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Amiri A, Abedanzadeh S, Davaeil B, Shaabani A, Moosavi-Movahedi AA. Protein click chemistry and its potential for medical applications. Q Rev Biophys 2024; 57:e6. [PMID: 38619322 DOI: 10.1017/s0033583524000027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
A revolution in chemical biology occurred with the introduction of click chemistry. Click chemistry plays an important role in protein chemistry modifications, providing specific, sensitive, rapid, and easy-to-handle methods. Under physiological conditions, click chemistry often overlaps with bioorthogonal chemistry, defined as reactions that occur rapidly and selectively without interfering with biological processes. Click chemistry is used for the posttranslational modification of proteins based on covalent bond formations. With the contribution of click reactions, selective modification of proteins would be developed, representing an alternative to other technologies in preparing new proteins or enzymes for studying specific protein functions in different biological processes. Click-modified proteins have potential in diverse applications such as imaging, labeling, sensing, drug design, and enzyme technology. Due to the promising role of proteins in disease diagnosis and therapy, this review aims to highlight the growing applications of click strategies in protein chemistry over the last two decades, with a special emphasis on medicinal applications.
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Affiliation(s)
- Ahmad Amiri
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | | | - Bagher Davaeil
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ahmad Shaabani
- Department of Chemistry, Shahid Beheshti University, Tehran, Iran
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2
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Kosara S, Singh R, Bhatia D. Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives. NANOSCALE ADVANCES 2024; 6:386-401. [PMID: 38235105 PMCID: PMC10790967 DOI: 10.1039/d3na00692a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024]
Abstract
DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.
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Affiliation(s)
- Sanjay Kosara
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
| | - Ramesh Singh
- Department of Mechanical Engineering, Colorado State University Fort Collins CO USA
| | - Dhiraj Bhatia
- Department of Biological Sciences and Engineering, Indian Institute of Technology Gandhinagar Palaj Gujarat 382355 India
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3
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Maingi V, Zhang Z, Thachuk C, Sarraf N, Chapman ER, Rothemund PWK. Digital nanoreactors to control absolute stoichiometry and spatiotemporal behavior of DNA receptors within lipid bilayers. Nat Commun 2023; 14:1532. [PMID: 36941256 PMCID: PMC10027858 DOI: 10.1038/s41467-023-36996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Interactions between membrane proteins are essential for cell survival but are often poorly understood. Even the biologically functional ratio of components within a multi-subunit membrane complex-the native stoichiometry-is difficult to establish. Here we demonstrate digital nanoreactors that can control interactions between lipid-bound molecular receptors along three key dimensions: stoichiometric, spatial, and temporal. Each nanoreactor is based on a DNA origami ring, which both templates the synthesis of a liposome and provides tethering sites for DNA-based receptors (modelling membrane proteins). Receptors are released into the liposomal membrane using strand displacement and a DNA logic gate measures receptor heterodimer formation. High-efficiency tethering of receptors enables the kinetics of receptors in 1:1 and 2:2 absolute stoichiometries to be observed by bulk fluorescence, which in principle is generalizable to any ratio. Similar single-molecule-in-bulk experiments using DNA-linked membrane proteins could determine native stoichiometry and the kinetics of membrane protein interactions for applications ranging from signalling research to drug discovery.
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Affiliation(s)
- Vishal Maingi
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
| | - Zhao Zhang
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA
| | - Chris Thachuk
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA.
| | - Namita Sarraf
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Edwin R Chapman
- Department of Neuroscience and Howard Hughes Medical Institute, University of Wisconsin-Madison, 1111 Highland Avenue, Madison, WI, 53705, USA.
| | - Paul W K Rothemund
- Department of Bioengineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation & Neural Systems, California Institute of Technology, Pasadena, CA, USA.
- Department of Computation + Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA.
