1
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Qin Y, Chen X, Willner I. Nucleic Acid-Modified Nanoparticles for Cancer Therapeutic Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025:e2500843. [PMID: 40420627 DOI: 10.1002/smll.202500843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 04/20/2025] [Indexed: 05/28/2025]
Abstract
Nanomaterials including metal or metal oxide nanoparticles, carbonous nanomaterial (e.g., carbon dots) or metal-organic framework nanoparticles provide porous, catalytically active surfaces and functional interfaces for binding of ions or molecular agents. By the conjugation of nucleic acids to the nanoparticles, hybrid nanostructures revealing emerging multimodal catalytic/photocatalytic activities, high loading capacities, and effective targeted cell permeation efficacies are formed. The review article exemplifies the application of nucleic acid-modified nanoparticles conjugates for therapeutic treatment of cancer cells. Stimuli-responsive reconfiguration of nucleic acid strands and the specific recognition and catalytic function of oligonucleotides associated with porous, catalytic, and photocatalytic nanoparticles yield hybrid composites demonstrating cooperative synergistic properties for medical applications. The targeted chemodynamic, photodynamic, photothermal and chemotherapeutic treatment of cancer cells by the oligonucleotide/nanoparticle conjugates is addressed. In addition, the application of oligonucleotide/nanoparticle conjugates for gene therapy treatment of cancer cells is discussed.
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Affiliation(s)
- Yunlong Qin
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Xinghua Chen
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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2
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Kwon H, Shin J, Sun S, Zhu R, Stainer S, Hinterdorfer P, Cho SJ, Kim DH, Oh YJ. Vertical DNA Nanostructure Arrays: Facilitating Functionalization on Macro-Scale Surfaces. ACS NANO 2025; 19:19353-19363. [PMID: 40200829 PMCID: PMC12120987 DOI: 10.1021/acsnano.5c03100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 04/04/2025] [Accepted: 04/04/2025] [Indexed: 04/10/2025]
Abstract
The capability for varied functionalization and precise control at the nanoscale are significant advantages of DNA nanostructures. In the assembly of DNA nanostructure, the surface-assisted growth method utilizing double-crossover (DX) tile structures facilitates nucleation at relatively low concentrations on the surface based on electrostatic interactions, thereby enabling crystal growth over large areas. However, in surface-assisted growth, the geometrical hindrance of vertical structures on the DX tile structure surface makes it challenging to conjugate DNA nanostructures into fabricated surfaces. Here, the surface-assisted growth method was employed to extend the DX tile growth for forming vertical structure arrays on the substrate, providing attachment sites for functionalization on uniformly covered substrates at the macroscopic scale. Additionally, the spacing of the vertical structure arrays was demonstrated to be controllable through the strategic design of the repeating unit tiles that construct the DX crystals.
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Affiliation(s)
- Hyeonjun Kwon
- School
of Chemical Engineering, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Jihoon Shin
- School
of Chemical Engineering, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Siqi Sun
- School
of Chemical Engineering, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020Linz, Austria
| | - Sarah Stainer
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020Linz, Austria
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020Linz, Austria
| | - Sang-Joon Cho
- Park
Systems, Corp., KANC 15F, Gwanggyo-ro 109, Suwon16229, Republic of Korea
| | - Dong-Hwan Kim
- School
of Chemical Engineering, Sungkyunkwan University, Suwon16419, Republic of Korea
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020Linz, Austria
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3
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Wang R, Wang Y, Lu B, Zhang W, Xia B, Xiao SJ. Construction of Double-layered DNA Tiles and Arrays from Double Crossover Motifs. Chembiochem 2025; 26:e202400898. [PMID: 39777971 DOI: 10.1002/cbic.202400898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 01/02/2025] [Accepted: 01/06/2025] [Indexed: 01/11/2025]
Abstract
DNA double crossover (DX) motifs including DAE (double crossover, antiparallel, even spacing) and DAO (double crossover, antiparallel, odd spacing) are well-known monolayered DNA building blocks for construction of 2D DNA arrays and tubes in nanoscale and microscale. Compared to the 3D architectures of DNA origami and single-stranded DNA bricks to build nanoscale 3D bundles, tessellations, gears, castles, etc., designs of double- and multi-layers of DX motifs for 3D architectures are still limited. Herein, we report two types of double-layered tiles derived from DAE motifs with single-stranded circular 42- and 64-nt oligonucleotides as scaffold strands. Further tiling of the tiles generated planar 3D crystalline domains and curved tubes, correspondingly. Finally, we applied the chiral index theory to derive the unit tube parameters of six E-tiling (inter-tile distance of even spacing) tubes and analyzed the causation of difference between these tubes.
