity and risks to human health.
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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Ouyang X, De Stefano M, Krissanaprasit A, Bank Kodal AL, Bech Rosen C, Liu T, Helmig S, Fan C, Gothelf KV. Docking of Antibodies into the Cavities of DNA Origami Structures. Angew Chem Int Ed Engl 2017; 56:14423-14427. [DOI: 10.1002/anie.201706765] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/18/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Xiangyuan Ouyang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education of China; Key Laboratory of Modern Separation Science in Shaanxi Province; College of Chemistry & Material Science; Northwest University; Xi'an 710127 China
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Mattia De Stefano
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Abhichart Krissanaprasit
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
- Present address: Department of Materials Science and Engineering; North Carolina State University; Raleigh NC 27606 USA
| | - Anne Louise Bank Kodal
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Christian Bech Rosen
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Tianqiang Liu
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Sarah Helmig
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
| | - Chunhai Fan
- Division of Physical Biology, Bioimaging Center; Shanghai Synchrotron Radiation Facility (SSRF); Shanghai Institute of Applied Physics, Chinese Academy of Sciences; Shanghai 201800 China
| | - Kurt V. Gothelf
- Center for DNA Nanotechnology (CDNA) at the Interdisciplinary Nanoscience Center (iNANO) and the D; epartment of Chemistry Aarhus University; 8000 Aarhus C Denmark
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Wu J, Yu F, Zhang Z, Chen Y, Du J. Highly sensitive self-complementary DNA nanoswitches triggered by polyelectrolytes. NANOSCALE 2016; 8:464-470. [PMID: 26627445 DOI: 10.1039/c5nr05193b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Dimerization of two homologous strands of genomic DNA/RNA is an essential feature of retroviral replication. Herein we show that a cationic comb-type copolymer (CCC), poly(L-lysine)-graft-dextran, accelerates the dimerization of self-complementary stem-loop DNA, frequently found in functional DNA/RNA molecules, such as aptamers. Furthermore, an anionic polymer poly(sodium vinylsulfonate) (PVS) dissociates CCC from the duplex shortly within a few seconds. Then single stem-loop DNA spontaneously transforms from its dimer. Thus we can easily control the dimer and stem-loop DNA by switching on/off CCC activity. Both polyelectrolytes and DNA concentrations are in the nanomole per liter range. The polyelectrolyte-assisted transconformation and sequences design strategy ensures the reversible state control with rapid response and effective switching under physiologically relevant conditions. A further application of this sensitive assembly is to construct an aptamer-type drug delivery system, bind or release functional molecules responding to its transconformation.
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Affiliation(s)
- Jincai Wu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Feng Yu
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Zheng Zhang
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Yong Chen
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
| | - Jie Du
- College of Materials and Chemistry Engineering, Hainan University, Haikou 570228, China.
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Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc Chem Res 2014; 47:1663-72. [PMID: 24617966 DOI: 10.1021/ar400308f] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".
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Affiliation(s)
- Yukiko Kamiya
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
- Ecotopia
Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
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Li H, LaBean TH, Leong KW. Nucleic acid-based nanoengineering: novel structures for biomedical applications. Interface Focus 2011; 1:702-24. [PMID: 23050076 PMCID: PMC3262286 DOI: 10.1098/rsfs.2011.0040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 01/21/2023] Open
Abstract
Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson-Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.
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Affiliation(s)
| | | | - Kam W. Leong
- Department of Biomedical Engineering, Duke University, 136 Hudson Hall, PO Box 90281, Durham, NC 27708, USA
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Campolongo MJ, Kahn JS, Cheng W, Yang D, Gupton-Campolongo T, Luo D. Adaptive DNA-based materials for switching, sensing, and logic devices. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm03854g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Niemeyer CM. Semisynthetic DNA-protein conjugates for biosensing and nanofabrication. Angew Chem Int Ed Engl 2010; 49:1200-16. [PMID: 20091721 DOI: 10.1002/anie.200904930] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conjugation with artificial nucleic acids allows proteins to be modified with a synthetically accessible, robust tag. This attachment is addressable in a highly specific manner by means of molecular recognition events, such as Watson-Crick hybridization. Such DNA-protein conjugates, with their combined properties, have a broad range of applications, such as in high-performance biomedical diagnostic assays, fundamental research on molecular recognition, and the synthesis of DNA nanostructures. This Review surveys current approaches to generate DNA-protein conjugates as well as recent advances in their applications. For example, DNA-protein conjugates have been assembled into model systems for the investigation of catalytic cascade reactions and light-harvesting devices. Such hybrid conjugates are also used for the biofunctionalization of planar surfaces for micro- and nanoarrays, and for decorating inorganic nanoparticles to enable applications in sensing, materials science, and catalysis.
