201
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Bolaños Quiñones VA, Zhu H, Solovev AA, Mei Y, Gracias DH. Origami Biosystems: 3D Assembly Methods for Biomedical Applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800230] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vladimir A. Bolaños Quiñones
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Hong Zhu
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Alexander A. Solovev
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Yongfeng Mei
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - David H. Gracias
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N Charles Street, 221 Maryland Hall Baltimore MD 21218 USA
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202
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Reddy Satyavolu NS, Pishevaresfahani N, Tan LH, Lu Y. DNA-Encoded Morphological Evolution of Bimetallic Pd@Au Core-shell Nanoparticles from a High-indexed Core. NANO RESEARCH 2018; 11:4549-4561. [PMID: 30906510 PMCID: PMC6424367 DOI: 10.1007/s12274-018-2035-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 02/22/2018] [Accepted: 02/25/2018] [Indexed: 05/28/2023]
Abstract
DNA-mediated synthesis of nanoparticles with different morphologies has proven to be a powerful method to synthesize and access many exclusive shapes and surface properties. While previous studies employ seeds that contain relatively low-energy facets, such as a simple cubic palladium seed in the synthesis of Pd-Au bimetallic nanoparticles, few studies have investigated whether DNA molecules can still exert their influence when the synthesis uses a seed that contains high-energy facets. Seeds that are enclosed by such high-energy facets or sites are known to act as easy nucleation sites in nanoparticles growth and could potentially suppress the effect of DNA. To answer this question, we herein report DNA-encoded control of morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed that contains high indexed facets. Based on detailed spectroscopic and SEM studies of time-dependent growth of the bimetallic nanoparticles, we found that each of 10-mer DNA molecules (T10, G10, C10 and A10) has a unique way of interacting with both the seed's surface and the precursor. Among them, the most important factor is the binding affinity of the nucleobase to the Pd surface, with the A10 possessing the highest binding affinity and thus capable of stabilizing the seed's high energy surfaces. Furthermore, for bases with lower binding affinity (T10, G10 and C10) than A10, the growth is completely dictated by the seed's surface energy initially, but the later growth can still be influenced by the different DNA sequences, resulting in four unique morphologically different Pd@Au bimetallic nanoparticles. The effect of these DNA molecules with medium binding affinity can only be observed when there is more deposition of Au. Based on the above results, a scheme for the DNA controlled growth is proposed. Together these results have provided insights into factors governing DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can readily be applied to other bimetallic systems that adopt seed-mediated synthesis.
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Affiliation(s)
- Nitya Sai Reddy Satyavolu
- The Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nikou Pishevaresfahani
- The Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li Huey Tan
- The Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- The Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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203
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Copp SM, Gorovits A, Swasey SM, Gudibandi S, Bogdanov P, Gwinn EG. Fluorescence Color by Data-Driven Design of Genomic Silver Clusters. ACS NANO 2018; 12:8240-8247. [PMID: 30059609 DOI: 10.1021/acsnano.8b03404] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
DNA nucleobase sequence controls the size of DNA-stabilized silver clusters, leading to their well-known yet little understood sequence-tuned colors. The enormous space of possible DNA sequences for templating clusters has challenged the understanding of how sequence selects cluster properties and has limited the design of applications that employ these clusters. We investigate the genomic role of DNA sequence for fluorescent silver clusters using a data-driven approach. Employing rapid parallel silver cluster synthesis and fluorimetry, we determine the fluorescence spectra of silver cluster products stabilized by 1432 distinct DNA oligomers. By applying pattern recognition algorithms to this large experimental data set, we discover certain DNA base patterns, or "motifs," that correlate to silver clusters with similar fluorescence spectra. These motifs are employed in machine learning classifiers to predictively design DNA template sequences for specific fluorescence color bands. Our method improves selectivity of templates by 330% for silver clusters with peak emission wavelengths beyond 660 nm. The discovered base motifs also provide physical insights into how DNA sequence controls silver cluster size and color. This predictive design approach for color of DNA-stabilized silver clusters exhibits the potential of machine learning and data mining to increase the precision and efficiency of nanomaterials design, even for a soft-matter-inorganic hybrid system characterized by an extremely large parameter space.
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Affiliation(s)
- Stacy M Copp
- Center for Integrated Nanotechnologies , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Alexander Gorovits
- Department of Computer Science , University at Albany-SUNY , 1400 Washington Ave. , Albany , New York 12222 , United States
| | | | - Sruthi Gudibandi
- Department of Computer Science , University at Albany-SUNY , 1400 Washington Ave. , Albany , New York 12222 , United States
| | - Petko Bogdanov
- Department of Computer Science , University at Albany-SUNY , 1400 Washington Ave. , Albany , New York 12222 , United States
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204
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Kou B, Chai Y, Yuan Y, Yuan R. Dynamical Regulation of Enzyme Cascade Amplification by a Regenerated DNA Nanotweezer for Ultrasensitive Electrochemical DNA Detection. Anal Chem 2018; 90:10701-10706. [DOI: 10.1021/acs.analchem.8b00477] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Beibei Kou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yali Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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205
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Fernandez-Castanon J, Bianchi S, Saglimbeni F, Di Leonardo R, Sciortino F. Microrheology of DNA hydrogel gelling and melting on cooling. SOFT MATTER 2018; 14:6431-6438. [PMID: 29952388 PMCID: PMC6295875 DOI: 10.1039/c8sm00751a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/16/2018] [Indexed: 05/18/2023]
Abstract
We present systematic characterisation by means of dynamic light scattering and particle tracking techniques of the viscosity and of the linear viscoelastic moduli, G'(ω) and G''(ω), for two different DNA hydrogels. These thermoreversible systems are composed of tetravalent DNA-made nanostars whose sticky sequence is designed to provide controlled interparticle bonding. While the first system forms a gel on cooling, the second one has been programmed to behave as a re-entrant gel, turning again to a fluid solution at low temperature. The frequency-dependent viscous and storage moduli and the viscosity reveal the different viscoelastic behavior of the two DNA hydrogels. Our results show how little variations in the design of the DNA sequences allow tuning of the mechanical response of these biocompatible all-DNA materials.
