201
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Su Y, Li D, Liu B, Xiao M, Wang F, Li L, Zhang X, Pei H. Rational Design of Framework Nucleic Acids for Bioanalytical Applications. Chempluschem 2019; 84:512-523. [DOI: 10.1002/cplu.201900118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Yuwei Su
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Bingyi Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Fei Wang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Xueli Zhang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
- Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
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202
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Sun H, Yang L, Thompson MP, Schara S, Cao W, Choi W, Hu Z, Zang N, Tan W, Gianneschi NC. Recent Advances in Amphiphilic Polymer-Oligonucleotide Nanomaterials via Living/Controlled Polymerization Technologies. Bioconjug Chem 2019; 30:1889-1904. [PMID: 30969752 DOI: 10.1021/acs.bioconjchem.9b00166] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past decade, the field of polymer-oligonucleotide nanomaterials has flourished because of the development of synthetic techniques, particularly living polymerization technologies, which provide access to polymers with well-defined architectures, precise molecular weights, and terminal or side-chain functionalities. Various "living" polymerization methods have empowered chemists with the ability to prepare functional polymer-oligonucleotide conjugates yielding a library of architectures, including linear diblock, comb, star, hyperbranched star, and gel morphologies. Since oligonucleotides are hydrophilic and synthetic polymers can be tailored with hydrophobicity, these amphiphilic polymer-oligonucleotide conjugates are capable of self-assembling into nanostructures with different shapes, leading to many high-value-added biomedical applications, such as drug delivery systems, gene regulation, and 3D-bioprinting. This review aims to highlight the main living polymerization approaches to polymer-oligonucleotide conjugates, including ring-opening metathesis polymerization, atom transfer radical polymerization (ATRP), reversible addition-fragmentation transfer polymerization (RAFT), and ring-opening polymerization of cyclic esters and N-carboxyanhydride. The self-assembly properties and resulting applications of polymer-DNA hybrid materials are highlighted as well.
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Affiliation(s)
- Hao Sun
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Lu Yang
- Department of Chemistry , University of Florida , P.O. Box 117200, Gainesville , Florida 32611-7200 , United States
| | - Matthew P Thompson
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Steve Schara
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Wei Cao
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Wonmin Choi
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Ziying Hu
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Nanzhi Zang
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
| | - Weihong Tan
- Department of Chemistry , University of Florida , P.O. Box 117200, Gainesville , Florida 32611-7200 , United States
| | - Nathan C Gianneschi
- Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, International Institute for Nanotechnology, and Simpson Querrey Institute , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
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203
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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204
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
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Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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205
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Kellis DL, Sarter C, Cannon BL, Davis PH, Graugnard E, Lee J, Pensack RD, Kolmar T, Jäschke A, Yurke B, Knowlton WB. An All-Optical Excitonic Switch Operated in the Liquid and Solid Phases. ACS NANO 2019; 13:2986-2994. [PMID: 30758934 DOI: 10.1021/acsnano.8b07504] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The excitonic circuitry found in photosynthetic organisms suggests an alternative to electronic circuits, but the assembly of optically active molecules to fabricate even simple excitonic devices has been hampered by the limited availability of suitable molecular scale assembly technologies. Here we have designed and operated a hybrid all-optical excitonic switch comprised of donor/acceptor chromophores and photochromic nucleotide modulators assembled with nanometer scale precision using DNA nanotechnology. The all-optical excitonic switch was operated successfully in both liquid and solid phases, exhibiting high ON/OFF switching contrast with no apparent cyclic fatigue through nearly 200 cycles. These findings, combined with the switch's small footprint and volume, estimated low energy requirement, and potential ability to switch at speeds in the 10s of picoseconds, establish a prospective pathway forward for all-optical excitonic circuits.
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Affiliation(s)
- Donald L Kellis
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Christopher Sarter
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Brittany L Cannon
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Paul H Davis
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Elton Graugnard
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Jeunghoon Lee
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Chemistry & Biochemistry , Boise State University , Boise , Idaho 83725 , United States
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology , Heidelberg University , 69120 Heidelberg , Germany
| | - Bernard Yurke
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
| | - William B Knowlton
- Micron School of Materials Science & Engineering , Boise State University , Boise , Idaho 83725 , United States
- Department of Electrical & Computer Engineering , Boise State University , Boise , Idaho 83725 , United States
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206
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Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. Nature 2019; 567:366-372. [DOI: 10.1038/s41586-019-1014-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/07/2019] [Indexed: 01/19/2023]
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207
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Li L, Zhang P, Li J, Wang Y, Wei Y, Hu J, Zhou X, Xu B, Li B. Measurement of nanomechanical properties of DNA molecules by PeakForce atomic force microscopy based on DNA origami. NANOSCALE 2019; 11:4707-4711. [PMID: 30834915 DOI: 10.1039/c8nr10354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Characterization of the stiffness of thin DNA strands remains difficult. By constructing bilayer DNA molecules, we investigated their mechanical properties using AFM. Increased DNA thickness through DNA origami greatly reduced the substrate effect when measuring Young's modulus, thus providing a more accurate picture of the inherent nanomechanical properties of DNA.
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Affiliation(s)
- Lin Li
- School of Science, Ningbo University, Ningbo 315211, Zhejiang, China.
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208
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Complex wireframe DNA nanostructures from simple building blocks. Nat Commun 2019; 10:1067. [PMID: 30842408 PMCID: PMC6403373 DOI: 10.1038/s41467-019-08647-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 01/18/2019] [Indexed: 11/08/2022] Open
Abstract
DNA nanostructures with increasing complexity have showcased the power of programmable self-assembly from DNA strands. At the nascent stage of the field, a variety of small branched objects consisting of a few DNA strands were created. Since then, a quantum leap of complexity has been achieved by a scaffolded 'origami' approach and a scaffold-free approach using single-stranded tiles/bricks-creating fully addressable two-dimensional and three-dimensional DNA nanostructures designed on densely packed lattices. Recently, wireframe architectures have been applied to the DNA origami method to construct complex structures. Here, revisiting the original wireframe framework entirely made of short synthetic strands, we demonstrate a design paradigm that circumvents the sophisticated routing and size limitations intrinsic to the scaffold strand in DNA origami. Under this highly versatile self-assembly framework, we produce a myriad of wireframe structures, including 2D arrays, tubes, polyhedra, and multi-layer 3D arrays.