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Affiliation(s)
- Ruoran Wang
- College of Science, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, P. R. China
| | - Yu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P. R. China E-amil
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P. R. China E-amil
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P. R. China E-amil
| | - Bing Xia
- College of Science, State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, 210037, P. R. China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P. R. China E-amil
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4
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Li X, Wang J, Baptist A, Wu W, Heuer‐Jungemann A, Zhang T. Crystalline Assemblies of DNA Nanostructures and Their Functional Properties. Angew Chem Int Ed Engl 2025; 64:e202416948. [PMID: 39576670 PMCID: PMC11735872 DOI: 10.1002/anie.202416948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Indexed: 01/18/2025]
Abstract
Self-assembly presents a remarkable approach for creating intricate structures by positioning nanomaterials in precise locations, with control over molecular interactions. For example, material arrays with interplanar distances similar to the wavelength of light can generate structural color through complex interactions like scattering, diffraction, and interference. Moreover, enzymes, plasmonic nanoparticles, and luminescent materials organized in periodic lattices are envisioned to create functional materials with various applications. Focusing on structural DNA nanotechnology, here, we summarized the recent developments of two- and three-dimensional lattices made purely from DNA nanostructures. We review DNA-based monomer design for different lattices, guest molecule assembly, and inorganic material coating techniques and discuss their functional properties and potential applications in photonic crystals, nanoelectronics, and bioengineering as well as future challenges and perspectives.
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Affiliation(s)
- Xueqiao Li
- Department of Applied Chemistry, School of Chemistry and Chemical EngineeringYantai UniversityYantai264005China
| | - Jiaoyang Wang
- Department of Applied Chemistry, School of Chemistry and Chemical EngineeringYantai UniversityYantai264005China
| | - Anna Baptist
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Center for NanoScience (CeNS)Ludwig-Maximilians-University81377MunichGermany
| | - Wenna Wu
- Department of Applied Chemistry, School of Chemistry and Chemical EngineeringYantai UniversityYantai264005China
| | - Amelie Heuer‐Jungemann
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Center for NanoScience (CeNS)Ludwig-Maximilians-University81377MunichGermany
| | - Tao Zhang
- Department of Applied Chemistry, School of Chemistry and Chemical EngineeringYantai UniversityYantai264005China
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5
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Cai B, Rong X, Sun Y, Liu L, Li Z. Engineered 3D DNA Crystals: A Molecular Design Perspective. SMALL METHODS 2025:e2401455. [PMID: 39777863 DOI: 10.1002/smtd.202401455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/24/2024] [Indexed: 01/11/2025]
Abstract
Recent advances in biomolecular self-assembly have transformed material science, enabling the creation of novel materials with unparalleled precision and functionality. Among these innovations, 3D DNA crystals have emerged as a distinctive class of macroscopic materials, engineered through the bottom-up approach by DNA self-assembly. These structures uniquely combine precise molecular ordering with high programmability, establishing their importance in advanced material design. This review delves into the molecular design of engineered 3D DNA crystals, classifying current crystal structures based on "crystal bond orientations" and examining key aspects of in-silico molecular design, self-assembly, and crystal modifications. The functionalization of 3D DNA crystals for applications in crystallization scaffolding, biocatalysis, biosensing, electrical and optical devices, as well as in the emerging fields of DNA computing and data storage are explored. Finally, the ongoing challenges are addressed and future directions to advance the field of engineered 3D DNA crystals are proposed.