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Affiliation(s)
| | - Silvio Bianchi
- CNR-NANOTEC, Soft and Living Matter Laboratory, Rome, I-00185, Italy
| | | | - Roberto Di Leonardo
- Dipartimento di Fisica, "Sapienza" Università di Roma, Rome, I-00185, Italy. and CNR-NANOTEC, Soft and Living Matter Laboratory, Rome, I-00185, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, "Sapienza" Università di Roma, Rome, I-00185, Italy. and CNR-ISC, UOS "Sapienza" Università di Roma, Rome, I-00186, Italy
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206
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Marenda M, Orlandini E, Micheletti C. Discovering privileged topologies of molecular knots with self-assembling models. Nat Commun 2018; 9:3051. [PMID: 30076306 PMCID: PMC6076300 DOI: 10.1038/s41467-018-05413-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
Despite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.
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Affiliation(s)
- Mattia Marenda
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136, Trieste, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia "Galileo Galilei", sezione INFN, Università degli Studi di Padova, via Marzolo 8, I-35131, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136, Trieste, Italy.
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207
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Chen X, Wang Q, Peng J, Long Q, Yu H, Li Z. Self-Assembly of Large DNA Origami with Custom-Designed Scaffolds. ACS APPLIED MATERIALS & INTERFACES 2018; 10:24344-24348. [PMID: 29989388 DOI: 10.1021/acsami.8b09222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
As a milestone in DNA self-assembly, DNA origami has demonstrated powerful applications in many fields. However, the scarce availability of long single-stranded DNA (ssDNA) limits the size and sequences of DNA origami nanostructures, which in turn impedes the further development. In this study, we present a robust strategy to produce long circular ssDNA scaffold strands with custom-tailored lengths and sequences. These ssDNA products were then used as scaffolds for constructing various DNA origami nanostructures. This scalable method produces ssDNA at low cost with high purity and high yield, which can enable production of custom-designed DNA origami for various applications.
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Affiliation(s)
- Xiaoxing Chen
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
| | - Qian Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
| | - Jin Peng
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
| | - Qipeng Long
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
| | - Zhe Li
- Department of Biomedical Engineering, College of Engineering and Applied Sciences , Nanjing University , Nanjing , Jiangsu 210093 , P. R. China
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208
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Complex silica composite nanomaterials templated with DNA origami. Nature 2018; 559:593-598. [DOI: 10.1038/s41586-018-0332-7] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
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209
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Ellipilli S, Phillips JD, Heemstra JM. Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite. Org Biomol Chem 2018; 16:4659-4664. [PMID: 29881861 DOI: 10.1039/c8ob00626a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available δ-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.
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Affiliation(s)
- Satheesh Ellipilli
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
| | - John D Phillips
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
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210
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Zhou K, Ke Y, Wang Q. Selective in Situ Assembly of Viral Protein onto DNA Origami. J Am Chem Soc 2018; 140:8074-8077. [PMID: 29932333 DOI: 10.1021/jacs.8b03914] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Engineering hybrid protein-DNA assemblies in a controlled manner has attracted particular attention, for their potential applications in biomedicine and nanotechnology due to their intricate folding properties and important physiological roles. Although DNA origami has served as a powerful platform for spatially arranging functional molecules, in situ assembly of proteins onto DNA origami is still challenging, especially in a precisely controlled and facile manner. Here, we demonstrate in situ assembly of tobacco mosaic virus (TMV) coat proteins onto DNA origami to generate programmable assembly of hybrid DNA origami-protein nanoarchitectures. The protein nanotubes of controlled length are precisely anchored on the DNA origami at selected locations using TMV genome-mimicking RNA strands. This study opens a new route to the organization of protein and DNA into sophisticated protein-DNA nanoarchitectures by harnessing the viral encapsidation mechanism and the programmability of DNA origami.
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Affiliation(s)
- Kun Zhou
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics , Chinese Academy of Sciences , Suzhou 215123 , China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine and i-Lab, CAS Center for Excellence in Brain Science, Suzhou Institute of Nano-Tech and Nano-Bionics , Chinese Academy of Sciences , Suzhou 215123 , China.,School of Nano-Tech and Nano-Bionics , University of Science and Technology of China , Hefei 230026 , China
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211
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Simultaneous and stoichiometric purification of hundreds of oligonucleotides. Nat Commun 2018; 9:2467. [PMID: 29941961 PMCID: PMC6018234 DOI: 10.1038/s41467-018-04870-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
Purification of oligonucleotides has traditionally relied on mobility-based separation methods. However, these are imperfect, biased, and difficult to scale high multiplex. Here, we present a method for simultaneous purification of many oligonucleotides that also normalizes concentrations. The method uses a rationally designed randomer capture probe to enrich for oligos with perfect 5′ sequences, based on the observation that synthesis errors are correlated: product molecules with one or more deletions in one region are also more likely to have deletions in other regions. Next-generation sequencing analysis of 64-plex 70 nt purification products show a median 78% purity, a significant improvement over polyacrylamide gel electrophoresis and high pressure liquid chromatography (60% median purity). Additionally, 89% of the oligo products are within a factor of 2 of the median concentration. Chemically synthesized DNA oligonucleotides (oligos) require purification to remove truncated species. Here, the authors developed a high-throughput method for oligo purification that also normalises the concentrations of the oligos in the final samples.
