101
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Lohmann F, Weigandt J, Valero J, Famulok M. Logic gating by macrocycle displacement using a double-stranded DNA [3]rotaxane shuttle. Angew Chem Int Ed Engl 2014; 53:10372-6. [PMID: 25078433 DOI: 10.1002/anie.201405447] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/31/2022]
Abstract
Molecular interlocked systems with mechanically trapped components can serve as versatile building blocks for dynamic nanostructures. Here we report the synthesis of unprecedented double-stranded (ds) DNA [2]- and [3]rotaxanes with two distinct stations for the hybridization of the macrocycles on the axle. In the [3]rotaxane, the release and migration of the "shuttle ring" mobilizes a second macrocycle in a highly controlled fashion. Different oligodeoxynucleotides (ODNs) employed as inputs induce structural changes in the system that can be detected as diverse logically gated output signals. We also designed nonsymmetrical [2]rotaxanes which allow unambiguous localization of the position of the macrocycle by use of atomic force microscopy (AFM). Either light irradiation or the use of fuel ODNs can drive the threaded macrocycle to the desired station in these shuttle systems. The DNA nanostructures introduced here constitute promising prototypes for logically gated cargo delivery and release shuttles.
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Affiliation(s)
- Finn Lohmann
- Life and Medical Science (LIMES) Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk Strasse 1, 53121 Bonn (Germany) http://www.famuloklab.de
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102
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Rajendran A, Endo M, Hidaka K, Shimada N, Maruyama A, Sugiyama H. A lock-and-key mechanism for the controllable fabrication of DNA origami structures. Chem Commun (Camb) 2014; 50:8743-6. [DOI: 10.1039/c4cc02244k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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103
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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104
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Chen N, Li J, Song H, Chao J, Huang Q, Fan C. Physical and biochemical insights on DNA structures in artificial and living systems. Acc Chem Res 2014; 47:1720-30. [PMID: 24588263 DOI: 10.1021/ar400324n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CONSPECTUS: Highly specific DNA base-pairing is the basis for both fulfilling its genetic role and constructing novel nanostructures and hybrid conjugates with inorganic nanomaterials (NMs). There exist many remarkable differences in the physical properties of single-stranded (ss) and double-stranded (ds) DNA, which play important roles in regulation of biological processes in nature. Rapid advances in nanoscience and nanotechnology pose new questions on how DNA and DNA structures interact with inorganic nanomaterials or cells and animals, which should be important for their biological and biomedical applications. In this Account, we intend to provide an overview on many facets of DNA and DNA structures in artificial and living systems, with the focus on their properties and functions at the interfaces of inorganic nanomaterials and biological systems. ssDNA, dsDNA, and DNA nanostructures interact with NMs in different ways. In particular, gold nanoparticles and graphene oxide exhibit strikingly different affinity toward ssDNA and dsDNA. Such binding differences can be coupled with optical properties of NMs. For example, DNA hybridization can effectively modulate the plasmonic and catalytic properties of gold nanoparticles. By exploitation of these interactions, there have been many ways for sensitive transduction of biomolecular recognition for various sensing applications. Alternatively, modulation of the properties of DNA and DNA structures with NMs has led to new tools for genetic analysis including genotyping and haplotyping. Self-assembled DNA nanostructures have emerged as a new type of NMs with pure biomolecules. These nanostructures can be designed in one, two, or three dimensions with various sizes, shapes, and geometries. They also have characteristics of uniform size, precise addressability, excellent water solubility, and biocompatibility. These nanostructures provide a new toolbox for biophysical studies with unparalleled advantages, for example, NMR-based protein structure determination and single-molecule studies. Also importantly, DNA nanostructures have proven highly useful in various applications including biological detection, bioreactors, and nanomedicine. In particular, DNA nanostructures exhibit high cellular permeability, a property that is not available for ssDNA and dsDNA, which is required for their drug delivery applications. DNA and DNA structures can also form hybrids with inorganic NMs. Notably, DNA anchored at the interface of inorganic NMs behaves differently from that at the macroscopic interface. Several types of DNA-NM conjugates have exerted beneficial effects for bioassays and in vitro translation of proteins. Even more interestingly, hybrid nanoconjugates demonstrate distinct properties under the context of biological systems such as cultured cells or animal models. These unprecedented properties not only arouse great interest in studying such interfaces but also open new opportunities for numerous applications in artificial and living systems.