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209
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Matthies M, Agarwal NP, Poppleton E, Joshi FM, Šulc P, Schmidt TL. Triangulated Wireframe Structures Assembled Using Single-Stranded DNA Tiles. ACS NANO 2019; 13:1839-1848. [PMID: 30624898 DOI: 10.1021/acsnano.8b08009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The field of structural DNA nanotechnology offers a wide range of design strategies with which to build structures with a desired aspect ratio, size, and shape. Compared with traditional close-packed DNA structures, triangulated wireframe structures require less material per surface or volume unit and improve the stability in biologically relevant conditions due to the reduced electrostatic repulsion. Herein, we expand the design space of the DNA single-stranded tile method to cover a range of anisotropic, finite, triangulated wireframe structures as well as a number of one-dimensional crystalline assemblies. These structures are composed of six-arm junctions with a single double helix as connecting edges that assemble in physiologically relevant salinities. For a reliable folding of the structures, single-stranded spacers 2-4 nucleotides long have to be introduced in the junction connecting neighboring arms. Coarse-grained molecular dynamics simulations using the oxDNA model suggests that the spacers prevent the stacking of DNA helices, thereby facilitating the assembly of planar geometries.
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Affiliation(s)
| | | | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute , Arizona State University , 1001 South McAllister Avenue , Tempe , Arizona 85281 , United States
| | | | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute , Arizona State University , 1001 South McAllister Avenue , Tempe , Arizona 85281 , United States
- School of Molecular Sciences Arizona State University , Physical Sciences Building, Room D-102 , PO Box 871604, Tempe , Arizona 85287-1604 , United States
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210
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Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges. ACS NANO 2019; 13:2083-2093. [PMID: 30605605 PMCID: PMC6679942 DOI: 10.1021/acsnano.8b08671] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
3D polyhedral wireframe DNA nanoparticles (DNA-NPs) fabricated using scaffolded DNA origami offer complete and independent control over NP size, structure, and asymmetric functionalization on the 10-100 nm scale. However, the complex DNA sequence design needed for the synthesis of these versatile DNA-NPs has limited their widespread use to date. While the automated sequence design algorithms DAEDALUS and vHelix-BSCOR apply to DNA-NPs synthesized using either uniformly dual or hybrid single-dual duplex edges, respectively, these DNA-NPs are relatively compliant mechanically and are therefore of limited utility for some applications. Further, these algorithms are incapable of handling DNA-NP edge designs composed of more than two duplexes, which are needed to enhance DNA-NP mechanical stiffness. As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. We also introduce a multiway vertex design that enables the fabrication of DNA-NPs with arbitrary edge lengths and vertex angles and apply it to synthesize a highly asymmetric origami object. Sequence designs are demonstrated to fold robustly into target DNA-NP shapes with high folding efficiency and structural fidelity that is verified using single particle cryo-electron microscopy and 3D reconstruction. In order to test its generality, we apply TALOS to design an in silico library of over 200 DNA-NPs of distinct symmetries and sizes, and for broad impact, we also provide the software as open source for the generation of custom NP designs.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Tyson R. Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kaiming Zhang
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - William P. Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shanshan Li
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
| | - Wah Chiu
- Department of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Author
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211
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Monferrer A, Zhang D, Lushnikov AJ, Hermann T. Versatile kit of robust nanoshapes self-assembling from RNA and DNA modules. Nat Commun 2019; 10:608. [PMID: 30723214 PMCID: PMC6363791 DOI: 10.1038/s41467-019-08521-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 01/16/2019] [Indexed: 11/09/2022] Open
Abstract
DNA and RNA have emerged as a material for nanotechnology applications that take advantage of the nucleic acids' ability to encode folding and programmable self-assembly through mainly base pairing. The two types of nucleic acid have rarely been used in combination to enhance structural diversity or for partitioning of functional and architectural roles. Here, we report a design and screening strategy to integrate combinations of RNA motifs as architectural joints and DNA building blocks as functional modules for programmable self-assembly of a versatile toolkit of polygonal nucleic acid nanoshapes. Clean incorporation of diverse DNA modules with various topologies attest to the extraordinary robustness of the RNA-DNA hybrid framework. The design and screening strategy enables systematic development of RNA-DNA hybrid nanoshapes as programmable platforms for applications in molecular recognition, sensor and catalyst development as well as protein interaction studies.
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Affiliation(s)
- Alba Monferrer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Douglas Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | | | - Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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212
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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213
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214
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Gerling T, Dietz H. Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies. Angew Chem Int Ed Engl 2019; 58:2680-2684. [PMID: 30694591 PMCID: PMC6984961 DOI: 10.1002/anie.201812463] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 11/07/2022]
Abstract
Stacking bonds formed between two blunt-ended DNA double helices can be used to reversibly stabilize higher-order complexes that are assembled from rigid DNA components. Typically, at low cation concentrations, stacking bonds break and thus higher-order complexes disassemble. Herein, we present a site-specific photochemical mechanism for the reversible covalent stabilization of stacking bonds in DNA assemblies. To this end, we modified one blunt end with the 3-cyanovinylcarbazole (cnv K) moiety and positioned a thymine residue (T) at the other blunt end. In the bound state, the two blunt-ended helices are stacked together, resulting in a co-localization of cnv K and T. Such a configuration induces the formation of a covalent bond across the stacking contact upon irradiation with 365 nm light. This bond can also be cleaved upon irradiation with 310 nm light, allowing repeated formation and cleavage of the same covalent bond on the timescale of seconds. Our system will expand the range of conditions under which stacking-bond-stabilized objects may be utilized.