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4
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Nucleic acid-based scaffold systems and application in enzyme cascade catalysis. Appl Microbiol Biotechnol 2022; 107:9-23. [DOI: 10.1007/s00253-022-12315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022]
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5
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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6
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022; 61:e202208367. [DOI: 10.1002/anie.202208367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Indexed: 12/18/2022]
Affiliation(s)
- Nada Farag
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Gianfranco Ercolani
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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7
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Farag N, Ercolani G, Del Grosso E, Ricci F. DNA Tile Self‐Assembly Guided by Base Excision Repair Enzymes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nada Farag
- Universita degli Studi di Roma Tor Vergata Chemistry ITALY
| | | | | | - Francesco Ricci
- University of Rome, Tor Vergata Department of Chemistry Via della Ricerca Scientifica 00133 Rome ITALY
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8
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Willaert RG, Kasas S. High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions Using DNA Origami Frames. Methods Mol Biol 2022; 2516:157-167. [PMID: 35922627 DOI: 10.1007/978-1-0716-2413-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Direct, live imaging of protein-DNA interactions under physiological conditions is invaluable for understanding the mechanism and kinetics of binding and understanding the topological changes of the DNA strand. The DNA origami technology allows for precise placement of target molecules in a designed nanostructure. Here, we describe a protocol for the self-assembly of DNA origami frames with 2 stretched DNA sequences containing the binding site of a transcription factor, i.e., the Protein FadR, which is a TetR-family tanscription factor regulator for fatty acid metabolism in the archaeal organism Sulfolobus acidocaldarius. These frames can be used to study the dynamics of transcription factor binding using high-speed AFM and obtain mechanistic insights into the mechanism of action of transcription factors.
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Affiliation(s)
- Ronnie G Willaert
- Research Group Structural Biology Brussels, Alliance Research Group VUB-UGent NanoMicrobiology (NAMI), Brussels, Belgium.
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Brussels, Belgium.
| | - Sandor Kasas
- International Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, Brussels, Belgium
- Laboratory of Biological Electron Microscopy, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Centre Universitaire Romand de Médecine Légale, UFAM, Université de Lausanne, Lausanne, Switzerland
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9
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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10
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Encoding hierarchical assembly pathways of proteins with DNA. Proc Natl Acad Sci U S A 2021; 118:2106808118. [PMID: 34593642 DOI: 10.1073/pnas.2106808118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
The structural and functional diversity of materials in nature depends on the controlled assembly of discrete building blocks into complex architectures via specific, multistep, hierarchical assembly pathways. Achieving similar complexity in synthetic materials through hierarchical assembly is challenging due to difficulties with defining multiple recognition areas on synthetic building blocks and controlling the sequence through which those recognition sites direct assembly. Here, we show that we can exploit the chemical anisotropy of proteins and the programmability of DNA ligands to deliberately control the hierarchical assembly of protein-DNA materials. Through DNA sequence design, we introduce orthogonal DNA interactions with disparate interaction strengths ("strong" and "weak") onto specific geometric regions of a model protein, stable protein 1 (Sp1). We show that the spatial encoding of DNA ligands leads to highly directional assembly via strong interactions and that, by design, the first stage of assembly increases the multivalency of weak DNA-DNA interactions that give rise to an emergent second stage of assembly. Furthermore, we demonstrate that judicious DNA design not only directs assembly along a given pathway but can also direct distinct structural outcomes from a single pathway. This combination of protein surface and DNA sequence design allows us to encode the structural and chemical information necessary into building blocks to program their multistep hierarchical assembly. Our findings represent a strategy for controlling the hierarchical assembly of proteins to realize a diverse set of protein-DNA materials by design.
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11
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Berger RML, Weck JM, Kempe SM, Hill O, Liedl T, Rädler JO, Monzel C, Heuer-Jungemann A. Nanoscale FasL Organization on DNA Origami to Decipher Apoptosis Signal Activation in Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101678. [PMID: 34057291 DOI: 10.1002/smll.202101678] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/13/2021] [Indexed: 05/27/2023]
Abstract
Cell signaling is initiated by characteristic protein patterns in the plasma membrane, but tools to decipher their molecular organization and activation are hitherto lacking. Among the well-known signaling pattern is the death inducing signaling complex with a predicted hexagonal receptor architecture. To probe this architecture, DNA origami-based nanoagents with nanometer precise arrangements of the death receptor ligand FasL are introduced and presented to cells. Mimicking different receptor geometries, these nanoagents act as signaling platforms inducing fastest time-to-death kinetics for hexagonal FasL arrangements with 10 nm inter-molecular spacing. Compared to naturally occurring soluble FasL, this trigger is faster and 100× more efficient. Nanoagents with different spacing, lower FasL number or higher coupling flexibility impede signaling. The results present DNA origami as versatile signaling scaffolds exhibiting unprecedented control over molecular number and geometry. They define molecular benchmarks in apoptosis signal initiation and constitute a new strategy to drive particular cell responses.