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212
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Chen Y, Ke G, Ma Y, Zhu Z, Liu M, Liu Y, Yan H, Yang CJ. A Synthetic Light-Driven Substrate Channeling System for Precise Regulation of Enzyme Cascade Activity Based on DNA Origami. J Am Chem Soc 2018; 140:8990-8996. [DOI: 10.1021/jacs.8b05429] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yahong Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Guoliang Ke
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yanli Ma
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute and School of Molecular Sciences at Arizona State University, Tempe, Arizona 85287, United States
| | - Chaoyong James Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200127, China
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213
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Ye D, Zuo X, Fan C. DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:171-195. [PMID: 29490188 DOI: 10.1146/annurev-anchem-061417-010007] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.
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Affiliation(s)
- Dekai Ye
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Zuo
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
- Institute of Molecular Medicine, Renji Hospital, Schools of Medicine and Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
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214
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Chen T, Ren L, Liu X, Zhou M, Li L, Xu J, Zhu X. DNA Nanotechnology for Cancer Diagnosis and Therapy. Int J Mol Sci 2018; 19:ijms19061671. [PMID: 29874867 PMCID: PMC6032219 DOI: 10.3390/ijms19061671] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/27/2018] [Accepted: 06/01/2018] [Indexed: 01/03/2023] Open
Abstract
Cancer is one of the leading causes of mortality worldwide, because of the lack of accurate diagnostic tools for the early stages of cancer. Thus, early diagnosis, which provides important information for a timely therapy of cancer, is of great significance for controlling the development of the disease and the proliferation of cancer cells and for improving the survival rates of patients. To achieve the goals of early diagnosis and timely therapy of cancer, DNA nanotechnology may be effective, since it has emerged as a valid technique for the fabrication of various nanoscale structures and devices. The resultant DNA-based nanoscale structures and devices show extraordinary performance in cancer diagnosis, owing to their predictable secondary structures, small sizes, and high biocompatibility and programmability. In particular, the rapid development of DNA nanotechnologies, such as molecular assembly technologies, endows DNA-based nanomaterials with more functionalization and intellectualization. Here, we summarize recent progress made in the development of DNA nanotechnology for the fabrication of functional and intelligent nanomaterials and highlight the prospects of this technology in cancer diagnosis and therapy.
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Affiliation(s)
- Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Institute of Biomedical Engineering, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China.
| | - Lingjie Ren
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Xiaohao Liu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Mengru Zhou
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Lingling Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Jingjing Xu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Institute of Biomedical Engineering, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China.
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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215
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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216
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Huang R, He N, Li Z. Recent progresses in DNA nanostructure-based biosensors for detection of tumor markers. Biosens Bioelectron 2018. [DOI: 10.1016/j.bios.2018.02.053] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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217
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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218
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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219
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Chidchob P, Sleiman HF. Recent advances in DNA nanotechnology. Curr Opin Chem Biol 2018; 46:63-70. [PMID: 29751162 DOI: 10.1016/j.cbpa.2018.04.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/14/2018] [Accepted: 04/20/2018] [Indexed: 12/28/2022]
Abstract
DNA is a powerful guiding molecule to achieve the precise construction of arbitrary structures and high-resolution organization of functional materials. The combination of sequence programmability, rigidity and highly specific molecular recognition in this molecule has resulted in a wide range of exquisitely designed DNA frameworks. To date, the impressive potential of DNA nanomaterials has been demonstrated from fundamental research to technological advancements in materials science and biomedicine. This review presents a summary of some of the most recent developments in structural DNA nanotechnology regarding new assembly approaches and efforts in translating DNA nanomaterials into practical use. Recent work on incorporating blunt-end stacking and hydrophobic interactions as orthogonal instruction rules in DNA assembly, and several emerging applications of DNA nanomaterials will also be highlighted.
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Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada.
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220
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Suzuki Y, Sugiyama H, Endo M. Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801983] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences; Tohoku University; 6-3 Aramaki aza Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences; 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
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences; 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
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221
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Suzuki Y, Sugiyama H, Endo M. Complexing DNA Origami Frameworks through Sequential Self-Assembly Based on Directed Docking. Angew Chem Int Ed Engl 2018; 57:7061-7065. [PMID: 29644771 DOI: 10.1002/anie.201801983] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/01/2018] [Indexed: 01/08/2023]
Abstract
Ordered DNA origami arrays have the potential to compartmentalize space into distinct periodic domains that can incorporate a variety of nanoscale objects. Herein, we used the cavities of a preassembled 2D DNA origami framework to incorporate square-shaped DNA origami structures (SQ-origamis). The framework was self-assembled on a lipid bilayer membrane from cross-shaped DNA origami structures (CR-origamis) and subsequently exposed to the SQ-origamis. High-speed AFM revealed the dynamic adsorption/desorption behavior of the SQ-origamis, which resulted in continuous changing of their arrangements in the framework. These dynamic SQ-origamis were trapped in the cavities by increasing the Mg2+ concentration or by introducing sticky-ended cohesions between extended staples, both from the SQ- and CR-origamis, which enabled the directed docking of the SQ-origamis. Our study offers a platform to create supramolecular structures or systems consisting of multiple DNA origami components.