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Affiliation(s)
- Christof M Niemeyer
- Technische Universität Dortmund, Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Strasse 6, 44227 Dortmund, Germany.
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Niemeyer C. Halbsynthetische DNA-Protein-Konjugate für Biosensorik und Nanofabrikation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200904930] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Numajiri K, Kuzuya A, Komiyama M. Asymmetric Secondary and Tertiary Streptavidin/DNA Complexes Selectively Formed in a Nanometer-Scale DNA Well. Bioconjug Chem 2010; 21:338-44. [DOI: 10.1021/bc900426p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kentaro Numajiri
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Akinori Kuzuya
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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Irrgang J, Ksienczyk J, Lapiene V, Niemeyer CM. Analysis of Non-Covalent Bioconjugation of Colloidal Nanoparticles by Means of Atomic Force Microscopy and Data Clustering. Chemphyschem 2009; 10:1483-91. [DOI: 10.1002/cphc.200800693] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Jonkheijm P, Weinrich D, Schröder H, Niemeyer CM, Waldmann H. Chemical strategies for generating protein biochips. Angew Chem Int Ed Engl 2008; 47:9618-47. [PMID: 19025742 DOI: 10.1002/anie.200801711] [Citation(s) in RCA: 510] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein biochips are at the heart of many medical and bioanalytical applications. Increasing interest has been focused on surface activation and subsequent functionalization strategies for immobilizing these biomolecules. Different approaches using covalent and noncovalent chemistry are reviewed; particular emphasis is placed on the chemical specificity of protein attachment and on retention of protein function. Strategies for creating protein patterns (as opposed to protein arrays) are also outlined. An outlook on promising and challenging future directions for protein biochip research and applications is also offered.
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Affiliation(s)
- Pascal Jonkheijm
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology and Faculty of Chemistry, Chemical Biology, Technical University of Dortmund, Otto Hahn Strasse 11, 44227 Dortmund, Germany
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Jonkheijm P, Weinrich D, Schröder H, Niemeyer C, Waldmann H. Chemische Verfahren zur Herstellung von Proteinbiochips. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801711] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Tang K, Gan H, Li Y, Chi L, Sun T, Fuchs H. Stereoselective Interaction between DNA and Chiral Surfaces. J Am Chem Soc 2008; 130:11284-5. [DOI: 10.1021/ja8044184] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kangjian Tang
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Hui Gan
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Yong Li
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Lifeng Chi
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Taolei Sun
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
| | - Harald Fuchs
- Physikalisches Institut, Muenster University, D-48149 Muenster, Germany, Center for Nanotechnology, Muenster University, D-48151, Germany, and Department of Chemistry, Fudan University, Shanghai 200433, P. R. China
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Liang X, Nishioka H, Takenaka N, Asanuma H. A DNA nanomachine powered by light irradiation. Chembiochem 2008; 9:702-5. [PMID: 18253940 DOI: 10.1002/cbic.200700649] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xingguo Liang
- Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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Smith SS. Nucleoprotein assemblies at the nanoscale: medical implications. Nanomedicine (Lond) 2007; 1:427-36. [PMID: 17716145 DOI: 10.2217/17435889.1.4.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bionanotechnology is exploiting the rich structural knowledge now available on DNA and DNA-protein interactions to construct nucleoprotein-based devices that have the potential not only to contribute to our understanding of the structure and function of the proteins and nucleic acids involved but also to new approaches to problems in medicine. Assemblies under development currently are poised to contribute to diagnosis and therapy. Here, I discuss recent work in this emerging field.