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Affiliation(s)
- Ricarda M L Berger
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Johann M Weck
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Simon M Kempe
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Oliver Hill
- Apogenix AG, University of Heidelberg, Im Neuenheimer Feld 584, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Cornelia Monzel
- Experimental Medical Physics, Heinrich-Heine University, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and Center for Nanoscience (CeNS), Ludwig-Maximilians-University, Am Klopferspitz 18, 82152, Martinsried, Germany
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12
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Abstract
DNA nanotechnology has progressed from proof-of-concept demonstrations of structural design towards application-oriented research. As a natural material with excellent self-assembling properties, DNA is an indomitable choice for various biological applications, including biosensing, cell modulation, bioimaging and drug delivery. However, a major impediment to the use of DNA nanostructures in biological applications is their susceptibility to attack by nucleases present in the physiological environment. Although several DNA nanostructures show enhanced resistance to nuclease attack compared with duplexes and plasmid DNA, this may be inadequate for practical application. Recently, several strategies have been developed to increase the nuclease resistance of DNA nanostructures while retaining their functions, and the stability of various DNA nanostructures has been studied in biological fluids, such as serum, urine and cell lysates. This Review discusses the approaches used to modulate nuclease resistance in DNA nanostructures and provides an overview of the techniques employed to evaluate resistance to degradation and quantify stability.
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Affiliation(s)
- Arun Richard Chandrasekaran
- grid.265850.c0000 0001 2151 7947The RNA Institute, University at Albany, State University of New York, Albany, NY USA
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13
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Schaffter SW, Schneider J, Agrawal DK, Pacella MS, Rothchild E, Murphy T, Schulman R. Reconfiguring DNA Nanotube Architectures via Selective Regulation of Terminating Structures. ACS NANO 2020; 14:13451-13462. [PMID: 33048538 DOI: 10.1021/acsnano.0c05340] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular assemblies inside cells often undergo structural reconfiguration in response to stimuli to alter their function. Adaptive reconfiguration of cytoskeletal networks, for example, enables cellular shape change, movement, and cargo transport and plays a key role in driving complex processes such as division and differentiation. The cellular cytoskeleton is a self-assembling polymer network composed of simple filaments, so reconfiguration often occurs through the rearrangement of its component filaments' connectivities. DNA nanotubes have emerged as promising building blocks for constructing programmable synthetic analogs of cytoskeletal networks. Nucleating seeds can control when and where nanotubes grow, and capping structures can bind nanotube ends to stop growth. Such seeding and capping structures, collectively called termini, can organize nanotubes into larger architectures. However, these structures cannot be selectively activated or inactivated in response to specific stimuli to rearrange nanotube architectures, a key property of cytoskeletal networks. Here, we demonstrate how selective regulation of the binding affinity of DNA nanotube termini for DNA nanotube monomers or nanotube ends can direct the reconfiguration of nanotube architectures. Using DNA hybridization and strand displacement reactions that specifically activate or inactivate four orthogonal nanotube termini, we demonstrate that nanotube architectures can be reconfigured by selective addition or removal of distinct termini. Finally, we show how terminus activation could be a sensitive detector and amplifier of a DNA sequence signal. These results could enable the development of adaptive and multifunctional materials or diagnostic tools.