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramaki aza Aoba, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences, 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
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences, 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
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222
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Kogikoski S, Kubota LT. Electrochemical behavior of self-assembled DNA–gold nanoparticle lattice films. Electrochem commun 2018. [DOI: 10.1016/j.elecom.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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223
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Oruc B, Celik S, Hayat Soytas S, Unal H. DNA Directed Self-Assembly of Single Walled Carbon Nanotubes into Three-Way Junction Nanostructures. ACS OMEGA 2018; 3:4157-4162. [PMID: 30023887 PMCID: PMC6044768 DOI: 10.1021/acsomega.8b00306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/05/2018] [Indexed: 05/19/2023]
Abstract
Utilization of a self-assembled two-dimensional DNA nanostructure to arrange single-walled carbon nanotubes (SWNTs) into predetermined structures at controllable angles is presented. A specially designed DNA three-way junction (3WJ) composed of three double-stranded DNA arms containing single-stranded overhang sequences was prepared by annealing of partially complementary ssDNA sequences and ultrasonicated with SWNTs, resulting in DNA-3WJ/SWNT hybrid nanostructures. Utilization of DNA-3WJ not only allowed the precise dispersion of SWNTs but also acted as a rigid template for the self-assembly of SWNTs into three-armed junctions at an angle of approximately 120° to each other as visualized by scanning electron microscopy and atomic force microscopy. Prepared DNA-3WJ/SWNT nanostructures were also demonstrated to have the appropriate binding sites for fluorophores, providing a simple method for the fluorescent labeling of SWNTs. When ssDNA sequences forming the DNA-3WJ are ultrasonicated with SWNTs, followed by annealing of resulting ssDNA wrapped SWNTs, instead of hybrid junctions composed of three SWNT molecules, a web-like structure composed of interconnected SWNT junctions was obtained. The design approaches demonstrated here provide simple methods for the arrangement of SWNTs into desired nanostructures utilizing pre-assembled DNA nanostructures as linkers in aqueous solution through noncovalent interactions which can greatly contribute to efforts along the controlled assembly of SWNTs.
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Affiliation(s)
- Betul Oruc
- Faculty
of Engineering and Natural Sciences, Sabanci
University, 34956 Istanbul, Turkey
| | - Suleyman Celik
- Sabanci
University SUNUM Nanotechnology Research Center, 34956 Istanbul, Turkey
| | - Serap Hayat Soytas
- Sabanci
University SUNUM Nanotechnology Research Center, 34956 Istanbul, Turkey
| | - Hayriye Unal
- Sabanci
University SUNUM Nanotechnology Research Center, 34956 Istanbul, Turkey
- E-mail: (H.U.)
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224
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Ellis E, Moorthy S, Chio WIK, Lee TC. Artificial molecular and nanostructures for advanced nanomachinery. Chem Commun (Camb) 2018; 54:4075-4090. [PMID: 29484317 DOI: 10.1039/c7cc09133h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Artificial nanomachines can be broadly defined as manmade molecular and nanosystems that are capable of performing useful tasks, very often, by means of doing mechanical work at the nanoscale. Recent advances in nanoscience allow these tiny machines to be designed and made with unprecedented sophistication and complexity, showing promise in novel applications, including molecular assemblers, self-propelling nanocarriers and in vivo molecular computation. This Feature Article overviews and compares major types of nanoscale machines, including molecular machines, self-assembled nanomachines and hybrid inorganic nanomachines, to reveal common structural features and operating principles across different length scales and material systems. We will focus on systems with feature size between 1 and 100 nm, where classical laws of physics meet those of quantum mechanics, giving rise to a spectrum of exotic physiochemical properties. Concepts of nanomachines will be illustrated by selected seminal work along with state-of-the-art progress, including our own contribution, across the fields. The Article will conclude with a brief outlook of this exciting research area.
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Affiliation(s)
- Elizabeth Ellis
- Department of Chemistry, University College London (UCL), UK and Institute for Materials Research and Engineering (IMRE), Agency for Science Technology and Research (A*STAR), Singapore
| | - Suresh Moorthy
- Department of Chemistry, University College London (UCL), UK and Institute for Materials Discovery, University College London (UCL), UK.
| | - Weng-I Katherine Chio
- Department of Chemistry, University College London (UCL), UK and Singapore Bioimaging Consortium (SBIC), Agency for Science Technology and Research (A*STAR), Singapore
| | - Tung-Chun Lee
- Department of Chemistry, University College London (UCL), UK and Institute for Materials Discovery, University College London (UCL), UK.
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225
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Quantifying absolute addressability in DNA origami with molecular resolution. Nat Commun 2018; 9:1600. [PMID: 29686288 PMCID: PMC5913233 DOI: 10.1038/s41467-018-04031-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Self-assembled DNA nanostructures feature an unprecedented addressability with sub-nanometer precision and accuracy. This addressability relies on the ability to attach functional entities to single DNA strands in these structures. The efficiency of this attachment depends on two factors: incorporation of the strand of interest and accessibility of this strand for downstream modification. Here we use DNA-PAINT super-resolution microscopy to quantify both incorporation and accessibility of all individual strands in DNA origami with molecular resolution. We find that strand incorporation strongly correlates with the position in the structure, ranging from a minimum of 48% on the edges to a maximum of 95% in the center. Our method offers a direct feedback for the rational refinement of the design and assembly process of DNA nanostructures and provides a long sought-after quantitative explanation for efficiencies of DNA-based nanomachines. Self-assembled DNA nanostructures hold potential as nanomachines or platforms for organized chemical synthesis, but methods for assembly quality control are lacking. Here the authors use DNA-PAINT to quantify the incorporation and accessibility of individual strands in a DNA origami platform with molecular resolution.