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Affiliation(s)
- Steven S Smith
- City of Hope National Medical Center and Beckman Research Institute, Duarte, CA 91010, USA.
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Roulon T, Le Cam E, Escudé C. A new supramolecular structure made of two different plasmids linked by a circular oligonucleotide. Chembiochem 2006; 7:912-5. [PMID: 16671125 DOI: 10.1002/cbic.200500478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thibaut Roulon
- Laboratoire Régulation et Dynamique des Génomes, Département Régulations, Développement et Diversité Moléculaire, USM 050, Muséum National d'Histoire Naturelle, CNRS UMR5153, INSERM U565, Case Postale 26, 43 rue Cuvier, 75231 Paris Cedex 05, France
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Clark J, Smith SS. Application of Nanoscale Bioassemblies to Clinical Laboratory Diagnostics. Adv Clin Chem 2006; 41:23-48. [PMID: 28682750 DOI: 10.1016/s0065-2423(05)41002-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This chapter summarizes progress in several approaches and devices that will improve and augment existing diagnostic techniques. The term bionanotechnology has been used to describe the science that supports the construction of nanoscale bioassemblies. In each of the present applications to diagnostics, bionanotechnological devices play a largely passive role. Cell surface targeting with an antibody, a growth factor, or a small molecule ligand achieves a new level of sophistication, however, it is still a passive approach. While the induced conformational changes associated with the binding of dendrimers or molecular beacons are somewhat more complex responses to the local environment, they are still largely passive mechanistically. Dynamic devices that change color with time of incubation based on the presence or absence of secondary or tertiary cellular markers within a population exhibiting a primary marker would be of considerable utility. Dynamic nanoscale devices of this type await the application of the rules of assembly associated with the scaffolds described earlier and perhaps the discovery and application of new rules of assembly and new scaffolds.
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Affiliation(s)
- Jarrod Clark
- City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Steven S Smith
- City of Hope National Medical Center and Beckman Research Institute, Duarte, California
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Abstract
DNA has many physical and chemical properties that make it a powerful material for molecular constructions at the nanometer length scale. In particular, its ability to form duplexes and other secondary structures through predictable nucleotide-sequence-directed hybridization allows for the design of programmable structural motifs which can self-assemble to form large supramolecular arrays, scaffolds, and even mechanical and logical nanodevices. Despite the large variety of structural motifs used as building blocks in the programmed assembly of supramolecular DNA nanoarchitectures, the various modules share underlying principles in terms of the design of their hierarchical configuration and the implemented nucleotide sequences. This Review is intended to provide an overview of this fascinating and rapidly growing field of research from the structural design point of view.
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Affiliation(s)
- Udo Feldkamp
- Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Universität Dortmund, Germany.
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Anselmi C, DeSantis P, Scipioni A. Nanoscale mechanical and dynamical properties of DNA single molecules. Biophys Chem 2005; 113:209-21. [PMID: 15620506 DOI: 10.1016/j.bpc.2004.09.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Revised: 09/13/2004] [Accepted: 09/13/2004] [Indexed: 11/30/2022]
Abstract
Experimental evidence suggests DNA mechanical properties, in particular intrinsic curvature and flexibility, have a role in many relevant biological processes. Systematic investigations about the origin of DNA curvature and flexibility have been carried out; however, most of the applied experimental techniques need simplifying models to interpret the data, which can affect the results. Progress in the direct visualization of macromolecules allows the analysis of morphological properties and structural changes of DNAs directly from the digitised micrographs of single molecules. In addition, the statistical analysis of a large number of molecules gives information both on the local intrinsic curvature and the flexibility of DNA tracts at nanometric scale in relatively long sequences. However, it is necessary to extend the classical worm-like chain model (WLC) for describing conformations of intrinsically straight homogeneous polymers to DNA. This review describes the various methodologies proposed by different authors.