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Affiliation(s)
- Samuel W Schaffter
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Joanna Schneider
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Deepak K Agrawal
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael S Pacella
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric Rothchild
- Material Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Terence Murphy
- Our Lady of Lourdes High School, Poughkeepsie, New York 12603, United States
| | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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14
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Morya V, Walia S, Mandal BB, Ghoroi C, Bhatia D. Functional DNA Based Hydrogels: Development, Properties and Biological Applications. ACS Biomater Sci Eng 2020; 6:6021-6035. [DOI: 10.1021/acsbiomaterials.0c01125] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Vinod Morya
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Shanka Walia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Biman B Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam India
| | - Chinmay Ghoroi
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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15
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Abstract
DNA is now well-established as a nanoscale building material with applications in fields such as biosensing and molecular computation. Molecular processes such as logic gates, nucleic acid circuits, and multiplexed detection have used different readout strategies to measure the output signal. In biosensing, this output can be the diagnosis of a disease biomarker, whereas in molecular computation, the output can be the result of a mathematical operation carried out using DNA. Recent developments have shown that the output of such processes can be displayed graphically as a macroscopic symbol or an alphanumeric character on multiwell plates, microarray chips, gels, lateral flow devices, and DNA origami surfaces. This review discusses the concepts behind such graphical readouts of molecular events, available display platforms, and the advantages and challenges in adapting such methods for practical use. Graphical display systems have the potential to be used in the creation of intelligent computing and sensing devices by which nanoscale binding events are translated into macroscopic visual readouts.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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16
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Loretan M, Domljanovic I, Lakatos M, Rüegg C, Acuna GP. DNA Origami as Emerging Technology for the Engineering of Fluorescent and Plasmonic-Based Biosensors. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E2185. [PMID: 32397498 PMCID: PMC7254321 DOI: 10.3390/ma13092185] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/23/2022]
Abstract
DNA nanotechnology is a powerful and promising tool for the development of nanoscale devices for numerous and diverse applications. One of the greatest potential fields of application for DNA nanotechnology is in biomedicine, in particular biosensing. Thanks to the control over their size, shape, and fabrication, DNA origami represents a unique opportunity to assemble dynamic and complex devices with precise and predictable structural characteristics. Combined with the addressability and flexibility of the chemistry for DNA functionalization, DNA origami allows the precise design of sensors capable of detecting a large range of different targets, encompassing RNA, DNA, proteins, small molecules, or changes in physico-chemical parameters, that could serve as diagnostic tools. Here, we review some recent, salient developments in DNA origami-based sensors centered on optical detection methods (readout) with a special emphasis on the sensitivity, the selectivity, and response time. We also discuss challenges that still need to be addressed before this approach can be translated into robust diagnostic devices for bio-medical applications.
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Affiliation(s)
- Morgane Loretan
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
| | - Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland;
| | - Mathias Lakatos
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland;
| | - Guillermo P. Acuna
- Photonic Nanosystems, Department of Physics, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 3, PER08, 1700 Fribourg, Switzerland; (M.L.); (G.P.A.)
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17
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Li F, Wang D, Zhou J, Men D, Zhan XE. Design and biosynthesis of functional protein nanostructures. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1142-1158. [PMID: 32253589 DOI: 10.1007/s11427-019-1641-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023]
Abstract
Proteins are one of the major classes of biomolecules that execute biological functions for maintenance of life. Various kinds of nanostructures self-assembled from proteins have been created in nature over millions of years of evolution, including protein nanowires, layers and nanocages. These protein nanostructures can be reconstructed and equipped with desired new functions. Learning from and manipulating the self-assembly of protein nanostructures not only help to deepen our understanding of the nature of life but also offer new routes to fabricate novel nanomaterials for diverse applications. This review summarizes the recent research progress in this field, focusing on the characteristics, functionalization strategies, and applications of protein nanostructures.
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Affiliation(s)
- Feng Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Dianbing Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xian-En Zhan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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18
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Chandrasekaran AR, Punnoose JA, Zhou L, Dey P, Dey BK, Halvorsen K. DNA nanotechnology approaches for microRNA detection and diagnosis. Nucleic Acids Res 2019; 47:10489-10505. [PMID: 31287874 PMCID: PMC6847506 DOI: 10.1093/nar/gkz580] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.
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Affiliation(s)
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
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19
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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20
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Dong Y, Mao Y. DNA Origami as Scaffolds for Self‐Assembly of Lipids and Proteins. Chembiochem 2019; 20:2422-2431. [DOI: 10.1002/cbic.201900073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/22/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuanchen Dong
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- Present address: CAS Key Laboratory of Colloid Interfaces and Chemical ThermodynamicsInstitute of ChemistryChinese Academy of Sciences No. 2 Zhongguancun Beiyijie Beijing 100190 P.R. China
| | - Youdong Mao
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteDepartment of MicrobiologyHarvard Medical School 450 Brookline Avenue Boston MA 02215 USA
- Intel Parallel Computing Center for Structural BiologyDana-Farber Cancer Institute 450 Brookline Avenue Boston MA 02215 USA
- State Key Laboratory for Artificial Microstructures and Mesoscopic PhysicsSchool of PhysicsCenter for Quantitative BiologyPeking University Beijing 100871 P.R. China
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21
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Azéma L, Bonnet-Salomon S, Endo M, Takeuchi Y, Durand G, Emura T, Hidaka K, Dausse E, Sugiyama H, Toulmé JJ. Triggering nucleic acid nanostructure assembly by conditional kissing interactions. Nucleic Acids Res 2019; 46:1052-1058. [PMID: 29272518 PMCID: PMC5814900 DOI: 10.1093/nar/gkx1267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids are biomolecules of amazing versatility. Beyond their function for information storage they can be used for building nano-objects. We took advantage of loop–loop or kissing interactions between hairpin building blocks displaying complementary loops for driving the assembly of nucleic acid nano-architectures. It is of interest to make the interaction between elementary units dependent on an external trigger, thus allowing the control of the scaffold formation. To this end we exploited the binding properties of structure-switching aptamers (aptaswitch). Aptaswitches are stem–loop structured oligonucleotides that engage a kissing complex with an RNA hairpin in response to ligand-induced aptaswitch folding. We demonstrated the potential of this approach by conditionally assembling oligonucleotide nanorods in response to the addition of adenosine.