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226
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Huang X, Song J, Yung BC, Huang X, Xiong Y, Chen X. Ratiometric optical nanoprobes enable accurate molecular detection and imaging. Chem Soc Rev 2018; 47:2873-2920. [PMID: 29568836 PMCID: PMC5926823 DOI: 10.1039/c7cs00612h] [Citation(s) in RCA: 446] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploring and understanding biological and pathological changes are of great significance for early diagnosis and therapy of diseases. Optical sensing and imaging approaches have experienced major progress in this field. Particularly, an emergence of various functional optical nanoprobes has provided enhanced sensitivity, specificity, targeting ability, as well as multiplexing and multimodal capabilities due to improvements in their intrinsic physicochemical and optical properties. However, one of the biggest challenges of conventional optical nanoprobes is their absolute intensity-dependent signal readout, which causes inaccurate sensing and imaging results due to the presence of various analyte-independent factors that can cause fluctuations in their absolute signal intensity. Ratiometric measurements provide built-in self-calibration for signal correction, enabling more sensitive and reliable detection. Optimizing nanoprobe designs with ratiometric strategies can surmount many of the limitations encountered by traditional optical nanoprobes. This review first elaborates upon existing optical nanoprobes that exploit ratiometric measurements for improved sensing and imaging, including fluorescence, surface enhanced Raman scattering (SERS), and photoacoustic nanoprobes. Next, a thorough discussion is provided on design strategies for these nanoprobes, and their potential biomedical applications for targeting specific biomolecule populations (e.g. cancer biomarkers and small molecules with physiological relevance), for imaging the tumor microenvironment (e.g. pH, reactive oxygen species, hypoxia, enzyme and metal ions), as well as for intraoperative image guidance of tumor-resection procedures.
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Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China. and Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
| | - Jibin Song
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA. and MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Bryant C Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
| | - Xiaohua Huang
- Department of Chemistry, University of Memphis, 213 Smith Chemistry Bldg., Memphis, TN 38152, USA
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
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227
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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228
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Pfeifer W, Saccà B. Synthetic DNA filaments: from design to applications. Biol Chem 2018; 399:773-785. [DOI: 10.1515/hsz-2018-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/25/2018] [Indexed: 01/06/2023]
Abstract
Abstract
Natural filaments, such as microtubules and actin filaments, are fundamental components of the cell. Despite their relatively simple linear structure, filaments play a number of crucial roles in living organisms, from scaffolding to cellular adhesion and motility. The mechanical properties of natural filaments mostly rely on the structural features of the component units and on the way they are connected together, thus providing an ideal molecular model for emulation purposes. In this review, we describe the progresses done in this field using DNA for the rational design of synthetic filamentous-like materials with tailored structural and physical characteristics. We firstly survey the strategies that have been adopted until now for the construction of individual DNA building components and their programmable self-assembly into linear oligomeric structures. We then describe the theoretical models of polymer elasticity applied to calculate the bending strength of DNA filaments, expressed in terms of persistence length. Finally, we report some of the most exciting examples of truly biomimetic DNA filaments, which are capable of mimicking not only the sophisticated structural features of their natural counterparts but also their responsiveness to external stimuli, thus resulting in active motion and growing networks between distant loci.
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Affiliation(s)
- Wolfgang Pfeifer
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
| | - Barbara Saccà
- Centre for Medical Biotechnology (ZMB) and Centre for Nano Integration Duisburg-Essen (CENIDE) , University of Duisburg-Essen, Universitätstraße 2 , D-45117 Essen , Germany
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229
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Miyata T, Shimada N, Maruyama A, Kawai K. Fluorescence Redox Blinking Adaptable to Structural Analysis of Nucleic Acids. Chemistry 2018; 24:6755-6761. [DOI: 10.1002/chem.201705668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Takafumi Miyata
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta, Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Naohiko Shimada
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta, Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta, Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1, Ibaraki Osaka 567-0047 Japan
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230
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Bui H, Shah S, Mokhtar R, Song T, Garg S, Reif J. Localized DNA Hybridization Chain Reactions on DNA Origami. ACS NANO 2018; 12:1146-1155. [PMID: 29357217 DOI: 10.1021/acsnano.7b06699] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The field of DNA nanoscience has demonstrated many exquisite DNA nanostructures and intricate DNA nanodevices. However, the operation of each step of prior demonstrated DNA nanodevices requires the diffusion of DNA strands, and the speed of these devices is limited by diffusion kinetics. Here we demonstrate chains of localized DNA hybridization reactions on the surface of a self-assembled DNA origami rectangle. The localization design for our DNA nanodevices does not rely on the diffusion of DNA strands for each step, thus providing faster reaction kinetics. The locality also provides considerable increased scalability, since localized components of the devices can be reused in other locations. A variety of techniques, including atomic force microscopy, total internal reflection fluorescence, and ensemble fluorescence spectroscopy, are used to confirm the occurrence of localized DNA hybridization reactions on the surface of DNA origami. There are many potential biological applications for our localized DNA nanodevices, and the localization design is extensible to applications involving DNA nanodevices operating on other molecular surfaces, such as those of the cell.
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Affiliation(s)
- Hieu Bui
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
- National Research Council , 500 Fifth Street NW, Keck 576, Washington, DC 20001, United States
| | - Shalin Shah
- Department of Electrical and Computer Engineering, Duke University Durham, North Carolina 27708, United States
| | - Reem Mokhtar
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Tianqi Song
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - Sudhanshu Garg
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
| | - John Reif
- Department of Computer Science, Duke University , Durham, North Carolina 27708, United States
- Department of Electrical and Computer Engineering, Duke University Durham, North Carolina 27708, United States
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231
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Cozzoli L, Gjonaj L, Stuart MCA, Poolman B, Roelfes G. Responsive DNA G-quadruplex micelles. Chem Commun (Camb) 2018; 54:260-263. [PMID: 29231221 DOI: 10.1039/c7cc07899d] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel and versatile design of DNA-lipid conjugates is presented. The assembly of the DNA headgroups into G-quadruplex structures is essential for the formation of micelles and their stability. By hybridization with a complementary oligonucleotide the micelles were destabilized, resulting in cargo release. In combination with a hairpin DNA aptamer as complementary strand, the release is obtained selectively by the presence of ATP.