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Affiliation(s)
- Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haiyun Song
- Key
Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Chao
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Sychrotron Radiation Facility (SSRF), CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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105
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Endo M, Sugiyama H. Single-molecule imaging of dynamic motions of biomolecules in DNA origami nanostructures using high-speed atomic force microscopy. Acc Chem Res 2014; 47:1645-53. [PMID: 24601497 DOI: 10.1021/ar400299m] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
CONSPECTUS: Direct imaging of molecular motions is one of the most fundamental issues for elucidating the physical properties of individual molecules and their reaction mechanisms. Atomic force microscopy (AFM) enables direct molecular imaging, especially for biomolecules in the physiological environment. Because AFM can visualize the molecules at nanometer-scale spatial resolution, a versatile observation scaffold is needed for the precise imaging of molecule interactions in the reactions. The emergence of DNA origami technology allows the precise placement of desired molecules in the designed nanostructures and enables molecules to be detected at the single-molecule level. In our study, the DNA origami system was applied to visualize the detailed motions of target molecules in reactions using high-speed AFM (HS-AFM), which enables the analysis of dynamic motions of biomolecules in a subsecond time resolution. In this system, biochemical properties such as the placement of various double-stranded DNAs (dsDNAs) containing unrestricted DNA sequences, modified nucleosides, and chemical functions can be incorporated. From a physical point of view, the tension and rotation of dsDNAs can be controlled by placement into the DNA nanostructures. From a topological point of view, the orientations of dsDNAs and various shapes of dsDNAs including Holliday junctions can be incorporated for studies on reaction mechanisms. In this Account, we describe the combination of the DNA origami system and HS-AFM for imaging various biochemical reactions including enzymatic reactions and DNA structural changes. To observe the behaviors and reactions of DNA methyltransferase and DNA repair enzymes, the substrate dsDNAs were incorporated into the cavity of the DNA frame, and the enzymes that bound to the target dsDNA were observed using HS-AFM. DNA recombination was also observed using the recombination substrates and Holliday junction intermediates placed in the DNA frame, and the direction of the reactions was controlled by introducing structural stress to the substrates. In addition, the movement of RNA polymerase and its reaction were visualized using a template dsDNA attached to the origami structure. To observe DNA structural changes, G-quadruplex formation and disruption, the switching behaviors of photoresponsive oligonucleotides, and B-Z transition were visualized using the DNA frame observation system. For the formation and disruption of G-quadruplex and double-helix DNA, the two dsDNA chains incorporated into the DNA frame could amplify the small structural change to the global structural change, which enabled the visualization of their association and dissociation by HS-AFM. The dynamic motion of the helical rotation induced by the B-Z transition was also directly imaged in the DNA frame. Furthermore, the stepwise motions of mobile DNA along the DNA track were visualized on the DNA origami surface. These target-orientated observation systems should contribute to the detailed analysis of biomolecule motions in real time and at molecular resolution.
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Affiliation(s)
- Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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106
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Tsukanov R, Tomov TE, Liber M, Berger Y, Nir E. Developing DNA nanotechnology using single-molecule fluorescence. Acc Chem Res 2014; 47:1789-98. [PMID: 24828396 DOI: 10.1021/ar500027d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
CONSPECTUS: An important effort in the DNA nanotechnology field is focused on the rational design and manufacture of molecular structures and dynamic devices made of DNA. As is the case for other technologies that deal with manipulation of matter, rational development requires high quality and informative feedback on the building blocks and final products. For DNA nanotechnology such feedback is typically provided by gel electrophoresis, atomic force microscopy (AFM), and transmission electron microscopy (TEM). These analytical tools provide excellent structural information; however, usually they do not provide high-resolution dynamic information. For the development of DNA-made dynamic devices such as machines, motors, robots, and computers this constitutes a major problem. Bulk-fluorescence techniques are capable of providing dynamic information, but because only ensemble averaged information is obtained, the technique may not adequately describe the dynamics in the context of complex DNA devices. The single-molecule fluorescence (SMF) technique offers a unique combination of capabilities that make it an excellent tool for guiding the development of DNA-made devices. The technique has been increasingly used in DNA nanotechnology, especially for the analysis of structure, dynamics, integrity, and operation of DNA-made devices; however, its capabilities are not yet sufficiently familiar to the community. The purpose of this Account is to demonstrate how different SMF tools can be utilized for the development of DNA devices and for structural dynamic investigation of biomolecules in general and DNA molecules in particular. Single-molecule diffusion-based Förster resonance energy transfer and alternating laser excitation (sm-FRET/ALEX) and immobilization-based total internal reflection fluorescence (TIRF) techniques are briefly described and demonstrated. To illustrate the many applications of SMF to DNA nanotechnology, examples of SMF studies of DNA hairpins and Holliday junctions and of the interactions of DNA strands with DNA origami and origami-related devices such as a DNA bipedal motor are provided. These examples demonstrate how SMF can be utilized for measurement of distances and conformational distributions and equilibrium and nonequilibrium kinetics, to monitor structural integrity and operation of DNA devices, and for isolation and investigation of minor subpopulations including malfunctioning and nonreactive devices. Utilization of a flow-cell to achieve measurements of dynamics with increased time resolution and for convenient and efficient operation of DNA devices is discussed briefly. We conclude by summarizing the various benefits provided by SMF for the development of DNA nanotechnology and suggest that the method can significantly assist in the design and manufacture and evaluation of operation of DNA devices.