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Affiliation(s)
- Laurent Azéma
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | | | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science, Kyoto University, Kyoto 606-8501, Japan
| | - Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Guillaume Durand
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eric Dausse
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science, Kyoto University, Kyoto 606-8501, Japan
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22
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Kizer ME, Linhardt RJ, Chandrasekaran AR, Wang X. A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805386. [PMID: 30985074 DOI: 10.1002/smll.201805386] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Precise control of DNA base pairing has rapidly developed into a field full of diverse nanoscale structures and devices that are capable of automation, performing molecular analyses, mimicking enzymatic cascades, biosensing, and delivering drugs. This DNA-based platform has shown the potential of offering novel therapeutics and biomolecular analysis but will ultimately require clever modification to enrich or achieve the needed "properties" and make it whole. These modifications total what are categorized as the molecular hero suit of DNA nanotechnology. Like a hero, DNA nanostructures have the ability to put on a suit equipped with honing mechanisms, molecular flares, encapsulated cargoes, a protective body armor, and an evasive stealth mode.
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Affiliation(s)
- Megan E Kizer
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | | | - Xing Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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23
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Monferrer A, Zhang D, Lushnikov AJ, Hermann T. Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules. Nat Commun 2019; 10:608. [PMID: 30723214 PMCID: PMC6363791 DOI: 10.1038/s41467-019-08521-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/16/2019] [Indexed: 11/09/2022] Open
Abstract
DNA and RNA have emerged as a material for nanotechnology applications that take advantage of the nucleic acids' ability to encode folding and programmable self-assembly through mainly base pairing. The two types of nucleic acid have rarely been used in combination to enhance structural diversity or for partitioning of functional and architectural roles. Here, we report a design and screening strategy to integrate combinations of RNA motifs as architectural joints and DNA building blocks as functional modules for programmable self-assembly of a versatile toolkit of polygonal nucleic acid nanoshapes. Clean incorporation of diverse DNA modules with various topologies attest to the extraordinary robustness of the RNA-DNA hybrid framework. The design and screening strategy enables systematic development of RNA-DNA hybrid nanoshapes as programmable platforms for applications in molecular recognition, sensor and catalyst development as well as protein interaction studies.
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Affiliation(s)
- Alba Monferrer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Douglas Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | | | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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24
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Dang DT, van Onzen AHAM, Dorland YL, Brunsveld L. Cucurbit[8]uril Reactivation of an Inactivated Caspase-8 Mutant Reveals Differentiated Enzymatic Substrate Processing. Chembiochem 2018; 19:2490-2494. [PMID: 30300966 PMCID: PMC6391946 DOI: 10.1002/cbic.201800521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 01/26/2023]
Abstract
Caspase‐8 constructs featuring an N‐terminal FGG sequence allow for selective twofold recognition by cucurbit[8]uril, which leads to an increase of the enzymatic activity in a cucurbit[8]uril dose‐dependent manner. This supramolecular switching has enabled for the first time the study of the same caspase‐8 in its two extreme states; as full monomer and as cucurbit[8]uril induced dimer. A mutated, fully monomeric caspase‐8 (D384A), which is enzymatically inactive towards its natural substrate caspase‐3, could be fully reactivated upon addition of cucurbit[8]uril. In its monomeric state caspase‐8 (D384A) still processes a small synthetic substrate, but not the natural caspase‐3 substrate, highlighting the close interplay between protein dimerization and active site rearrangement for substrate selectivity. The ability to switch the caspase‐8 activity by a supramolecular system thus provides a flexible approach to studying the activity of a protein at different oligomerization states.