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Affiliation(s)
- Baoshuo Cai
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiao Rong
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yifan Sun
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06484, USA
- Nanobiology Institute, Yale University, West Haven, CT, 06484, USA
| | - Zhe Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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6
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Zhao ZH, Han BL, Su HF, Guo QL, Wang WX, Zhuo JQ, Guo YN, Liu JL, Luo GG, Cui P, Sun D. Buckling cluster-based H-bonded icosahedral capsules and their propagation to a robust zeolite-like supramolecular framework. Nat Commun 2024; 15:9401. [PMID: 39477935 PMCID: PMC11525653 DOI: 10.1038/s41467-024-53640-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 10/16/2024] [Indexed: 11/02/2024] Open
Abstract
Hydrogen-bonded assembly of multiple components into well-defined icosahedral capsules akin to virus capsids has been elusive. In parallel, constructing robust zeolitic-like cluster-based supramolecular frameworks (CSFs) without any coordination covalent bonding linkages remains challenging. Herein, we report a cluster-based pseudoicosahedral H-bonded capsule Cu60, which is buckled by the self-organization of judiciously designed constituent copper clusters and anions. The spontaneous formation of the icosahedron in the solid state takes advantage of 48 charge-assisted CH···F hydrogen bonds between cationic clusters and anions (PF6-), and is highly sensitive to the surface protective ligands on the clusters with minor structural modification inhibiting its formation. Most excitingly, an extended three-periodic robust zeolitic-like CSF, is constructed by edge-sharing the resultant icosahedrons. The perpendicular channels of the CSF feature unusual 3D orthogonal double-helical patterns. The CSF material not only keeps its single-crystal character in the desolvated phase, but also exhibits excellent chemical and thermal stabilities as well as long-lived phosphorescence emission.
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Affiliation(s)
- Zhan-Hua Zhao
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China
| | - Bao-Liang Han
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan, PR China
| | - Hai-Feng Su
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, PR China
| | - Qi-Lin Guo
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China
| | - Wen-Xin Wang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan, PR China
| | - Jing-Qiu Zhuo
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China
| | - Yong-Nan Guo
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China
| | - Jia-Long Liu
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China
| | - Geng-Geng Luo
- College of Materials Science and Engineering, Huaqiao University, Xiamen, PR China.
| | - Ping Cui
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan, PR China
| | - Di Sun
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, State Key Laboratory of Crystal Materials, Shandong University, Jinan, PR China.
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7
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Ouyang Y, Zhang P, Willner I. DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications. Angew Chem Int Ed Engl 2024; 63:e202411118. [PMID: 39037936 DOI: 10.1002/anie.202411118] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 07/24/2024]
Abstract
Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.
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Affiliation(s)
- Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Pu Zhang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Current address: Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P.R. China
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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8
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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. Nat Commun 2024; 15:6636. [PMID: 39107287 PMCID: PMC11303717 DOI: 10.1038/s41467-024-50348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/09/2024] [Indexed: 08/10/2024] Open
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology. The biochemical and biophysical properties of these motifs determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
- Department of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA.
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9
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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.563609. [PMID: 38014227 PMCID: PMC10680705 DOI: 10.1101/2023.11.15.563609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
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10
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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11
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Sun Z, Ren Y, Zhu W, Xiao Y, Wu H. DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment. Analyst 2024; 149:599-613. [PMID: 38221846 DOI: 10.1039/d3an01871g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.
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Affiliation(s)
- Zhaorong Sun
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Yingjie Ren
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Wenjun Zhu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Yuliang Xiao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Han Wu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- Institute of Brain Science and Brain-inspired Research, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
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12
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Feng F, Zhang L, Zheng P, Xiao SJ. Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds. Chembiochem 2023; 24:e202300420. [PMID: 37464981 DOI: 10.1002/cbic.202300420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.