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Affiliation(s)
- Roman Tsukanov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Toma E. Tomov
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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107
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Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404043] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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108
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Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H. Single-Molecule Mechanochemical Sensing Using DNA Origami Nanostructures. Angew Chem Int Ed Engl 2014; 53:8137-41. [DOI: 10.1002/anie.201404043] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Indexed: 01/01/2023]
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109
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Pibiri E, Holzmeister P, Lalkens B, Acuna GP, Tinnefeld P. Single-molecule positioning in zeromode waveguides by DNA origami nanoadapters. NANO LETTERS 2014; 14:3499-503. [PMID: 24773477 DOI: 10.1021/nl501064b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Nanotechnology is challenged by the need to connect top-down produced nanostructures with the bottom-up world of chemistry. A nanobiotechnological prime example is the positioning of single polymerase molecules in small holes in metal films, so-called zeromode waveguides (ZMWs), which is required for single-molecule real-time DNA sequencing. In this work, we present nanoadapters made of DNA (DNA origami) that match the size of the holes so that exactly one nanoadapter fits in each hole. By site-selective functionalization of the DNA origami nanoadapters, we placed single dye molecules in the ZMWs, thus optimizing the hole usage and improving the photophysical properties of dyes compared to stochastically immobilized molecules.
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Affiliation(s)
- Enrico Pibiri
- NanoBioSciences Group, Institute for Physical and Theoretical Chemistry Braunschweig , Hans-Sommer-Strasse 10, 38106 Braunschweig, Lower Saxony, Germany
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110
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Acuna G, Grohmann D, Tinnefeld P. Enhancing single-molecule fluorescence with nanophotonics. FEBS Lett 2014; 588:3547-52. [DOI: 10.1016/j.febslet.2014.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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111
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Yuan Z, Chen YC, Li HW, Chang HT. Fluorescent silver nanoclusters stabilized by DNA scaffolds. Chem Commun (Camb) 2014; 50:9800-15. [DOI: 10.1039/c4cc02981j] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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112
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Kumar A, Kumar V. Biotemplated Inorganic Nanostructures: Supramolecular Directed Nanosystems of Semiconductor(s)/Metal(s) Mediated by Nucleic Acids and Their Properties. Chem Rev 2014; 114:7044-78. [DOI: 10.1021/cr4007285] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
| | - Vinit Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee-247667, India
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113
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Gates EP, Dearden AM, Woolley AT. DNA‐templated lithography and nanofabrication for the fabrication of nanoscale electronic circuitry. Crit Rev Anal Chem 2014; 44:354-70. [DOI: 10.1080/10408347.2014.910636] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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114
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Abstract
Validating and testing a fluorescence microscope or a microscopy method requires defined samples that can be used as standards. DNA origami is a new tool that provides a framework to place defined numbers of small molecules such as fluorescent dyes or proteins in a programmed geometry with nanometer precision. The flexibility and versatility in the design of DNA origami microscopy standards makes them ideally suited for the broad variety of emerging super-resolution microscopy methods. As DNA origami structures are durable and portable, they can become a universally available specimen to check the everyday functionality of a microscope. The standards are immobilized on a glass slide, and they can be imaged without further preparation and can be stored for up to 6 months. We describe a detailed protocol for the design, production and use of DNA origami microscopy standards, and we introduce a DNA origami rectangle, bundles and a nanopillar as fluorescent nanoscopic rulers. The protocol provides procedures for the design and realization of fluorescent marks on DNA origami structures, their production and purification, quality control, handling, immobilization, measurement and data analysis. The procedure can be completed in 1-2 d.