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Affiliation(s)
- Thomas Gerling
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
| | - Hendrik Dietz
- Physik Department, Walter Schottky Institute, Technische Universität München, Am Coulombwall 4a, 85748, Garching, Germany
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215
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Gerling T, Dietz H. Reversible Covalent Stabilization of Stacking Contacts in DNA Assemblies. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Thomas Gerling
- Physik DepartmentWalter Schottky InstituteTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Hendrik Dietz
- Physik DepartmentWalter Schottky InstituteTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
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216
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Du Y, Pan J, Choi JH. A review on optical imaging of DNA nanostructures and dynamic processes. Methods Appl Fluoresc 2019; 7:012002. [PMID: 30523978 DOI: 10.1088/2050-6120/aaed11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA self-assembly offers a powerful means to construct complex nanostructures and program dynamic molecular processes such as strand displacement. DNA nanosystems pack high structural complexity in a small scale (typically, <100 nm) and span dynamic features over long periods of time, which bring new challenges for characterizations. The spatial and temporal features of DNA nanosystems require novel experimental methods capable of high resolution imaging over long time periods. This article reviews recent advances in optical imaging methods for characterizing self-assembled DNA nanosystems, with particular emphasis on super-resolved fluorescence microscopy. Several advanced strategies are developed to obtain accurate and detailed images of intricate DNA nanogeometries and to perform precise tracking of molecular motions in dynamic processes. We present state-of-the-art instruments and imaging strategies including localization microscopy and spectral imaging. We discuss how they are used in biological studies and biomedical applications, and also provide current challenges and future outlook. Overall, this review serves as a practical guide in optical microscopy for the field of DNA nanotechnology.
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Affiliation(s)
- Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907
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217
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Jun H, Zhang F, Shepherd T, Ratanalert S, Qi X, Yan H, Bathe M. Autonomously designed free-form 2D DNA origami. SCIENCE ADVANCES 2019; 5:eaav0655. [PMID: 30613779 PMCID: PMC6314877 DOI: 10.1126/sciadv.aav0655] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/21/2018] [Indexed: 05/20/2023]
Abstract
Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.
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Affiliation(s)
- Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fei Zhang
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Tyson Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Xiaodong Qi
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- The Biodesign Institute and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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218
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Galeotti F, Pisco M, Cusano A. Self-assembly on optical fibers: a powerful nanofabrication tool for next generation "lab-on-fiber" optrodes. NANOSCALE 2018; 10:22673-22700. [PMID: 30500026 DOI: 10.1039/c8nr06002a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Self-assembly offers a unique resource for the preparation of discrete structures at the nano- and microscale, which are either not accessible by other fabrication techniques or require highly expensive and technologically demanding processes. The possibility of obtaining spontaneous organization of separated components, whether they are molecules, polymers, nano- or micro-objects, into a larger functional unit, enables the development of ready-to-use plug and play devices and components at lower costs. Expanding the applicability of self-assembly approaches at the nanoscale to non-conventional substrates would open up new avenues towards multifunctional platforms customized for specific applications. Recently, the combination of the amazing morphological and optical features of self-assembled patterns with the intrinsic properties of optical fibers to conduct light to a remote location has demonstrated the potentiality to open up new intriguing scenarios featuring unprecedented functionalities and performances. The integration of advanced materials and structures at the nanoscale with optical fiber substrates is the idea behind the so-called lab-on-fiber technology, which is an emerging technology at the forefront of nanophotonics and nanotechnology research. Self-assembly processes can have a key role in implementing cost-effective solutions suitable for the mass production of technologically advanced platforms based on optical fibers towards their real market exploitation. Novel lab-on-fiber optrodes would arise from the sustainable integration of functional materials at the nano- and microscale onto optical fiber substrates. Such devices are able to be easily integrated in hypodermic needles and catheters for in vivo theranostics and point-of-care diagnostics, opening up new frontiers in multidisciplinary technological development to be exploited in life science applications. This work is conceived to provide an overview of the latest strategies, based on self-assembly processes, which have been implemented for the realization of lab-on-fiber optrodes with particular emphasis on the perspectives and challenges that lie ahead. We discuss the main fabrication techniques and strategies aimed at developing new multifunctional optical fiber nanoprobes and their application in real scenarios. Finally, we highlight some of the other self-assembly processes that have not yet been applied to optical fiber sensors, but have the potentiality to be exploited in the fabrication of future lab-on-fiber devices.
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Affiliation(s)
- F Galeotti
- Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche (ISMAC-CNR), 20133 Milano, Italy.
| | - M Pisco
- Divisione di Optoelettronica, Dipartimento di Ingegneria, Università del Sannio, 82100 Benevento, Italy.
| | - A Cusano
- Divisione di Optoelettronica, Dipartimento di Ingegneria, Università del Sannio, 82100 Benevento, Italy.
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219
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Jorge AF, Eritja R. Overview of DNA Self-Assembling: Progresses in Biomedical Applications. Pharmaceutics 2018; 10:E268. [PMID: 30544945 PMCID: PMC6320858 DOI: 10.3390/pharmaceutics10040268] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/14/2022] Open
Abstract
Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.
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Affiliation(s)
- Andreia F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain.