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Affiliation(s)
- Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
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13
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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14
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Baig MMFA, Ma J, Gao X, Khan MA, Ali A, Farid A, Zia AW, Noreen S, Wu H. Exploring the robustness of DNA nanotubes framework for anticancer theranostics toward the 2D/3D clusters of hypopharyngeal respiratory tumor cells. Int J Biol Macromol 2023; 236:123988. [PMID: 36907299 DOI: 10.1016/j.ijbiomac.2023.123988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/13/2023] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
This study aimed to develop a robust approach for the early diagnosis and treatment of tumors. Short circular DNA nanotechnology synthesized a stiff and compact DNA nanotubes (DNA-NTs) framework. TW-37, a small molecular drug, was loaded into DNA-NTs for BH3-mimetic therapy to elevate the intracellular cytochrome-c levels in 2D/3D hypopharyngeal tumor (FaDu) cell clusters. After anti-EGFR functionalization, the DNA-NTs were tethered with a cytochrome-c binding aptamer, which can be applied to evaluate the elevated intracellular cytochrome-c levels via in situ hybridization (FISH) analysis and fluorescence resonance energy transfer (FRET). The results showed that DNA-NTs were enriched within the tumor cells via anti-EGFR targeting with a pH-responsive controlled release of TW-37. In this way, it initiated the triple inhibition of "BH3, Bcl-2, Bcl-xL, and Mcl-1". The triple inhibition of these proteins caused Bax/Bak oligomerization, leading to the perforation of the mitochondrial membrane. This led to the elevation of intracellular cytochrome-c levels, which reacted with the cytochrome-c binding aptamer to produce FRET signals. In this way, we successfully targeted 2D/3D clusters of FaDu tumor cells and achieved the tumor-specific and pH-triggered release of TW-37, causing tumor cell apoptosis. This pilot study suggests that anti-EGFR functionalized, TW-37 loaded, and cytochrome-c binding aptamer tethered DNA-NTs might be the hallmark for early tumor diagnosis and therapy.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Jinwei Ma
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiuli Gao
- Microbiological and Biochemical Pharmaceutical Engineering Research Center of Guizhou Province, State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Atif Ali
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Abdul Wasy Zia
- Institute of Mechanical, Process, and Energy Engineering, School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, United Kingdom
| | - Sobia Noreen
- Department of Pharmaceutical Technology, Institute of Pharmacy, University of Innsbruck, Innsbruck 6020, Austria
| | - Hongkai Wu
- Department of Chemistry and the Hong Kong Branch of Chinese National Engineering Research Centre for Tissue Restoration, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Department of Chemical and Biological Engineering, Division of Biomedical Engineering, School of Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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15
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Walczak M, Brady RA, Leathers A, Kotar J, Di Michele L. Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures. J Chem Phys 2023; 158:084501. [PMID: 36859089 DOI: 10.1063/5.0132484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.
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Affiliation(s)
- Michal Walczak
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ryan A Brady
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Adrian Leathers
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Jurij Kotar
- Department of Physics-Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
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16
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Li S, Wang Y, Ge W, Zhang W, Lu B, Feng F, Ni C, Xiao SJ. Tuning the Roundabout of Four-Point-Star Tiles with the Core Arm Length of Three Half-Turns for 2D DNA Arrays. Chemistry 2023; 29:e202202863. [PMID: 36251733 DOI: 10.1002/chem.202202863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 11/05/2022]
Abstract
By rationally adjusting the weaving modes of point-star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point-star tiles with the core arm length at two DNA half-turns, we improved the weaving modes of our newly reported four-point-star tiles with the core arm length at three half-turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E-tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one-locus and/or dual-locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio-chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.
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Affiliation(s)
- Shijie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Yantong Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Ge
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Caihong Ni
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Ave., Nanjing, Jiangsu, 210023, P.R. China
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17
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Baig MMFA, Gao X, Farid A, Zia AW, Abbas M, Wu H. Synthesis of stable 2D micro-assemblies of DNA tiles achieved via intrinsic curvatures in the skeleton of DNA duplexes coupled with the flexible support of the twisted side-arms. APPLIED NANOSCIENCE 2022. [DOI: 10.1007/s13204-022-02616-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Zhang T, Wei B. Design of Orthogonal DNA Sticky-End Cohesion Based on Configuration-Specific Molecular Recognition. J Am Chem Soc 2022; 144:18479-18484. [PMID: 36173287 DOI: 10.1021/jacs.2c07181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In sticky-end cohesion, sequence complementarity is the key to design specific recognition among many DNA nanostructure units. The binding orthogonality usually arises from sticky-end pairs of different sequences. Instead of creating orthogonal species of sticky-end bonds based on sequence complementarity, we restricted the sticky-end sequence diversity down to the fixed C-G pair and explored orthogonal recognition of the synthetic DNA constructs based solely on the configurational match. From our comprehensive investigations of 2D tessellation and 3D crystallization, we demonstrated the new configuration-specific sticky-end cohesion to program specific and precise molecular recognition of synthetic structural units for high-order DNA self-assembly.