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115
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Yamamoto S, De D, Hidaka K, Kim KK, Endo M, Sugiyama H. Single molecule visualization and characterization of Sox2-Pax6 complex formation on a regulatory DNA element using a DNA origami frame. NANO LETTERS 2014; 14:2286-2292. [PMID: 24660747 DOI: 10.1021/nl4044949] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report the use of atomic force microscopy (AFM) to study Sox2-Pax6 complex formation on the regulatory DNA element at a single molecule level. Using an origami DNA scaffold containing two DNA strands with different levels of tensile force, we confirmed that DNA bending is necessary for Sox2 binding. We also demonstrated that two transcription factors bind cooperatively by observing the increased occupancy of Sox2-Pax6 on the DNA element compared to that of Sox2 alone.
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Affiliation(s)
- Seigi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University , Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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116
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A protein adaptor to locate a functional protein dimer on molecular switchboard. Methods 2014; 67:142-50. [DOI: 10.1016/j.ymeth.2013.10.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/09/2013] [Accepted: 10/16/2013] [Indexed: 01/25/2023] Open
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117
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DNA from natural sources in design of functional devices. Methods 2014; 67:105-15. [DOI: 10.1016/j.ymeth.2014.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 02/20/2014] [Accepted: 03/02/2014] [Indexed: 01/01/2023] Open
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118
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Long W, Zou W, Li X, Jiang W, Li X, Chen J. Tracing photon transmission in dye-doped DNA-CTMA optical nanofibers. OPTICS EXPRESS 2014; 22:6249-6256. [PMID: 24663973 DOI: 10.1364/oe.22.006249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We experimentally demonstrate the novel phenomena of photoluminescence (PL) and fluorescence resonance energy transfer (FRET) assisted three-color PL separating in DNA optical nanofibers consisting of the stretched and connected DNA-cetyltrimethyl ammonium wires. The PL experiments are performed to comparatively trace photon transmission between single dye-doped DNA-CTMA optical nanofiber and PMMA optical nanofiber. A cascade FRET including DNA minor groove binder and DNA intercalators is used to further trace photon transmission inside DNA-CTMA wire. These experimental results will help to intrigue the new applications of DNA-CTMA as molecular waveguide in optobioelectronics area.
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119
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DNA origami based assembly of gold nanoparticle dimers for surface-enhanced Raman scattering. Nat Commun 2014; 5:3448. [DOI: 10.1038/ncomms4448] [Citation(s) in RCA: 340] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/13/2014] [Indexed: 12/17/2022] Open
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120
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Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and single-molecule visualization of the solution-state structures of G-hairpin and G-triplex intermediates. Angew Chem Int Ed Engl 2014; 53:4107-12. [PMID: 24623581 DOI: 10.1002/anie.201308903] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Revised: 12/17/2013] [Indexed: 01/11/2023]
Abstract
We present the direct and single-molecule visualization of the in-pathway intermediates of the G-quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high-speed atomic force microscopy (HS-AFM) for direct visualization, we captured images of the unprecedented solution-state structures of a tetramolecular antiparallel and (3+1)-type G-quadruplex intermediates, such as G-hairpin and G-triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid-state, single-molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G-quadruplexes.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502 (Japan); Current address: Faculty of Medicine and Life Science Center of TARA, University of Tsukuba, 1-1-1 Tennodai, Tsukuba-shi, Ibaraki-ken 305-8577 (Japan)
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121
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Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308903] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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122
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Digital imprinting of RNA recognition and processing on a self-assembled nucleic acid matrix. Sci Rep 2014; 3:2550. [PMID: 23989631 PMCID: PMC3757352 DOI: 10.1038/srep02550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/08/2013] [Indexed: 11/08/2022] Open
Abstract
The accelerating progress of research in nanomedicine and nanobiotechnology has included initiatives to develop highly-sensitive, high-throughput methods to detect biomarkers at the single-cell level. Current sensing approaches, however, typically involve integrative instrumentation that necessarily must balance sensitivity with rapidity in optimizing biomarker detection quality. We show here that laterally-confined, self-assembled monolayers of a short, double-stranded(ds)[RNA-DNA] chimera enable permanent digital detection of dsRNA-specific inputs. The action of ribonuclease III and the binding of an inactive, dsRNA-binding mutant can be permanently recorded by the input-responsive action of a restriction endonuclease that cleaves an ancillary reporter site within the dsDNA segment. The resulting irreversible height change of the arrayed ds[RNA-DNA], as measured by atomic force microscopy, provides a distinct digital output for each dsRNA-specific input. These findings provide the basis for developing imprinting-based bio-nanosensors, and reveal the versatility of AFM as a tool for characterizing the behaviour of highly-crowded biomolecules at the nanoscale.