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220
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Ge Z, Gu H, Li Q, Fan C. Concept and Development of Framework Nucleic Acids. J Am Chem Soc 2018; 140:17808-17819. [PMID: 30516961 DOI: 10.1021/jacs.8b10529] [Citation(s) in RCA: 173] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zhilei Ge
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongzhou Gu
- Center for Biotechnology and Biomedical Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- 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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221
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Krerowicz SJ, Hernandez-Ortiz JP, Schwartz DC. Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules. ACS APPLIED MATERIALS & INTERFACES 2018; 10:41215-41223. [PMID: 30403478 PMCID: PMC6453721 DOI: 10.1021/acsami.8b18157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
As the interest in DNA nanotechnology increases, so does the need for larger and more complex DNA structures. In this work, we describe two methods of using large, double-stranded (ds) DNA to self-assemble sequence-specific, nonrepetitive microscale structures. A model system restructures T7 DNA (40 kb) through sequence-specific biotinylation followed by intramolecular binding to a 40 nm diameter neutravidin bead to create T7 "rosettes". This model system informed the creation of "nodal DNA" where "nodes" with single-stranded DNA flaps are attached to a large dsDNA insert so that a complementary oligonucleotide "strap" bridges the two nodes for restructuring to form a DNA "bolo". To do this in high yield, several methodologies were developed, including a protection/deprotection scheme using RNA/RNase H and dialysis chambers, which remove excess straps while retaining large DNA molecules. To assess these restructuring processes, the DNA was adsorbed onto supported lipid bilayers, allowing for a visual assay of their structure using single-molecule fluorescence microscopy. Good agreement between the expected and observed fluorescence intensity measurements of the individual features of restructured DNA for both the DNA rosettes and bolos gives us a high degree of confidence that both processes give sequence-specific restructuring of large, dsDNA molecules to create microscale objects.
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Affiliation(s)
- Samuel J.W. Krerowicz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Juan P. Hernandez-Ortiz
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Departamento de Materiales y Nanotecnología, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Colombia/Wisconsin One-Health Consortium, Universidad Nacional de Colombia- Medellín, Medellín 050034, Colombia
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222
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Madhanagopal BR, Zhang S, Demirel E, Wady H, Chandrasekaran AR. DNA Nanocarriers: Programmed to Deliver. Trends Biochem Sci 2018; 43:997-1013. [DOI: 10.1016/j.tibs.2018.09.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/16/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022]
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223
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Sun Y, Zhang F, Jiang S, Wang Z, Ni R, Wang H, Zhou W, Li X, Stang PJ. Assembly of Metallacages into Soft Suprastructures with Dimensions of up to Micrometers and the Formation of Composite Materials. J Am Chem Soc 2018; 140:17297-17307. [PMID: 30424604 DOI: 10.1021/jacs.8b11199] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This work provides a platform for the rapid generation of superstructure assemblies with a wide range of lengths that can be used to access a variety of metal-organic complex-based soft superstructures. Metallacage-based microneedles that are nanometers in diameter and millimeters in length were generated in dichloromethane and ethyl acetate; their size could be controlled by adjusting the ratio of the two solvents. Interestingly, microflower structures could be formed by further assembly of the microneedles during solvent evaporation. Our study establishes a feasible method designed to broaden the range of suprastructures with emissions from blue and green to red through the co-assembly of lysine-modified perylene. Similar to the co-assembly of lysine-modified perylene with microflowers, chlorophyll-a and vitamin B12 were introduced into the microflowers during the assembly process, which may be exploited in studies of energy capture and nerve repair in the future.
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Affiliation(s)
- Yan Sun
- School of Chemistry and Chemical Engineering , Yangzhou University , Yangzhou , Jiangsu 225002 , P. R. China.,Department of Chemistry , University of Utah , 315 South 1400 East, Room 2020 , Salt Lake City , Utah 84112 , United States
| | - Fengmin Zhang
- Testing Center of Yangzhou University , Yangzhou , Jiangsu 225002 , P. R. China
| | - Shaowei Jiang
- School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , P. R. China
| | - Zhifeng Wang
- Testing Center of Yangzhou University , Yangzhou , Jiangsu 225002 , P. R. China
| | - Ruidong Ni
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue , Tampa , Florida 33620 , United States
| | - Heng Wang
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue , Tampa , Florida 33620 , United States
| | - Weidong Zhou
- Testing Center of Yangzhou University , Yangzhou , Jiangsu 225002 , P. R. China
| | - Xiaopeng Li
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue , Tampa , Florida 33620 , United States
| | - Peter J Stang
- Department of Chemistry , University of Utah , 315 South 1400 East, Room 2020 , Salt Lake City , Utah 84112 , United States
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224
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Bisker G, England JL. Nonequilibrium associative retrieval of multiple stored self-assembly targets. Proc Natl Acad Sci U S A 2018; 115:E10531-E10538. [PMID: 30348806 PMCID: PMC6233095 DOI: 10.1073/pnas.1805769115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many biological systems rely on the ability to self-assemble different target structures using the same set of components. Equilibrium self-assembly suffers from a limited capacity in such cases, due to an increasing number of decoy states that grows rapidly with the number of targets encoded. Moreover, improving the kinetic stability of a target at equilibrium carries the price of introducing kinetic traps, leading to slower assembly. Using a toy physical model of interacting particles, we demonstrate that local driving can improve both the assembly time and kinetic stability of multitarget self-assembly, as well as reduce fluctuations around the target configuration. We further show that the local drive can result in a steady-state probability distribution over target structures that deviates from the Boltzmann distribution in a way that depends on the types of interactions that stabilize the targets. Our results illustrate the role that nonequilibrium driving plays in overcoming tradeoffs that are inherent to equilibrium assemblies.