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Affiliation(s)
- Liliana Cozzoli
- Stratingh Institute for Chemistry, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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232
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Norouzi A, Ravan H, Mohammadi A, Hosseinzadeh E, Norouzi M, Fozooni T. Aptamer-integrated DNA nanoassembly: A simple and sensitive DNA framework to detect cancer cells. Anal Chim Acta 2018. [PMID: 29534792 DOI: 10.1016/j.aca.2018.02.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of powerful techniques to detect cancer cells at early stages plays a notable role in diagnosing and prognosing cancer patients and reducing mortality. This paper reports on a novel functional DNA nanoassembly capable of detecting cancer cells based on structural DNA nanotechnology. DNA nanoassemblies were constructed by the self-assembly of a DNA concatemer to a plenty of sticky-ended three-way junctions. While an aptamer moiety guided the nanoassembly to the target cancer cell, the peroxidase-mimicking DNAzymes embedded in the nanoassemblies were used as the sensing element to produce colorimetric signals. As proof-of-concept, as low as 175 cancer cells were detected by the assay, and color change was clearly distinguished by the naked eyes. The proposed system enjoys potential applications for point-of-care cancer diagnosis, with its excellent sensitivity and selectivity.
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Affiliation(s)
- Akram Norouzi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hadi Ravan
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Abbas Mohammadi
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.
| | - Elyas Hosseinzadeh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdieh Norouzi
- Department of Nursing, Islamic Azad University of Kerman, Kerman, Iran
| | - Tahereh Fozooni
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
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233
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Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. J Struct Biol 2018; 201:100-107. [DOI: 10.1016/j.jsb.2017.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 08/11/2017] [Accepted: 09/02/2017] [Indexed: 11/17/2022]
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234
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Tian T, Li J, Xie C, Sun Y, Lei H, Liu X, Xia J, Shi J, Wang L, Lu W, Fan C. Targeted Imaging of Brain Tumors with a Framework Nucleic Acid Probe. ACS APPLIED MATERIALS & INTERFACES 2018; 10:3414-3420. [PMID: 29299920 DOI: 10.1021/acsami.7b17927] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Development of agents for delivering drugs and imaging probes across the blood-brain barrier (BBB) remains a major challenge. In this study, we designed a biocompatible framework nucleic acid (FNA)-based imaging probe for brain tumor-targeting. We employed a typical type of FNAs, tetrahedral DNA nanostructures (TDNs), as the building block, which were modified with angiopep-2 (ANG), a 19-mer peptide derived from human Kunitz domain of aprotinin. This probe exhibited high binding efficiency with low-density lipoprotein receptor-related protein-1 (LRP-1) of BBB and glioma. We found that ANG-functionalized TDNs (ANG-TDNs) stayed intact for at least 12 h in serum, and that ANG modification effectively enhanced cellular uptake of TDNs in brain capillary endothelial cells and Uppsala 87 malignant glioma (U87MG) cells. Remarkably, studies in both in vitro and in vivo models revealed that ANG-TDNs could cross the BBB. Especially, in vivo imaging showed strong fluorescent signals in U87MG human glioblastoma xenograft in nude mice. This study establishes that the FNA-based platform provides a new theranostic tool for the study and therapy of brain tumors.
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Affiliation(s)
- Tian Tian
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Interdisciplinary Integrative Biomedical Research, Shanghai University of Traditional Chinese Medicine , Shanghai 201203, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Cao Xie
- Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, China
| | - Yanhong Sun
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Haozhi Lei
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Xinyi Liu
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiaoyun Xia
- School of Chemistry and Biology Engineering, Changsha University of Science and Technology , Changsha 410004, China
| | - Jiye Shi
- UCB Pharma , Slough, SL1 14EN Berkshire, U.K
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University , Shanghai 201203, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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235
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Wang K, He MQ, Zhai FH, Wang J, He RH, Yu YL. Autonomous DNA nanomachine based on cascade amplification of strand displacement and DNA walker for detection of multiple DNAs. Biosens Bioelectron 2018; 105:159-165. [PMID: 29412940 DOI: 10.1016/j.bios.2018.01.044] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 01/06/2023]
Abstract
DNA can be modified to function as a scaffold for the construction of a DNA nanomachine, which can then be used in analytical applications if the DNA nanomachine can be triggered by the presence of a diagnostic DNA or some other analyte. We herein propose a novel and powerful DNA nanomachine that can detect DNA via combining the tandem strand displacement reactions and a DNA walker. Three different DNA sensing platforms are described, where the whole DNA machine was constructed on a gold electrode (GE). This cascade multiple amplification strategy exhibited an excellent sensitivity. Under optimal conditions, the electrochemical sensor could achieve a detection limit of 36 fM with a linear range from 50 to 500 fM. In particular, the electrochemical sensor could easily distinguish the base mutations. More interestingly, the DNA nanomachine could be used to construct analog AND and OR logic gates. We demonstrate that electrochemical signals generated from the different input combinations can be used to distinguish multiple target DNAs. The practical applicability of the present biosensor is demonstrated by the detection of target DNA in human serum with satisfactory results, which holds great potential for a future application in clinical diagnosis.
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Affiliation(s)
- Kun Wang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Meng-Qi He
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Fu-Heng Zhai
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jin Wang
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Rong-Huan He
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
| | - Yong-Liang Yu
- Department of Chemistry, College of Sciences, Northeastern University, Box 332, Shenyang 110819, China.