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123
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Rajendran A, Endo M, Hidaka K, Thao Tran PL, Teulade-Fichou MP, Mergny JL, Sugiyama H. G-quadruplex-binding ligand-induced DNA synapsis inside a DNA origami frame. RSC Adv 2014. [DOI: 10.1039/c3ra45676e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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124
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The Power of Single-Molecule FRET Microscopy Applied to DNA Nanotechnology. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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125
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Yang Y, Endo M, Suzuki Y, Hidaka K, Sugiyama H. Direct observation of the dual-switching behaviors corresponding to the state transition in a DNA nanoframe. Chem Commun (Camb) 2014; 50:4211-3. [DOI: 10.1039/c4cc00489b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The dual-switching behaviors of photoresponsive DNAs and the G-quadruplex in the DNA nanoframe were successfully visualized by high-speed atomic force microscopy.
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Affiliation(s)
- Yangyang Yang
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501, Japan
- CREST
- Japan Science and Technology Corporation (JST)
| | - Yuki Suzuki
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
- CREST
| | - Kumi Hidaka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
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126
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Kang S, Nieuwenhuis AF, Mathwig K, Mampallil D, Lemay SG. Electrochemical single-molecule detection in aqueous solution using self-aligned nanogap transducers. ACS NANO 2013; 7:10931-10937. [PMID: 24279688 DOI: 10.1021/nn404440v] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Electrochemical detection of individual molecular tags in nanochannels may enable cost-effective, massively parallel analysis and diagnostics platforms. Here we demonstrate single-molecule detection of prototypical analytes in aqueous solution based on redox cycling in 40 nm nanogap transducers. These nanofluidic devices are fabricated using standard microfabrication techniques combined with a self-aligned approach that minimizes gap size and dead volume. We demonstrate the detection of three common redox mediators at physiological salt concentrations.
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Affiliation(s)
- Shuo Kang
- MESA+ Institute for Nanotechnology, University of Twente , PO Box 217, 7500 AE Enschede, The Netherlands
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127
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Gorelick RJ, Sugiyama H. HIV-1 nucleocapsid proteins as molecular chaperones for tetramolecular antiparallel G-quadruplex formation. J Am Chem Soc 2013; 135:18575-85. [PMID: 24224650 PMCID: PMC3898174 DOI: 10.1021/ja409085j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Phong Lan Thao Tran
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Jean-Louis Mergny
- Univ. Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
| | - Robert J. Gorelick
- SAIC-Frederick, Inc, Frederick National Laboratory for Cancer Research, P. O. Box B, Frederick, Maryland 21702-1201, USA
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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128
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Rajendran A, Endo M, Sugiyama H. State-of-the-Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins. Chem Rev 2013; 114:1493-520. [DOI: 10.1021/cr300253x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Arivazhagan Rajendran
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Hiroshi Sugiyama
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho
Sakyo-ku, Kyoto 606-8502, Japan
- Institute
for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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129
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Pedersen RO, Loboa EG, LaBean TH. Sensitization of transforming growth factor-β signaling by multiple peptides patterned on DNA nanostructures. Biomacromolecules 2013; 14:4157-60. [PMID: 24206086 DOI: 10.1021/bm4011722] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We report sensitization of a cellular signaling pathway by addition of functionalized DNA nanostructures. Signaling by transforming growth factor β (TGFβ) has been shown to be dependent on receptor clustering. By patterning a DNA nanostructure with closely spaced peptides that bind to TGFβ receptor, we observe increased sensitivity of NMuMG cells to TGFβ ligand. This is evidenced by translocation of secondary messenger proteins to the nucleus and stimulation of an inducible luciferase reporter at lower concentrations of TGFβ ligand. We believe this represents an important initial step toward realization of DNA as a self-assembling and biologically compatible material for use in tissue engineering and drug delivery.