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Affiliation(s)
- Gili Bisker
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jeremy L England
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139;
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225
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Brady RA, Brooks NJ, Foderà V, Cicuta P, Di Michele L. Amphiphilic-DNA Platform for the Design of Crystalline Frameworks with Programmable Structure and Functionality. J Am Chem Soc 2018; 140:15384-15392. [PMID: 30351920 DOI: 10.1021/jacs.8b09143] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reliable preparation of functional, ordered, nanostructured frameworks would be a game changer for many emerging technologies, from energy storage to nanomedicine. Underpinned by the excellent molecular recognition of nucleic acids, along with their facile synthesis and breadth of available functionalizations, DNA nanotechnology is widely acknowledged as a prime route for the rational design of nanostructured materials. Yet, the preparation of crystalline DNA frameworks with programmable structure and functionality remains a challenge. Here we demonstrate the potential of simple amphiphilic DNA motifs, dubbed "C-stars", as a versatile platform for the design of programmable DNA crystals. In contrast to all-DNA materials, in which structure depends on the precise molecular details of individual building blocks, the self-assembly of C-stars is controlled uniquely by their topology and symmetry. Exploiting this robust self-assembly principle, we design a range of topologically identical, but structurally and chemically distinct C-stars that following a one-pot reaction self-assemble into highly porous, functional, crystalline frameworks. Simple design variations allow us to fine-tune the lattice parameter and thus control the partitioning of macromolecules within the frameworks, embed responsive motifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.
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Affiliation(s)
- Ryan A Brady
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Nicholas J Brooks
- Department of Chemistry , Imperial College London , London SW7 2AZ , United Kingdom
| | - Vito Foderà
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory , University of Cambridge , Cambridge CB3 0HE , United Kingdom
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226
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227
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228
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Zhou L, Marras AE, Huang CM, Castro CE, Su HJ. Paper Origami-Inspired Design and Actuation of DNA Nanomachines with Complex Motions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802580. [PMID: 30369060 DOI: 10.1002/smll.201802580] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/19/2018] [Indexed: 05/26/2023]
Abstract
Significant progress in DNA nanotechnology has accelerated the development of molecular machines with functions like macroscale machines. However, the mobility of DNA self-assembled nanorobots is still dramatically limited due to challenges with designing and controlling nanoscale systems with many degrees of freedom. Here, an origami-inspired method to design transformable DNA nanomachines is presented. This approach integrates stiff panels formed by bundles of double-stranded DNA connected with foldable creases formed by single-stranded DNA. To demonstrate the method, a DNA version of the paper origami mechanism called a waterbomb base (WBB) consisting of six panels connected by six joints is constructed. This nanoscale WBB can follow four distinct motion paths to transform between five distinct configurations including a flat square, two triangles, a rectangle, and a fully compacted trapezoidal shape. To achieve this, the sequence specificity of DNA base-pairing is leveraged for the selective actuation of joints and the ion-sensitivity of base-stacking interactions is employed for the flattening of joints. In addition, higher-order assembly of DNA WBBs into reconfigurable arrays is achieved. This work establishes a foundation for origami-inspired design for next generation synthetic molecular robots and reconfigurable nanomaterials enabling more complex and controllable motion.
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Affiliation(s)
- Lifeng Zhou
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Alexander E Marras
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Chao-Min Huang
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hai-Jun Su
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
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229
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Madge J, Bourne D, Miller MA. Controlling Fragment Competition on Pathways to Addressable Self-Assembly. J Phys Chem B 2018; 122:9815-9825. [PMID: 30256103 DOI: 10.1021/acs.jpcb.8b08096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building blocks, each of which occupies a defined location in the target. The requirement that each type of building block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap, since they cannot be combined. Here, we introduce a "completability" algorithm to quantify competition between self-assembling fragments and use it to deduce general principles for suppressing the effects of fragment incompatibility in the self-assembly of small addressable clusters. Competition originates from loops in the bonding network of the target structure, but loops may be needed to provide structural rigidity and thermodynamic stability. An optimal compromise can be achieved by careful choice of bonding networks and by promoting semihierarchical pathways that rule out competition between early fragments. These concepts are illustrated in simulations of self-assembly in two contrasting addressable targets of 20 unique components each.
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230
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Liu Y, Parks FC, Zhao W, Flood AH. Sequence-Controlled Stimuli-Responsive Single–Double Helix Conversion between 1:1 and 2:2 Chloride-Foldamer Complexes. J Am Chem Soc 2018; 140:15477-15486. [DOI: 10.1021/jacs.8b09899] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yun Liu
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Fred C. Parks
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Amar H. Flood
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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231
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Pardee K. Perspective: Solidifying the impact of cell-free synthetic biology through lyophilization. Biochem Eng J 2018; 138:91-97. [PMID: 30740032 PMCID: PMC6358126 DOI: 10.1016/j.bej.2018.07.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/20/2022]
Abstract
Cell-free synthetic biology is an exciting and new branch in the field of synthetic biology. Based on in vitro transcription and translation systems, this application-focused domain builds on decades of cell-free biochemistry and protein expression to operate synthetic gene networks outside of cellular environments. This has brought new and perhaps even unexpected advantages. Chief among these is the ability to operate genetically encoded tools in a sterile and abiotic format. Recent work has extended this advantage by freeze-drying these cell-free systems into dried pellets or embedded paper-based reactions. Taken together, these new ideas have solved the longstanding challenge of how to deploy poised synthetic gene networks in a biosafe mode outside of the laboratory. There is significant excitement in the potential of this newfound venue and the community has begun to extend proof-of-concept demonstrations in important and creative ways. Here I explore these new efforts and provide my thoughts on the challenges and opportunities ahead for freeze-dried, cell-free synthetic biology.