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Affiliation(s)
- Tianqing Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Bryan Wei
- School of Life Sciences, Tsinghua University, Beijing 100084, China.,Tsinghua University-Peking University Center for Life Sciences, Tsinghua University, Beijing 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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19
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Baig MMFA, Gao X, Khan MA, Farid A, Zia AW, Wu H. Nanoscale packing of DNA tiles into DNA macromolecular lattices. Int J Biol Macromol 2022; 220:520-527. [PMID: 35988727 DOI: 10.1016/j.ijbiomac.2022.08.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/05/2022]
Abstract
Nanoscale double-crossovers (DX), antiparallel (A), and even half-turns-perimeter (E) DNA tiles (DAE-tiles) with rectangular shapes can be packed into large arrays of micrometer-scale lattices. But the features and mechanical strength of DNA assembly made from differently shaped large-sized DAE DNA tiles and the effects of various geometries on the final DNA assembly are yet to be explored. Herein, we focused on examining DNA lattices synthesized from DX bi-triangular, DNA tiles (T) with concave and convex regions along the perimeter of the tiles. The bi-triangular DNA tiles "T(A) and T(B)" were synthesized by self-assembling the freshly prepared short circular scaffold (S) strands "S(A) and S(B)", each of 106 nucleotides (NT) lengths. The tiles "T(A) and T(B)" were then coupled together to get assembled via sticky ends. It resulted in the polymerization of DNA tiles into large-sized DNA lattices with giant micrometer-scale dimensions to form the "T(A) + T(B)" assembly. These DNA macro-frameworks were visualized "in the air" under atomic force microscopy (AFM) employing tapping mode. We have characterized how curvature in DNA tiles may undergo transitions and transformations to adjust the overall torque, strain, twists, and the topology of the final self-assembly array of DNA tiles. According to our results, our large-span DX tiles assembly "T(A) + T(B)" despite the complicated curvatures and mechanics, was successfully packed into giant DNA lattices of the width of 30-500 nm and lengths of 500 nm to over 10 μm. Conclusively, the micrometer-scale "T(A) + T(B)" framework assembly was rigid, stable, stiff, and exhibited enough tensile strength to form monocrystalline lattices.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Chemistry, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| | - Xiuli Gao
- Microbiological and Biochemical Pharmaceutical Engineering Research Center of Guizhou Province, State Key Laboratory of Functions and Applications of Medicinal Plants, School of Pharmacy, Guizhou Medical University, Guiyang 550025, China.
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Abdul Wasy Zia
- Department of Mechanical and Construction Engineering, Marie Curie Research Unit, Northumbria University, Newcastle, United Kingdom
| | - Hongkai Wu
- Department of Chemistry, School of Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Department of Chemical and Biological Engineering, Division of Biomedical Engineering, School of Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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20
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The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. Nat Commun 2022; 13:3112. [PMID: 35662248 PMCID: PMC9166708 DOI: 10.1038/s41467-022-30779-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/04/2022] [Indexed: 12/31/2022] Open
Abstract
The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context. Engineered crystal architectures from DNA have become a foundational goal for nanotechnological precise arrangement. Here, the authors systematically investigate the structures of 36 immobile Holliday junction sequences and identify the features allowing the crystallisation of most of them, while 6 are considered fatal.
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21
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Zhou X, Lin S, Yan H. Interfacing DNA nanotechnology and biomimetic photonic complexes: advances and prospects in energy and biomedicine. J Nanobiotechnology 2022; 20:257. [PMID: 35658974 PMCID: PMC9164479 DOI: 10.1186/s12951-022-01449-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
Self-assembled photonic systems with well-organized spatial arrangement and engineered optical properties can be used as efficient energy materials and as effective biomedical agents. The lessons learned from natural light-harvesting antennas have inspired the design and synthesis of a series of biomimetic photonic complexes, including those containing strongly coupled dye aggregates with dense molecular packing and unique spectroscopic features. These photoactive components provide excellent features that could be coupled to multiple applications including light-harvesting, energy transfer, biosensing, bioimaging, and cancer therapy. Meanwhile, nanoscale DNA assemblies have been employed as programmable and addressable templates to guide the formation of DNA-directed multi-pigment complexes, which can be used to enhance the complexity and precision of artificial photonic systems and show the potential for energy and biomedical applications. This review focuses on the interface of DNA nanotechnology and biomimetic photonic systems. We summarized the recent progress in the design, synthesis, and applications of bioinspired photonic systems, highlighted the advantages of the utilization of DNA nanostructures, and discussed the challenges and opportunities they provide.