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Affiliation(s)
- Dung T Dang
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and, Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Arthur H A M van Onzen
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and, Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Yvonne L Dorland
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and, Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering, and, Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
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25
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Bösch CD, Jevric J, Bürki N, Probst M, Langenegger SM, Häner R. Supramolecular Assembly of DNA-Phenanthrene Conjugates into Vesicles with Light-Harvesting Properties. Bioconjug Chem 2018; 29:1505-1509. [DOI: 10.1021/acs.bioconjchem.8b00263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Caroline D. Bösch
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Jovana Jevric
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Nutcha Bürki
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Markus Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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26
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Kuzyk A, Jungmann R, Acuna GP, Liu N. DNA Origami Route for Nanophotonics. ACS PHOTONICS 2018; 5:1151-1163. [PMID: 30271812 PMCID: PMC6156112 DOI: 10.1021/acsphotonics.7b01580] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/06/2018] [Accepted: 02/11/2018] [Indexed: 05/21/2023]
Abstract
The specificity and simplicity of the Watson-Crick base pair interactions make DNA one of the most versatile construction materials for creating nanoscale structures and devices. Among several DNA-based approaches, the DNA origami technique excels in programmable self-assembly of complex, arbitrary shaped structures with dimensions of hundreds of nanometers. Importantly, DNA origami can be used as templates for assembly of functional nanoscale components into three-dimensional structures with high precision and controlled stoichiometry. This is often beyond the reach of other nanofabrication techniques. In this Perspective, we highlight the capability of the DNA origami technique for realization of novel nanophotonic systems. First, we introduce the basic principles of designing and fabrication of DNA origami structures. Subsequently, we review recent advances of the DNA origami applications in nanoplasmonics, single-molecule and super-resolution fluorescent imaging, as well as hybrid photonic systems. We conclude by outlining the future prospects of the DNA origami technique for advanced nanophotonic systems with tailored functionalities.
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Affiliation(s)
- Anton Kuzyk
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Department
of Neuroscience and Biomedical Engineering, Aalto University School of Science, P.O. Box 12200, FI-00076 Aalto, Finland
| | - Ralf Jungmann
- Department
of Physics and Center for Nanoscience, Ludwig
Maximilian University, 80539 Munich, Germany
- Max
Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Guillermo P. Acuna
- Institute
for Physical & Theoretical Chemistry, and Braunschweig Integrated
Centre of Systems Biology (BRICS), and Laboratory for Emerging Nanometrology
(LENA), Braunschweig University of Technology, Rebenring 56, 38106 Braunschweig, Germany
| | - Na Liu
- Max
Planck Institute for Intelligent Systems, Heisenbergstrasse 3, D-70569 Stuttgart, Germany
- Kirchhoff
Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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27
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Wenz NL, Piasecka S, Kalinowski M, Schneider A, Richert C, Wege C. Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. NANOSCALE 2018; 10:6496-6510. [PMID: 29569670 DOI: 10.1039/c7nr07743b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.
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Affiliation(s)
- Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sylwia Piasecka
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Matthäus Kalinowski
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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28
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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29
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Tang MSL, Shiu SCC, Godonoga M, Cheung YW, Liang S, Dirkzwager RM, Kinghorn AB, Fraser LA, Heddle JG, Tanner JA. An aptamer-enabled DNA nanobox for protein sensing. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2018; 14:1161-1168. [PMID: 29410111 DOI: 10.1016/j.nano.2018.01.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
DNA nanostructures can show dynamic responses to molecular triggers for a wide variety of applications. While DNA sequence signal triggers are now well-established, there is a critical need for a broader diversity of molecular triggers to drive dynamic responses in DNA nanostructures. DNA aptamers are ideal; they can both seamlessly integrate into DNA nanostructure scaffolds and transduce molecular recognition into functional responses. Here, we report construction and optimization of a DNA origami nanobox locked by a pair of DNA double strands where one strand is a DNA aptamer targeting the malaria biomarker protein Plasmodium falciparum lactate dehydrogenase. The protein acts as the key which enables box opening. We observe highly specific protein-mediated box opening by both transmission electron microscopy and fluorescence. Aptamer-enabled DNA boxes have significant potential for enabling direct responses to proteins and other biomolecules in nanoscale diagnostics, drug delivery and sensing devices.