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Affiliation(s)
- Ronnie O Pedersen
- Department of Chemistry, Duke University , 124 Science Drive, Durham, North Carolina 27708-0354, United States
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130
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Endo M, Inoue M, Suzuki Y, Masui C, Morinaga H, Hidaka K, Sugiyama H. Regulation of B-Z Conformational Transition and Complex Formation with a Z-Form Binding Protein by Introduction of Constraint to Double-Stranded DNA by using a DNA Nanoscaffold. Chemistry 2013; 19:16887-90. [DOI: 10.1002/chem.201303830] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Indexed: 11/06/2022]
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131
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Endo M, Yamamoto S, Tatsumi K, Emura T, Hidaka K, Sugiyama H. RNA-templated DNA origami structures. Chem Commun (Camb) 2013; 49:2879-81. [PMID: 23446278 DOI: 10.1039/c3cc38804b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using the RNA transcript as a template, RNA-templated DNA origami structures were constructed by annealing with designed DNA staple strands. RNA-templated DNA origami structures were folded to form seven-helix bundled rectangular structures and six-helix bundled tubular structures. The chemically modified RNA-DNA hybrid origami structures were prepared by using RNA templates containing modified uracils.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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132
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Zhang H, Li F, Dever B, Wang C, Li XF, Le XC. DNA-Assemblierung mittels Affinitätsbindung für die ultraempfindliche Proteindetektion. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201210022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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133
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Zhang H, Li F, Dever B, Wang C, Li XF, Le XC. Assembling DNA through affinity binding to achieve ultrasensitive protein detection. Angew Chem Int Ed Engl 2013; 52:10698-705. [PMID: 24038633 DOI: 10.1002/anie.201210022] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 03/17/2013] [Indexed: 11/06/2022]
Abstract
Recent advances in DNA assembly and affinity binding have enabled exciting developments of nanosensors and ultrasensitive assays for specific proteins. These sensors and assays share three main attractive features: 1) the detection of proteins can be accomplished by the detection of amplifiable DNA, thereby dramatically enhancing the sensitivity; 2) assembly of DNA is triggered by affinity binding of two or more probes to a single target molecule, thereby resulting in increased specificity; and 3) the assay is conducted in solution with no need for separation, thus making the assay attractive for potential point-of-care applications. We illustrate here the principle of assembling DNA through affinity binding, and we highlight novel applications to the detection of proteins.
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Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G3 (Canada) http://www.ualberta.ca/∼xcle
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134
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Wu N, Czajkowsky DM, Zhang J, Qu J, Ye M, Zeng D, Zhou X, Hu J, Shao Z, Li B, Fan C. Molecular Threading and Tunable Molecular Recognition on DNA Origami Nanostructures. J Am Chem Soc 2013; 135:12172-5. [DOI: 10.1021/ja403863a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Na Wu
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Daniel M. Czajkowsky
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjin Zhang
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jianxun Qu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ming Ye
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dongdong Zeng
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xingfei Zhou
- Physics Department, Ningbo University, Zhejiang 315211, China
| | - Jun Hu
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Zhifeng Shao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bin Li
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology,
and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai
Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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135
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Hernández-Ainsa S, Bell NAW, Thacker VV, Göpfrich K, Misiunas K, Fuentes-Perez ME, Moreno-Herrero F, Keyser UF. DNA origami nanopores for controlling DNA translocation. ACS NANO 2013; 7:6024-30. [PMID: 23734828 DOI: 10.1021/nn401759r] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We combine DNA origami structures with glass nanocapillaries to reversibly form hybrid DNA origami nanopores. Trapping of the DNA origami onto the nanocapillary is proven by imaging fluorescently labeled DNA origami structures and simultaneous ionic current measurements of the trapping events. We then show two applications highlighting the versatility of these DNA origami nanopores. First, by tuning the pore size we can control the folding of dsDNA molecules ("physical control"). Second, we show that the specific introduction of binding sites in the DNA origami nanopore allows selective detection of ssDNA as a function of the DNA sequence ("chemical control").
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Affiliation(s)
- Silvia Hernández-Ainsa
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
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136
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Rajendran A, Endo M, Hidaka K, Tran PLT, Mergny JL, Sugiyama H. Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame. Nucleic Acids Res 2013; 41:8738-47. [PMID: 23863846 PMCID: PMC3794576 DOI: 10.1093/nar/gkt592] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Guanine-rich oligonucleotides often show a strong tendency to form supramolecular architecture, the so-called G-quadruplex structure. Because of the biological significance, it is now considered to be one of the most important conformations of DNA. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G-G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands. In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time. The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex.