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Affiliation(s)
- Claudio Anselmi
- Dipartimento di Chimica, Università di Roma "La Sapienza", I-00185 Rome, Italy
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Abstract
The structural properties that enable DNA to serve so effectively as genetic material can also be used for other purposes. The complementarity that leads to the pairing of the strands of the DNA double helix can be exploited to assemble more complex motifs, based on branched structures. These structures have been used as the basis of larger 2D and 3D constructions. In addition, they have been used to make nanomechanical devices. These devices range from DNA-based shape-shifting structures to gears and walkers, a DNA-stress gauge and even a translation device. The devices are activated by mechanisms as diverse as small molecules, proteins and, most intriguingly, other molecules of DNA.
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Affiliation(s)
- Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA.
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Abstract
The molecular recognition properties of DNA molecules combined with the distinct mechanical properties of single and double strands of DNA can be utilized for the construction of nanodevices, which can perform ever more tasks with possible applications ranging from nanoconstruction to intelligent drug delivery. With the help of DNA it is possible to construct machinelike devices that are capable of rotational motion, pulling and stretching, or even unidirectional motion. It is possible to devise autonomous nanodevices, to grab and release molecules, and also to perform simple information-processing tasks.
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Affiliation(s)
- Friedrich C Simmel
- Department of Physics and Center for Nanoscience, LMU Munich, Geschwister Scholl Platz 1, 80539 Munich, Germany.
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Abstract
DNA is a unique material for nanotechnology since it is possible to use base sequences to encode instructions for assembly in a predetermined fashion at the nanometre scale. Synthetic oligonucleotides are readily obtained by automated synthesis and numerous techniques have been developed for conjugating DNA with other materials. The exact spatial positioning of materials is crucial for the future development of complex nanodevices and the emerging field of DNA-nanotechnology is now exploring DNA-programmed processes for the assembly of organic compounds, biomolecules, and inorganic materials.
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Affiliation(s)
- Kurt V Gothelf
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark.
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Hazarika P, Ceyhan B, Niemeyer CM. Reversible Switching of DNA-Gold Nanoparticle Aggregation. Angew Chem Int Ed Engl 2004; 43:6469-71. [PMID: 15578785 DOI: 10.1002/anie.200461887] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Pompi Hazarika
- Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Universität Dortmund, Dortmund, Germany
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Hazarika P, Ceyhan B, Niemeyer CM. Reversible Switching of DNA-Gold Nanoparticle Aggregation. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461887] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
The nanometer scale is a special place where all sciences meet and develop a particularly strong interdisciplinarity. While biology is a source of inspiration for nanoscientists, chemistry has a central role in turning inspirations and methods from biological systems to nanotechnological use. DNA is the biological molecule by which nanoscience and nanotechnology is mostly fascinated. Nature uses DNA not only as a repository of the genetic information, but also as a controller of the expression of the genes it contains. Thus, there are codes embedded in the DNA sequence that serve to control recognition processes on the atomic scale, such as the base pairing, and others that control processes taking place on the nanoscale. From the chemical point of view, DNA is the supramolecular building block with the highest informational content. Nanoscience has therefore the opportunity of using DNA molecules to increase the level of complexity and efficiency in self-assembling and self-directing processes.
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Affiliation(s)
- Bruno Samorì
- Department of Biochemistry G. Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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Clark J, Singer EM, Korns DR, Smith SS. Design and analysis of nanoscale bioassemblies. Biotechniques 2004; 36:992-6, 998-1001. [PMID: 15211750 DOI: 10.2144/04366rv01] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bionanotechnology is an emerging field in nanotechnology. In general, it uses concepts from chemistry, biochemistry, and molecular biology to identify components and processes for the construction of self-assembling materials and devices. Distant goals of the science of bionanotechnology range from developing programmable nanoscale devices that can sample or alter their environments to developing assemblies capable of Darwinian evolution. At the heart of these approaches is the concept of the production of supramolecular assemblies (SMAs; also known as supramolecular aggregates) by programmed self-assembly in an aqueous medium. Ordered arrays, planar and closed-shell tilings, dynamic machines, and switches have been designed and constructed by using DNA-DNA, protein-protein, and protein-nucleic acid biospecificities. We review the designs and the analytical techniques that have been employed in the production of SMAs that do not occur in nature.