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236
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Tee S, Wang Z. How Well Can DNA Rupture DNA? Shearing and Unzipping Forces inside DNA Nanostructures. ACS OMEGA 2018; 3:292-301. [PMID: 30023776 PMCID: PMC6044922 DOI: 10.1021/acsomega.7b01692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/26/2017] [Indexed: 05/26/2023]
Abstract
A purely DNA nanomachine must support internal stresses across short DNA segments with finite rigidity, producing effects that can be qualitatively very different from experimental observations of isolated DNA in fixed-force ensembles. In this article, computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-stranded segments and how well this stress can discriminate between unzipping or shearing geometries. This discrimination is found to be maximized at an optimal length but deteriorates as the driving duplex is either lengthened or shortened. This differs markedly from a fixed-force ensemble and has implications for the design parameters and limitations of dynamic DNA nanomachines.
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237
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Méndez‐Arriaga JM, Maldonado CR, Dobado JA, Galindo MA. Silver(I)‐Mediated Base Pairs in DNA Sequences Containing 7‐Deazaguanine/Cytosine: towards DNA with Entirely Metallated Watson–Crick Base Pairs. Chemistry 2018; 24:4583-4589. [DOI: 10.1002/chem.201705131] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- José M. Méndez‐Arriaga
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - Carmen R. Maldonado
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - José A. Dobado
- Grupo de Modelización y Diseño Molecular, Departamento de Química OrgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
| | - Miguel A. Galindo
- Departamento de Química InorgánicaUniversidad de Granada Avd Fuentenueva s/n 18071 Spain
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238
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Han M, Fan Q, Zhang Y, Xu L, Yu C, Su X. Non-classical hydrogen bond triggered strand displacement for analytical applications and DNA nanostructure assembly. NEW J CHEM 2018. [DOI: 10.1039/c7nj05141g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel strand displacement triggered by the non-classical hydrogen bond between cyanuric acid and adenine exhibits a fast reaction rate.
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Affiliation(s)
- Manli Han
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Qingsheng Fan
- Sino-erman Joint Research Institution
- Nanchang University
- Nanchang 330047
- China
| | - Yi Zhang
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Changyuan Yu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Xin Su
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
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239
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Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
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240
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Gao M, Daniel D, Zou H, Jiang S, Lin S, Huang C, Hecht SM, Chen S. Rapid detection of a dengue virus RNA sequence with single molecule sensitivity using tandem toehold-mediated displacement reactions. Chem Commun (Camb) 2018; 54:968-971. [DOI: 10.1039/c7cc09131a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Novel tandem toehold-mediated displacement reactions were developed to detect dengue virus RNA. As few as 6 copies of RNA per sample were detected.
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Affiliation(s)
- Mingxuan Gao
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
| | - Douglas Daniel
- Biodesign Center for Innovations in Medicine, Arizona State University
- Tempe 85287
- USA
| | - Hongyan Zou
- College of Pharmaceutical Sciences, Southwest University
- Chongqing
- P. R. China
- Ministry of Education Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Southwest University
- Chongqing
| | - Shuoxing Jiang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University
- Tempe 85287
- USA
| | - Su Lin
- Biodesign Center for Innovations in Medicine, Arizona State University
- Tempe 85287
- USA
| | - Chengzhi Huang
- College of Pharmaceutical Sciences, Southwest University
- Chongqing
- P. R. China
- Ministry of Education Key Laboratory of Luminescence and Real-Time Analytical Chemistry, Southwest University
- Chongqing
| | - Sidney M. Hecht
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, Arizona State University
- Tempe 85287
- USA
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241
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Wei G, Wang C, Ma L, Li F, Gao Z, Yan M. Multi-dimensional architecture materials of amino acids and metal ions. NEW J CHEM 2018. [DOI: 10.1039/c8nj02925c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple self-assembly method for the preparation of functional multi-dimensional architecture materials.
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Affiliation(s)
- Guangcheng Wei
- Department of Pharmacy Science
- Binzhou Medical University
- Yantai
- China
| | - Chunhua Wang
- Department of Pharmacy Science
- Binzhou Medical University
- Yantai
- China
| | - Liying Ma
- Department of Pharmacy Science
- Binzhou Medical University
- Yantai
- China
| | - Feng Li
- Experiment Teaching Center
- Binzhou Medical University
- Yantai
- China
| | - Zonghua Gao
- Department of Pharmacy Science
- Binzhou Medical University
- Yantai
- China
| | - Miaomiao Yan
- Experiment Teaching Center
- Binzhou Medical University
- Yantai
- China
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242
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Huang D, Freeley M, Palma M. Single-Molecule Patterning via DNA Nanostructure Assembly: A Reusable Platform. Methods Mol Biol 2018; 1811:231-251. [PMID: 29926457 DOI: 10.1007/978-1-4939-8582-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we describe a facile strategy of general applicability for controlling the immobilization of individual nanomoieties on nanopatterned surfaces with single-molecule control. We combine the ability of DNA nanostructures as programmable platforms, with a one-step Focused Ion Beam nanopatterning, to demonstrate the controlled immobilization of DNA origami functionalized with individual quantum dots (QDs) at predesigned positions on glass coverslips and silicon substrates. Remarkably, the platform developed is reusable after a simple cleaning process, and can be designed to display different geometrical arrangements.
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Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Mark Freeley
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Matteo Palma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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243
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Sharma R, Schreck JS, Romano F, Louis AA, Doye JPK. Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model. ACS NANO 2017; 11:12426-12435. [PMID: 29083876 DOI: 10.1021/acsnano.7b06470] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
As detailed structural characterizations of large complex DNA nanostructures are hard to obtain experimentally, particularly if they have substantial flexibility, coarse-grained modeling can potentially provide an important complementary role. Such modeling can provide a detailed view of both the average structure and the structural fluctuations, as well as providing insight into how the nanostructure's design determines its structural properties. Here, we present a case study of jointed DNA nanostructures using the oxDNA model. In particular, we consider archetypal hinge and sliding joints, as well as more complex structures involving a number of such coupled joints. Our results highlight how the nature of the motion in these structures can sensitively depend on the precise details of the joints. Furthermore, the generally good agreement with experiments illustrates the power of this approach and suggests the use of such modeling to prescreen the properties of putative designs.