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Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan, Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan, CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan and University of Bordeaux, INSERM, U869, ARNA Laboratory, 2 rue Robert Escarpit, Pessac, F-33607, France
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137
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Wang ZG, Song C, Ding B. Functional DNA nanostructures for photonic and biomedical applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:2210-2222. [PMID: 23733711 DOI: 10.1002/smll.201300141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Indexed: 06/02/2023]
Abstract
DNA nanostructures, especially DNA origami, receive close interest because of the programmable control over their shape and size, precise spatial addressability, easy and high-yield preparation, mechanical flexibility, and biocompatibility. They have been used to organize a variety of nanoscale elements for specific functions, resulting in unprecedented improvements in the field of nanophotonics and nanomedical research. In this review, the discussion focuses on the employment of DNA nanostructures for the precise organization of noble metal nanoparticles to build interesting plasmonic nanoarchitectures, for the fabrication of visualized sensors and for targeted drug delivery. The effects offered by DNA nanostructures are highlighted in the areas of nanoantennas, collective plasmonic behaviors, single-molecule analysis, and cancer-cell targeting or killing. Finally, the challenges in the field of DNA nanotechnology for realistic application are discussed and insights for future directions are provided.
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Affiliation(s)
- Zhen-Gang Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
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138
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De Silva L, Yao L, Wang Y, Xu S. Well-Defined and Sequence-Specific Noncovalent Binding Forces of DNA. J Phys Chem B 2013; 117:7554-8. [DOI: 10.1021/jp403817b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lashan De Silva
- Department
of Chemistry and ‡Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, United
States
| | - Li Yao
- Department
of Chemistry and ‡Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, United
States
| | - Yuhong Wang
- Department
of Chemistry and ‡Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, United
States
| | - Shoujun Xu
- Department
of Chemistry and ‡Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, United
States
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139
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Making connections--strategies for single molecule fluorescence biophysics. Curr Opin Chem Biol 2013; 17:691-8. [PMID: 23769868 PMCID: PMC3989056 DOI: 10.1016/j.cbpa.2013.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/02/2013] [Accepted: 05/17/2013] [Indexed: 11/28/2022]
Abstract
The single-molecule approach yields exciting insights for many biomolecular applications. There are significant challenges to achieve main-stream single-molecule measurements. New labelling chemistries enable multiple tagged molecules in vitro and in live cells. Single-molecule pull-down expands the toolbox complementing co-immunoprecipitation. Breaking the single-molecule concentration barrier is within reach.
Fluorescence spectroscopy and fluorescence microscopy carried out on the single molecule level are elegant methods to decipher complex biological systems; it can provide a wealth of information that frequently is obscured in the averaging of ensemble measurements. Fluorescence can be used to localise a molecule, study its binding with interaction partners and ligands, or to follow conformational changes in large multicomponent systems. Efficient labelling of proteins and nucleic acids is very important for any fluorescence method, and equally the development of novel fluorophores has been crucial in making biomolecules amenable to single molecule fluorescence methods. In this paper we review novel coupling strategies that permit site-specific and efficient labelling of proteins. Furthermore, we will discuss progressive single molecule approaches that allow the detection of individual molecules and biomolecular complexes even directly isolated from cellular extracts at much higher and much lower concentrations than has been possible so far.
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140
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Tørring T, Gothelf KV. DNA nanotechnology: a curiosity or a promising technology? F1000PRIME REPORTS 2013; 5:14. [PMID: 23710328 PMCID: PMC3643079 DOI: 10.12703/p5-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA nanotechnology, the design and self-assembly of artificial nucleic acid-based structures or systems, has developed with breathtaking pace in recent years. The technology offers an unparalleled ability to control structure and function at the molecular level and the sizes of the structures are expanding towards the micrometer domain. The question is whether the technology offers solutions to any real-life problems, or if it will remain an academic discipline. Here, we discuss this question by extrapolating from recent developments in the field.