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232
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Kielar C, Reddavide FV, Tubbenhauer S, Cui M, Xu X, Grundmeier G, Zhang Y, Keller A. Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-Based Drug Discovery. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Francesco V. Reddavide
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
- DyNAbind GmbH; Arnoldstr. 20 01307 Dresden Germany
| | - Stefan Tubbenhauer
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Meiying Cui
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Yixin Zhang
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
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233
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Kielar C, Reddavide FV, Tubbenhauer S, Cui M, Xu X, Grundmeier G, Zhang Y, Keller A. Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-Based Drug Discovery. Angew Chem Int Ed Engl 2018; 57:14873-14877. [DOI: 10.1002/anie.201806778] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/22/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Francesco V. Reddavide
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
- DyNAbind GmbH; Arnoldstr. 20 01307 Dresden Germany
| | - Stefan Tubbenhauer
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Meiying Cui
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
| | - Xiaodan Xu
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
| | - Yixin Zhang
- B CUBE-Center for Molecular Bioengineering; Technische Universität Dresden; Arnoldstr. 18 01307 Dresden Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry; Paderborn University; Warburger Str. 100 33098 Paderborn Germany
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234
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Xu W, Yin P, Dai M. Super-resolution Geometric Barcoding for Multiplexed miRNA Profiling. Angew Chem Int Ed Engl 2018; 57:14075-14079. [PMID: 30182521 DOI: 10.1002/anie.201807956] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/21/2018] [Indexed: 01/07/2023]
Abstract
MicroRNA (miRNA) expression profiles hold promise as biomarkers for diagnostics and prognosis of complex diseases. Herein, we report a super-resolution fluorescence imaging-based digital profiling method for specific, sensitive, and multiplexed detection of miRNAs. In particular, we applied the DNA-PAINT (point accumulation for imaging in nanoscale topography) method to implement a super-resolution geometric barcoding scheme for multiplexed single-molecule miRNA capture and digital counting. Using synthetic DNA nanostructures as a programmable miRNA capture nano-array, we demonstrated high-specificity (single nucleotide mismatch discrimination), multiplexed (8-plex, 2 panels), and sensitive measurements on synthetic miRNA samples, as well as applied one 8-plex panel to measure endogenous miRNAs levels in total RNA extract from HeLa cells.
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Affiliation(s)
- Weidong Xu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
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235
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Xu W, Yin P, Dai M. Super‐resolution Geometric Barcoding for Multiplexed miRNA Profiling. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Weidong Xu
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
| | - Mingjie Dai
- Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA 02115 USA
- Department of Systems Biology Harvard Medical School Boston MA 02115 USA
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236
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Chen PZ, Pollit L, Jones L, Gu FX. Functional Two- and Three-Dimensional Architectures of Immobilized Metal Nanoparticles. Chem 2018. [DOI: 10.1016/j.chempr.2018.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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237
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Abstract
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic paradigms of DNA nanotechnology, we present a rationally designed synthetic platform that functions in an analogous manner to create complex DNA nanostructures. Starting from one type of DNA nanostructure, DNA strand displacement circuits were designed to interact and pass along the information encoded in the initial structure to mediate the self-assembly of a different type of structure, the final output structure depending on the type of circuit triggered. Using this concept of a DNA structure "trans-assembling" a different DNA structure through nonlocal strand displacement circuitry, four different schemes were implemented. Specifically, 1D ladder and 2D double-crossover (DX) lattices were designed to kinetically trigger DNA circuits to activate polymerization of either ring structures or another type of DX lattice under enzyme-free, isothermal conditions. In each scheme, the desired multilayer reaction pathway was activated, among multiple possible pathways, ultimately leading to the downstream self-assembly of the correct output structure.
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Affiliation(s)
- Jihoon Shin
- Hazards Monitoring Bionano Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon 34141 , Korea
| | - Junghoon Kim
- Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
| | - Sung Ha Park
- Department of Physics , Sungkyunkwan University , Suwon 16419 , Korea
- Sungkyunkwan Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Tai Hwan Ha
- Hazards Monitoring Bionano Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Daejeon 34141 , Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology , Korea University of Science and Technology (UST) , Daejeon 34113 , Korea
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238
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Whitelam S. Strong bonds and far-from-equilibrium conditions minimize errors in lattice-gas growth. J Chem Phys 2018; 149:104902. [DOI: 10.1063/1.5034789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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239
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Atsumi H, Belcher AM. DNA Origami and G-Quadruplex Hybrid Complexes Induce Size Control of Single-Walled Carbon Nanotubes via Biological Activation. ACS NANO 2018; 12:7986-7995. [PMID: 30011182 DOI: 10.1021/acsnano.8b02720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA self-assembly has enabled the programmable fabrication of nanoarchitectures, and these nanoarchitectures combined with nanomaterials have provided several applications. Here, we develop an approach for cutting single-walled carbon nanotubes (SWNTs) of predetermined lengths, using DNA origami and G-quadruplex hybrid complexes. This approach is based on features of DNA: (1) wrapping SWNTs with DNA to improve the dispersibility of SWNTs in water; (2) using G-quadruplex DNA to confine hemin in close proximity to SWNTs and enhance the biological activation of hydrogen peroxide by hemin; and (3) forming DNA origami platforms to allow for the precise placement of G-quadruplexes, enabling size control. These integrated features of DNA allow for temporally efficient cutting of SWNTs into desired lengths, thus expanding the availability of SWNTs for applications in the fields of nanoelectronics, nanomedicine, nanomaterials, and quantum physics, as well as in fundamental studies.
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Affiliation(s)
- Hiroshi Atsumi
- The David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Angela M Belcher
- The David H. Koch Institute for Integrative Cancer Research , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
- Department of Materials Science and Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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240
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Lin T, Yan J, Ong LL, Robaszewski J, Lu HD, Mi Y, Yin P, Wei B. Hierarchical Assembly of DNA Nanostructures Based on Four-Way Toehold-Mediated Strand Displacement. NANO LETTERS 2018; 18:4791-4795. [PMID: 29989824 DOI: 10.1021/acs.nanolett.8b01355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Because of its attractive cost and yield, hierarchical assembly, in which constituent structures of lower hierarchy share a majority of components, is an appealing approach to scale up DNA self-assembly. A few strategies have already been investigated to combine preformed DNA nanostructures. In this study, we present a new hierarchical assembly method based on four-way toehold-mediated strand displacement to facilitate the combination of preformed DNA structural units. Employing such a method, we have constructed a series of higher-order structures composed of 5, 7, 9, 11, 13, and 15 preformed units respectively.