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Affiliation(s)
- Marco S L Tang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maia Godonoga
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan
| | - Yee-Wai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shaolin Liang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Roderick M Dirkzwager
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lewis A Fraser
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jonathan G Heddle
- Heddle Initiative Research Unit, RIKEN, Saitama, Japan; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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30
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Lapenta F, Aupič J, Strmšek Ž, Jerala R. Coiled coil protein origami: from modular design principles towards biotechnological applications. Chem Soc Rev 2018; 47:3530-3542. [DOI: 10.1039/c7cs00822h] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review illustrates the current state in designing coiled-coil-based proteins with an emphasis on coiled coil protein origami structures and their potential.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology
- National Institute of Chemistry
- Ljubljana
- Slovenia
- EN-FIST Centre of Excellence
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31
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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32
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Hou C, Guan S, Wang R, Zhang W, Meng F, Zhao L, Xu J, Liu J. Supramolecular Protein Assemblies Based on DNA Templates. J Phys Chem Lett 2017; 8:3970-3979. [PMID: 28792224 DOI: 10.1021/acs.jpclett.7b01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.
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Affiliation(s)
| | | | - Ruidi Wang
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada
| | - Wei Zhang
- Zhuhai United Laboratories Co., Ltd. , Nation High & New Technology Industry Development Zone, Zhuhai 519040, China
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33
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Avakyan N, Conway JW, Sleiman HF. Long-Range Ordering of Blunt-Ended DNA Tiles on Supported Lipid Bilayers. J Am Chem Soc 2017; 139:12027-12034. [PMID: 28783358 DOI: 10.1021/jacs.7b06572] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nicole Avakyan
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Justin W. Conway
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal QC H3A 0B8, Canada
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34
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Minagawa H, Onodera K, Fujita H, Sakamoto T, Akitomi J, Kaneko N, Shiratori I, Kuwahara M, Horii K, Waga I. Selection, Characterization and Application of Artificial DNA Aptamer Containing Appended Bases with Sub-nanomolar Affinity for a Salivary Biomarker. Sci Rep 2017; 7:42716. [PMID: 28256555 PMCID: PMC5335659 DOI: 10.1038/srep42716] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 01/12/2017] [Indexed: 12/21/2022] Open
Abstract
We have attained a chemically modified DNA aptamer against salivary α-amylase (sAA), which attracts researchers’ attention as a useful biomarker for assessing human psychobiological and social behavioural processes, although high affinity aptamers have not been isolated from a random natural DNA library to date. For the selection, we used the base-appended base (BAB) modification, that is, a modified-base DNA library containing (E)-5-(2-(N-(2-(N6-adeninyl)ethyl))carbamylvinyl)-uracil in place of thymine. After eight rounds of selection, a 75 mer aptamer, AMYm1, which binds to sAA with extremely high affinity (Kd < 1 nM), was isolated. Furthermore, we have successfully determined the 36-mer minimum fragment, AMYm1-3, which retains target binding activity comparable to the full-length AMYm1, by surface plasmon resonance assays. Nuclear magnetic resonance spectral analysis indicated that the minimum fragment forms a specific stable conformation, whereas the predicted secondary structures were suggested to be disordered forms. Thus, DNA libraries with BAB-modifications can achieve more diverse conformations for fitness to various targets compared with natural DNA libraries, which is an important advantage for aptamer development. Furthermore, using AMYm1, a capillary gel electrophoresis assay and lateral flow assay with human saliva were conducted, and its feasibility was demonstrated.
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Affiliation(s)
- Hirotaka Minagawa
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Kentaro Onodera
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
| | - Joe Akitomi
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Naoto Kaneko
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Ikuo Shiratori
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Katsunori Horii
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
| | - Iwao Waga
- Innovation Laboratory, NEC Solution Innovators, Ltd., 1-18-7, Shinkiba, Koto-Ku, Tokyo 136-8627, Japan
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Valsangkar V, Chandrasekaran AR, Wang R, Haruehanroengra P, Levchenko O, Halvorsen K, Sheng J. Click-based functionalization of a 2'-O-propargyl-modified branched DNA nanostructure. J Mater Chem B 2017; 5:2074-2077. [PMID: 32263680 DOI: 10.1039/c6tb03277j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA has emerged as a versatile building block for programmable self-assembly. DNA-based nanostructures have been widely applied in biosensing, bioimaging, drug delivery, molecular computation and macromolecular scaffolding. A variety of strategies have been developed to functionalize these nanostructures. In this study, we report a facile click-based strategy to incorporate a metal chelating ligand and a fluorescent tag into a three-point-star DNA tile containing 2'-O-propargyl groups. Such a strategy opens up the possibility of functionalizing pre-assembled DNA strands to construct platforms for metal or drug delivery.