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Affiliation(s)
- Jarrod Clark
- Kaplan Clinical Research Laboratory, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA, USA.
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Parviz B, Ryan D, Whitesides G. Using self-assembly for the fabrication of nano-scale electronic and photonic devices. ACTA ACUST UNITED AC 2003. [DOI: 10.1109/tadvp.2003.817971] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Niemeyer CM, Adler M, Gao S, Chi L. Supramolecular DNA-streptavidin nanocircles with a covalently attached oligonucleotide moiety. J Biomol Struct Dyn 2002; 20:223-30. [PMID: 12354074 DOI: 10.1080/07391102.2002.10506838] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Covalent hybrid conjugates consisting of streptavidin (STV) and a 24-mer single-stranded DNA oligonucleotide have been used as a starting material for the synthesis of supramolecular nanocircles. For this, the covalent hybrid conjugates were oligomerized by cross-linking with 5 ,5 -bis-biotinylated double-stranded DNA (dsDNA) fragments of various length. Heat denaturation of the resulting oligomeric conjugates and subsequent rapid cooling led to the formation of the nanocircles, in which the oligonucleotide-containing STV molecule is coupled with both ends of the circular bis-biotinylated dsDNA fragment. The circular structure of the bioconjugates was established by electrophoretic studies including Ferguson plot analysis as well as by scanning force microscopy (SFM) inspection. The formation process and the stability against degradation by ligand exchange with free D-biotin was compared for the nanocircles obtained from covalent oligonucleotide-STV hybrids and native STV. The former nanocircles revealed a decreased stability with respect to ring opening than the circles obtained from native STV. This suggested that the affinity of the covalent oligonucleotide-STV hybrid for binding biotinylated DNA is significantly decreased. Nevertheless, the single-stranded oligonucleotide moiety of the hybrid nanocircles can be used as a molecular handle for further functionalization. For instance, it was used for the selective DNA-directed immobilization at a surface, previously functionalized with complementary capture oligonucleotides. Moreover, we demonstrate that a pair of nanocircles, containing complementary oligonucleotide moieties, can be hybridized to form specific dimers, thereby generating a novel type of supramolecular DNA-protein nanostructures.
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Affiliation(s)
- Christof M Niemeyer
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Str. 6, D-44227 Dortmund.
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Niemeyer CM. Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science. Angew Chem Int Ed Engl 2001; 40:4128-4158. [DOI: 10.1002/1521-3773(20011119)40:22<4128::aid-anie4128>3.0.co;2-s] [Citation(s) in RCA: 2006] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2001] [Indexed: 01/04/2023]
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Niemeyer CM. Semi-synthetic nucleic acid-protein conjugates: applications in life sciences and nanobiotechnology. J Biotechnol 2001; 82:47-66. [PMID: 11999713 DOI: 10.1016/s1389-0352(01)00027-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Semi-synthetic conjugates of nucleic acids and proteins can be generated by either covalent coupling chemistry, or else by non-covalent biomolecular recognition systems, such as receptor-ligands of complementary nucleic acids. These nucleic acid-protein conjugates are versatile molecular tools which can be applied, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of laterally microstructured biochips containing functional biological groups, and the biomimetic 'bottom-up' synthesis of nanostructured supramolecular devices. This review summarizes the current state-of-the-art synthesis and characterization methods of artificial nucleic acid-protein conjugates, as well as applications and perspectives for future developments of such hybrid biomolecular components in life sciences and nanobiotechnology.
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Affiliation(s)
- C M Niemeyer
- Universität Bremen, FB2-UFT, Biotechnologie und Molekulare Genetik, Germany.
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Abstract
Semisynthetic DNA-protein conjugates are versatile molecular tools useful, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of highly functionalized laterally microstructured biochips, and the biomimetic "bottom-up" synthesis of nanostructured supramolecular devices. This concept paper summarizes the current state-of-the-art concerning the synthesis, characterization, and applications of such hybrid molecules, and also draws perspectives on future developments.
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Affiliation(s)
- C M Niemeyer
- Universität Bremen, Biotechnologie und Molekulare Genetik, Germany.
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