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Affiliation(s)
- Tong Lin
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Kowloon , Hong Kong SAR
| | - Jun Yan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
| | - Luvena L Ong
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology , MIT , Cambridge , Massachusetts 02139 , United States
| | - Joanna Robaszewski
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Hoang D Lu
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Yongli Mi
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Kowloon , Hong Kong SAR
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
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241
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Gerling T, Kube M, Kick B, Dietz H. Sequence-programmable covalent bonding of designed DNA assemblies. SCIENCE ADVANCES 2018; 4:eaau1157. [PMID: 30128357 PMCID: PMC6097813 DOI: 10.1126/sciadv.aau1157] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 05/17/2023]
Abstract
Bottom-up fabrication of custom nanostructures using the methods of DNA nanotechnology has great potential for applications in many areas of science and technology. One obstacle to applications concerns the constrained environmental conditions at which DNA objects retain their structure. We present a general, site-selective, and scalable method for creating additional covalent bonds that increase the structural stability of DNA nanostructures. Placement of thymidines in close proximity within DNA nanostructures allows the rational creation of sites for covalent cyclobutane pyrimidine dimer (CPD) bonds induced via ultraviolet irradiation. The additional covalent bonds may be used in a sequence-programmable fashion to link free strand termini, to bridge strand breaks at crossover sites, and to create additional interhelical connections. Thus designed multilayer DNA origami objects can remain stable at temperatures up to 90°C and in pure double-distilled water with no additional cations present. In addition, these objects show enhanced resistance against nuclease activity. Cryo-electron microscopy (cryo-EM) structural analysis of non-cross-linked and cross-linked objects indicated that the global shape and the internal network of crossovers are preserved after irradiation. A cryo-EM map of a CPD-stabilized multilayer DNA origami object determined at physiological ionic strength reveals a substantial swelling behavior, presumably caused by repulsive electrostatic forces that, without covalent stabilization, would cause disassembly at low ionic strength. Our method opens new avenues for applications of DNA nanostructures in a wider range of conditions.
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242
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Merindol R, Loescher S, Samanta A, Walther A. Pathway-controlled formation of mesostructured all-DNA colloids and superstructures. NATURE NANOTECHNOLOGY 2018; 13:730-738. [PMID: 29941888 PMCID: PMC6082344 DOI: 10.1038/s41565-018-0168-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 05/21/2023]
Abstract
DNA has traditionally been used for the programmable design of nanostructures by exploiting its sequence-defined supramolecular recognition. However, control on larger length scales or even hierarchical materials that translate to the macroscale remain difficult to construct. Here, we show that the polymer character of single-stranded DNA (ssDNA) can be activated via a nucleobase-specific lower critical solution temperature, which provides a unique access to mesoscale structuring mechanisms on larger length scales. We integrate both effects into ssDNA multiblock copolymers that code sequences for phase separation, hybridization and functionalization. Kinetic pathway guidance using temperature ramps balances the counteracting mesoscale phase separation during heating with nanoscale duplex recognition during cooling to yield a diversity of complex all-DNA colloids with control over the internal dynamics and of their superstructures. Our approach provides a facile and versatile platform to add mesostructural layers into hierarchical all-DNA materials. The high density of addressable ssDNA blocks opens routes for applications such as gene delivery, artificial evolution or spatially encoded (bio)materials.
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Affiliation(s)
- Rémi Merindol
- Institute for Macromolecular Chemistry, University of Freiburg, Freiburg, Germany
| | - Sebastian Loescher
- Freiburg Materials Research Center, University of Freiburg, Freiburg, Germany
| | - Avik Samanta
- Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Freiburg, Germany
| | - Andreas Walther
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.
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243
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Fonseca P, Romano F, Schreck JS, Ouldridge TE, Doye JPK, Louis AA. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J Chem Phys 2018; 148:134910. [PMID: 29626893 DOI: 10.1063/1.5019344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
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Affiliation(s)
- Pedro Fonseca
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, USA
| | - Thomas E Ouldridge
- Department of Bioengineering, Imperial College London, London SW7 2AZ, 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
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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244
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Ijäs H, Nummelin S, Shen B, Kostiainen MA, Linko V. Dynamic DNA Origami Devices: from Strand-Displacement Reactions to External-Stimuli Responsive Systems. Int J Mol Sci 2018; 19:E2114. [PMID: 30037005 PMCID: PMC6073283 DOI: 10.3390/ijms19072114] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 12/31/2022] Open
Abstract
DNA nanotechnology provides an excellent foundation for diverse nanoscale structures that can be used in various bioapplications and materials research. Among all existing DNA assembly techniques, DNA origami proves to be the most robust one for creating custom nanoshapes. Since its invention in 2006, building from the bottom up using DNA advanced drastically, and therefore, more and more complex DNA-based systems became accessible. So far, the vast majority of the demonstrated DNA origami frameworks are static by nature; however, there also exist dynamic DNA origami devices that are increasingly coming into view. In this review, we discuss DNA origami nanostructures that exhibit controlled translational or rotational movement when triggered by predefined DNA sequences, various molecular interactions, and/or external stimuli such as light, pH, temperature, and electromagnetic fields. The rapid evolution of such dynamic DNA origami tools will undoubtedly have a significant impact on molecular-scale precision measurements, targeted drug delivery and diagnostics; however, they can also play a role in the development of optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
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Affiliation(s)
- Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland.
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
- HYBER Center of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland.
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245
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Zhang T, Hartl C, Frank K, Heuer-Jungemann A, Fischer S, Nickels PC, Nickel B, Liedl T. 3D DNA Origami Crystals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1800273. [PMID: 29774971 DOI: 10.1002/adma.201800273] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/22/2018] [Indexed: 05/17/2023]
Abstract
3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 105 nm3 , which would also suffice to accommodate ribosome-sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small-angle X-ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site-specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications.