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141
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Carneiro KMM, Avakyan N, Sleiman HF. Long-range assembly of DNA into nanofibers and highly ordered networks. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:266-85. [DOI: 10.1002/wnan.1218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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142
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Rajendran A, Endo M, Hidaka K, Sugiyama H. Direct and Real-Time Observation of Rotary Movement of a DNA Nanomechanical Device. J Am Chem Soc 2013; 135:1117-23. [DOI: 10.1021/ja310454k] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku,
Tokyo 102-0075, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate
School of Science, Kyoto University, Kitashirakawa-oiwakecho,
Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material
Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho,
Sakyo-ku, Kyoto 606-8501, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku,
Tokyo 102-0075, Japan
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143
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Said H, Schüller VJ, Eber FJ, Wege C, Liedl T, Richert C. M1.3--a small scaffold for DNA origami . NANOSCALE 2013; 5:284-90. [PMID: 23160434 DOI: 10.1039/c2nr32393a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The DNA origami method produces programmable nanoscale objects that form when one long scaffold strand hybridizes to numerous oligonucleotide staple strands. One scaffold strand is dominating the field: M13mp18, a bacteriophage-derived vector 7249 nucleotides in length. The full-length M13 is typically folded by using over 200 staple oligonucleotides. Here we report the convenient preparation of a 704 nt fragment dubbed "M1.3" as a linear or cyclic scaffold and the assembly of small origami structures with just 15-24 staple strands. A typical M1.3 origami is large enough to be visualized by TEM, but small enough to show a cooperativity in its assembly and thermal denaturation that is reminiscent of oligonucleotide duplexes. Due to its medium size, M1.3 origami with globally modified staples is affordable. As a proof of principle, two origami structures with globally 5'-capped staples were prepared and were shown to give higher UV-melting points than the corresponding assembly with unmodified DNA. M1.3 has the size of a gene, not a genome, and may function as a model for gene-based nanostructures. Small origami with M1.3 as a scaffold may serve as a workbench for chemical, physical, and biological experiments.
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Affiliation(s)
- Hassan Said
- Institute for Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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144
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Endo M, Yang Y, Sugiyama H. DNA origami technology for biomaterials applications. Biomater Sci 2013; 1:347-360. [DOI: 10.1039/c2bm00154c] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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145
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Rajendran A, Endo M, Hidaka K, Sugiyama H. Control of the two-dimensional crystallization of DNA origami with various loop arrangements. Chem Commun (Camb) 2013; 49:686-8. [DOI: 10.1039/c2cc37257f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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146
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Yang Y, Endo M, Hidaka K, Sugiyama H. Photo-controllable DNA origami nanostructures assembling into predesigned multiorientational patterns. J Am Chem Soc 2012; 134:20645-53. [PMID: 23210720 DOI: 10.1021/ja307785r] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We demonstrate a novel strategy for constructing multidirectional programmed 2D DNA nanostructures in various unique patterns by introducing photoresponsive oligonucleotides (Azo-ODNs) into hexagonal DNA origami structures. We examined regulation of assembly and disassembly of DNA nanostructures reversibly by different photoirradiation conditions in a programmed manner. Azo-ODNs were incorporated to the hexagonal DNA origami structures, which were then employed as self-assembly units for building up nanosized architectures in regulated arrangements. By adjusting the numbers and the positions of Azo-ODNs in the hexagonal units, the specific nanostructures with face controlling can be achieved, resulting in construction of ring-shaped nanostructures. By combining DNA origami strategy with photoregulating system, remote controlling of assembly and disassembly of DNA nanostructures has been accomplished simply by photo irradiation.
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Affiliation(s)
- Yangyang Yang
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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147
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Nakagawa H, Toda M, Atsumi H, Hagihara M, Hayashi-Nishino M, Dohno C, Nakatani K. Assembly of a Small DNA Rectangular Parallelepiped Block into Higher Order Nanostructures. CHEM LETT 2012. [DOI: 10.1246/cl.2012.1550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Nakagawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Mariko Toda
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Hiroshi Atsumi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Masaki Hagihara
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Mitsuko Hayashi-Nishino
- Comprehensive Analysis Center, The Institute of Scientific and Industrial Research, Osaka University
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University
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148
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-Molecule Visualization of the Hybridization and Dissociation of Photoresponsive Oligonucleotides and Their Reversible Switching Behavior in a DNA Nanostructure. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205247] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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149
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Endo M, Yang Y, Suzuki Y, Hidaka K, Sugiyama H. Single-molecule visualization of the hybridization and dissociation of photoresponsive oligonucleotides and their reversible switching behavior in a DNA nanostructure. Angew Chem Int Ed Engl 2012; 51:10518-22. [PMID: 22965475 DOI: 10.1002/anie.201205247] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 12/20/2022]
Abstract
A framed photo of DNA: A pair of photoresponsive oligonucleotides containing azobenzene moieties was introduced into double-stranded DNA within the cavity of a DNA nanostructure (see scheme). The two dsDNAs, in contact at the center, were dissociated using UV irradiation and hybridized with visible light; this was directly observed using high-speed atomic force microscopy.
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Affiliation(s)
- Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan.
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150
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Endo M, Tatsumi K, Terushima K, Katsuda Y, Hidaka K, Harada Y, Sugiyama H. Direct Visualization of the Movement of a Single T7 RNA Polymerase and Transcription on a DNA Nanostructure. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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