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Affiliation(s)
- Vibhav Valsangkar
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA.
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36
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Irani AH, Owen JL, Mercadante D, Williams MAK. Molecular Dynamics Simulations Illuminate the Role of Counterion Condensation in the Electrophoretic Transport of Homogalacturonans. Biomacromolecules 2017; 18:505-516. [DOI: 10.1021/acs.biomac.6b01599] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Amir H. Irani
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jessie L. Owen
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - Martin A. K. Williams
- Institute
of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The MacDiarmid Institute
of Advanced Materials and Nanotechnology, Wellington, New Zealand
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37
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Mukhortava A, Schlierf M. Efficient Formation of Site-Specific Protein–DNA Hybrids Using Copper-Free Click Chemistry. Bioconjug Chem 2016; 27:1559-63. [DOI: 10.1021/acs.bioconjchem.6b00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann Mukhortava
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
| | - Michael Schlierf
- B CUBE − Center for
Molecular Bioengineering, Technische Universität Dresden, Arnoldstraße
18, 01307 Dresden, Germany
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38
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Chandrasekaran AR, Wady H, Subramanian HKK. Nucleic Acid Nanostructures for Chemical and Biological Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2689-2700. [PMID: 27040036 DOI: 10.1002/smll.201503854] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
The nanoscale features of DNA have made it a useful molecule for bottom-up construction of nanomaterials, for example, two- and three-dimensional lattices, nanomachines, and nanodevices. One of the emerging applications of such DNA-based nanostructures is in chemical and biological sensing, where they have proven to be cost-effective, sensitive and have shown promise as point-of-care diagnostic tools. DNA is an ideal molecule for sensing not only because of its specificity but also because it is robust and can function under a broad range of biologically relevant temperatures and conditions. DNA nanostructure-based sensors provide biocompatibility and highly specific detection based on the molecular recognition properties of DNA. They can be used for the detection of single nucleotide polymorphism and to sense pH both in solution and in cells. They have also been used to detect clinically relevant tumor biomarkers. In this review, recent advances in DNA-based biosensors for pH, nucleic acids, tumor biomarkers and cancer cell detection are introduced. Some challenges that lie ahead for such biosensors to effectively compete with established technologies are also discussed.
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Affiliation(s)
| | - Heitham Wady
- Upstate Medical University, State University of New York, Syracuse, NY, 13210, USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA
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39
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute; University at Albany, State University of New York; 1400 Washington Avenue Albany NY 12222 USA
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40
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Chandrasekaran AR, Anderson N, Kizer M, Halvorsen K, Wang X. Beyond the Fold: Emerging Biological Applications of DNA Origami. Chembiochem 2016; 17:1081-9. [PMID: 26928725 DOI: 10.1002/cbic.201600038] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/22/2023]
Abstract
The use of DNA as a material for nanoscale construction has blossomed in the past decade. This is largely attributable to the DNA origami technique, which has enabled construction of nanostructures ranging from simple two-dimensional sheets to complex three-dimensional objects with defined curves and edges. These structures are amenable to site-specific functionalization with nanometer precision, and have been shown to exhibit cellular biocompatibility and permeability. The DNA origami technique has already found widespread use in a variety of emerging biological applications such as biosensing, enzyme cascades, biomolecular analysis, biomimetics, and drug delivery. We highlight a few of these applications and comments on the prospects for this rapidly expanding field of research.
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Affiliation(s)
| | - Nate Anderson
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. , .,Center for Biotechnology and Interdisciplinary Studies (CBIS), Rensselaer Polytechnic Institute, Troy, NY, 12180, USA. ,
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Chandrasekaran AR. Designer DNA Architectures: Applications in Nanomedicine. Nanobiomedicine (Rij) 2016; 3:6. [PMID: 29942381 PMCID: PMC5998270 DOI: 10.5772/63228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022] Open
Abstract
DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeability, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.
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