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Affiliation(s)
- Tao Zhang
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Caroline Hartl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Kilian Frank
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Amelie Heuer-Jungemann
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Stefan Fischer
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Philipp C Nickels
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Bert Nickel
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität, Geschwister-Scholl-Platz 1, 80539, München, Germany
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246
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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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247
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Ye K, Kaplan DL, Bao G, Bettinger C, Forgacs G, Dong C, Khademhosseini A, Ke Y, Leong K, Sambanis A, Sun W, Yin P. Advanced Cell and Tissue Biomanufacturing. ACS Biomater Sci Eng 2018; 4:2292-2307. [PMID: 33435095 DOI: 10.1021/acsbiomaterials.8b00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This position paper assesses state-of-the-art advanced biomanufacturing and identifies paths forward to advance this emerging field in biotechnology and biomedical engineering, including new research opportunities and translational and corporate activities. The vision for the field is to see advanced biomanufacturing emerge as a discipline in academic and industrial communities as well as a technological opportunity to spur research and industry growth. To navigate this vision, the paths to move forward and to identify major barriers were a focal point of discussions at a National Science Foundation-sponsored workshop focused on the topic. Some of the major needs include but are not limited to the integration of specific scientific and engineering disciplines and guidance from regulatory agencies, infrastructure requirements, and strategies for reliable systems integration. Some of the recommendations, major targets, and opportunities were also outlined, including some "grand challenges" to spur interest and progress in the field based on the participants at the workshop. Many of these recommendations have been expanded, materialized, and adopted by the field. For instance, the formation of an initial collaboration network in the community was established. This report provides suggestions for the opportunities and challenges to help move the field of advanced biomanufacturing forward. The field is in the early stages of effecting science and technology in biomanufacturing with a bright and important future impact evident based on the rapid scientific advances in recent years and industry progress.
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Affiliation(s)
- Kaiming Ye
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Watson School of Engineering and Applied Science, Binghamton University, State University of New York (SUNY), Binghamton, New York 13902, United States
| | - David L Kaplan
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Gang Bao
- Department of Bioengineering, School of Engineering, Rice University, Houston, Texas 77005, United States
| | - Christopher Bettinger
- Department of Materials Science and Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gabor Forgacs
- Department of Bioengineering, College of Engineering, University of Missouri, Columbia, Missouri 65211, United States.,Modern Meadow, Inc., 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Cheng Dong
- Department of Biomedical Engineering, College of Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Ali Khademhosseini
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Yonggang Ke
- Department of Biomedical Engineering, College of Engineering, Georgia Tech, Atlanta, Georgia 30332, United States
| | - Kam Leong
- Department of Biomedical Engineering, School of Engineering and Applied Science, Columbia University, New York City, New York 10027, United States
| | | | - Wei Sun
- Department of Mechanical Engineering and Mechanics, College of Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.,Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Cambridge, Massachusetts 02138, United States
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248
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Coursault D, Sule N, Parker J, Bao Y, Scherer NF. Dynamics of the Optically Directed Assembly and Disassembly of Gold Nanoplatelet Arrays. NANO LETTERS 2018; 18:3391-3399. [PMID: 29717877 DOI: 10.1021/acs.nanolett.8b00199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The tremendous progress in nanoscience now allows the creation of static nanostructured materials for a broad range of applications. A further goal is to achieve dynamic and reconfigurable nanostructures. One approach involves nanoparticle-based optical matter, but so far, studies have only considered spherical constituents. A nontrivial issue is that nanoparticles with other shapes are expected to have different local electromagnetic field distributions and interactions with neighbors in optical-matter arrays. Therefore, one would expect their dynamics to be different as well. This paper reports the directed assembly of ordered arrays of gold nanoplatelets in optical line traps, demonstrating the reconfigurability of the array by altering the phase gradient via holographic-beam shaping. The weaker gradient forces and resultant slower motion of the nanoplatelets, as compared with plasmonic (Ag and Au) nanospheres, allow the precise study of their assembly and disassembly dynamics. Both temporal and spatial correlations are detected between particles separated by distances of hundreds of nanometers to several microns. Electrodynamics simulations reveal the presence of multipolar plasmon modes that induce short-range (near-field) and longer-range electrodynamic (e.g., optical binding) interactions. These interactions and the interferences between mutipolar plamon modes cause both the strong correlations and the nonuniform dynamics observed. Our study demonstrates new opportunities for the generation of complex addressable optical matter and the creation of novel active optical technology.
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Affiliation(s)
- Delphine Coursault
- James Franck Institute, University of Chicago , Chicago , Illinois 60637 , United States
| | - Nishant Sule
- James Franck Institute, University of Chicago , Chicago , Illinois 60637 , United States
| | - John Parker
- James Franck Institute, University of Chicago , Chicago , Illinois 60637 , United States
| | - Ying Bao
- James Franck Institute, University of Chicago , Chicago , Illinois 60637 , United States
- Department of Chemistry , Western Washington University , Bellingham , Washington 98225 , United States
| | - Norbert F Scherer
- James Franck Institute, University of Chicago , Chicago , Illinois 60637 , United States
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249
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Direct observation and rational design of nucleation behavior in addressable self-assembly. Proc Natl Acad Sci U S A 2018; 115:E5877-E5886. [PMID: 29891671 PMCID: PMC6042111 DOI: 10.1073/pnas.1806010115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems. To optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on a prototypical “DNA-brick” structure. By combining temperature-dependent dynamic light scattering and atomic force microscopy with coarse-grained simulations, we show how subtle changes in the nucleation pathway profoundly affect the yield of the correctly formed structures. In particular, we can increase the range of conditions over which self-assembly occurs by using stable multisubunit clusters that lower the nucleation barrier for assembling subunits in the interior of the structure. Consequently, modifying only a small portion of a structure is sufficient to optimize its assembly. Due to the generality of our coarse-grained model and the excellent agreement that we find with our experimental results, the design principles reported here are likely to apply generically to addressable, multicomponent self-assembly.
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250
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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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