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Affiliation(s)
- Rahul Sharma
- Department of Chemistry, Indian Institute of Technology Roorkee , Roorkee, 247667, India
| | - John S Schreck
- Department of Chemical Engineering, Columbia University , New York, New York 10027, United States
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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244
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Huang J, Ding HM, Xu Y, Zeng D, Zhu H, Zang DM, Bao SS, Ma YQ, Zheng LM. Chiral expression from molecular to macroscopic level via pH modulation in terbium coordination polymers. Nat Commun 2017; 8:2131. [PMID: 29242533 PMCID: PMC5730601 DOI: 10.1038/s41467-017-02260-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 11/16/2017] [Indexed: 12/21/2022] Open
Abstract
Chiral expression from the molecular to macroscopic level is common in biological systems, but is difficult to realise for coordination polymers (CPs). The assembly of homochiral CPs in both crystalline and helical forms can provide a bridge for understanding the relationship between the molecular and macroscopic scales of chirality. Herein, we report homochiral helices of [Tb(R- or S-pempH)3]∙2H2O (R - or S -1) (pempH2 = (1-phenylethylamino)methylphosphonic acid) and their crystalline counterparts (R - or S -3), which are formed at different pH of the reaction mixtures under hydrothermal conditions. By combining the experiments and molecular simulations, we propose that the formation of helices of R -1 or S -1 occurs via a hierarchical self-assembly route, which involves twisted packing due to the geometric incompatibility of the different types of chains. The observed chiral transcription from molecules to morphologies is significant for understanding bio-related self-assembly processes on the nano- to macro-scale.
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Affiliation(s)
- Jian Huang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Hong-Ming Ding
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China.,Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou, 215006, China
| | - Yan Xu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Dai Zeng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Hui Zhu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Dong-Mian Zang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Song-Song Bao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China.
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China. .,Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou, 215006, China.
| | - Li-Min Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China.
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245
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Triplex-quadruplex structural scaffold: a new binding structure of aptamer. Sci Rep 2017; 7:15467. [PMID: 29133961 PMCID: PMC5684193 DOI: 10.1038/s41598-017-15797-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 11/08/2022] Open
Abstract
Apart from the canonical Watson-Crick duplex, nucleic acids can often form other structures, e.g. G-quadruplex and triplex. These structures give nucleic acid additional functions besides coding for genetic information. Aptamers are one type of functional nucleic acids that bind to specific targets with high selectivity and affinity by folding into special tertiary structures. Despite the fact that numerous aptamers have been reported, only a few different types of aptamer structures are identified. Here we report a novel triplex-quadruplex hybrid scaffold formed by a codeine binding aptamer (CBA). CBA and its derivatives are G-rich DNA sequences. Codeine binding can induce the formation of a complex structure for this aptamer containing a G-quadruplex and a G·GC triplex, while codeine is located at the junction of the triplex and quadruplex. When split CBA into two moieties, codeine does not bind either moieties individually, but can bind them together by inducing the formation of the triplex-quadruplex scaffold. This structure formation induced by codeine binding is shown to inhibit polymerase reaction, which shows a potential application of the aptamer sequence in gene regulations.
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246
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Kim H, Arbutina K, Xu A, Liu H. Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al 2O 3 and its application in imprinting lithography. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2363-2375. [PMID: 29181293 PMCID: PMC5687006 DOI: 10.3762/bjnano.8.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/02/2017] [Indexed: 06/01/2023]
Abstract
We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al2O3. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O3 oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films.
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Affiliation(s)
- Hyojeong Kim
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Kristin Arbutina
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Anqin Xu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
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247
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Centola M, Valero J, Famulok M. Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure. J Am Chem Soc 2017; 139:16044-16047. [DOI: 10.1021/jacs.7b08839] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mathias Centola
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
| | - Julián Valero
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Michael Famulok
- LIMES
Chemical Biology Unit, Universität Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
- Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
- Center
of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Straße
1, 53121 Bonn, Germany
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248
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Pan K, Bricker WP, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res 2017; 45:6284-6298. [PMID: 28482032 PMCID: PMC5499760 DOI: 10.1093/nar/gkx378] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/25/2017] [Indexed: 12/22/2022] Open
Abstract
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson–Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5–100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone.
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Affiliation(s)
- Keyao Pan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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249
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250
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Control of enzyme reactions by a reconfigurable DNA nanovault. Nat Commun 2017; 8:992. [PMID: 29051565 PMCID: PMC5648847 DOI: 10.1038/s41467-017-01072-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/16/2017] [Indexed: 12/21/2022] Open
Abstract
Biological systems use compartmentalisation as a general strategy to control enzymatic reactions by precisely regulating enzyme–substrate interactions. With the advent of DNA nanotechnology, it has become possible to rationally design DNA-based nano-containers with programmable structural and dynamic properties. These DNA nanostructures have been used to cage enzymes, but control over enzyme–substrate interactions using a dynamic DNA nanostructure has not been achieved yet. Here we introduce a DNA origami device that functions as a nanoscale vault: an enzyme is loaded in an isolated cavity and the access to free substrate molecules is controlled by a multi-lock mechanism. The DNA vault is characterised for features such as reversible opening/closing, cargo loading and wall porosity, and is shown to control the enzymatic reaction catalysed by an encapsulated protease. The DNA vault represents a general concept to control enzyme–substrate interactions by inducing conformational changes in a rationally designed DNA nanodevice. DNA nanostructures can cage enzymes but currently fall short of controlling their reactions with substrates. Here, the authors enclose an enzyme inside a dynamic DNA vault, which regulates its access to substrate molecules—and thus its enzymatic activity—through a multi-lock mechanism.
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