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Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Su Lin
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA. .,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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22
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Jiang C, Lu B, Zhang W, Ohayon YP, Feng F, Li S, Seeman NC, Xiao SJ. Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist. J Am Chem Soc 2022; 144:6759-6769. [PMID: 35385657 DOI: 10.1021/jacs.1c13601] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The overwinding and underwinding of DNA duplexes between junctions have been used in designing left- and right-handed DNA origami nanostructures, respectively. For DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the tiles has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile's intrinsic curvature in DNA nanostructures have so far never been addressed. In this work, we designed three types of tile cores built around a circular scaffold using three- and four-branched junctions. Joining the tile cores with arms having two kinds of inter-tile distances, an odd and an even number of DNA half-turns, tended to form planar 2D lattices and tubes, respectively. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the tubes and thereby the tile conformation of dihedrals with addressable faces. DNA tubes with either right- or left-handed chirality were obtained by the coupling of the intrinsic curvature of the tiles with the arm twist. We were able to assign the chiral indices (n,m) to a tube with its structure resolved by AFM at the single-tile level and therefore to estimate the global curvature of the tube (or its component tile) using a regular polygon model that approximated its transverse section. A deeper understanding of the integrated actions of different types of twisting forces on DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.
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Affiliation(s)
- Chuan Jiang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Biao Lu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shijie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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23
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Insua I, Bergueiro J, Méndez-Ardoy A, Lostalé-Seijo I, Montenegro J. Bottom-up supramolecular assembly in two dimensions. Chem Sci 2022; 13:3057-3068. [PMID: 35414883 PMCID: PMC8926289 DOI: 10.1039/d1sc05667k] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/19/2022] [Indexed: 01/17/2023] Open
Abstract
The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. Attracted by the interesting properties of two-dimensional inorganic analogues, monomers of different chemical natures are being explored for the assembly of dynamic 2D systems. Although many important discoveries have been already achieved, great challenges are still to be addressed in this field. Hierarchical multicomponent assembly, directional non-covalent growth and internal structural control are a just a few of the examples that will be discussed in this perspective about the exciting present and the bright future of two-dimensional supramolecular assemblies. The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. This perspective discusses the main strategies to direct the supramolecular self-assembly of organic monomers in 2D.![]()
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Affiliation(s)
- Ignacio Insua
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Julian Bergueiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Alejandro Méndez-Ardoy
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Irene Lostalé-Seijo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Spain
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24
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Affiliation(s)
- Jason S. Kahn
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
| | - Oleg Gang
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Department of Applied Physics and Applied Mathematics Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
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25
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Narayanan RP, Abraham L. Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots. Curr Top Med Chem 2022; 22:668-685. [PMID: 35023457 DOI: 10.2174/1568026622666220112143401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 12/01/2021] [Accepted: 12/05/2021] [Indexed: 11/22/2022]
Abstract
DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.
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Affiliation(s)
- Raghu Pradeep Narayanan
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
| | - Leeza Abraham
- Centre for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe-85281, USA
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26
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Poppleton E, Mallya A, Dey S, Joseph J, Šulc P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res 2022; 50:D246-D252. [PMID: 34747480 PMCID: PMC8728195 DOI: 10.1093/nar/gkab1000] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Swarup Dey
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Joel Joseph
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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27
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Du Y, Zhou X, Jin J, Liang H, Men Y, Jiang W. A two-stage energy tuning strategy via salt and glycine programmed DNA-engineered crystals. Chem Commun (Camb) 2021; 57:13578-13581. [PMID: 34846054 DOI: 10.1039/d1cc05432e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To obtain high-quality DNA-engineered crystals at room temperature, a two-stage energy tuning strategy by first adding NaCl and then glycine (Gly) is proposed. The addition of Gly can exquisitely balance the attraction and repulsion energies for crystallization. The state transition induced by energy rather than temperature is significant for a biosystem.
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Affiliation(s)
- Yanqiu Du
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China. .,College of Materials and Textile Engineering, Jiaxing University, Jiaxing 314001, P. R. China
| | - Xiang Zhou
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jing Jin
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
| | - Haojun Liang
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Yongfeng Men
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
| | - Wei Jiang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
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28
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wen Wang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chunyu Chen
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Simon Vecchioni
- Department of Chemistry New York University New York New York 10003 USA
| | - Tianqing Zhang
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Chengxian Wu
- School of Life Sciences Tsinghua University-Peking University Center for Life Sciences Center for Synthetic and Systems Biology Tsinghua University Beijing 100084 China
| | - Yoel P. Ohayon
- Department of Chemistry New York University New York New York 10003 USA
| | - Ruojie Sha
- Department of Chemistry New York University New York New York 10003 USA
| | - Nadrian C. Seeman
- Department of Chemistry New York University New York New York 10003 USA
| | - 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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29
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Wang W, Chen C, Vecchioni S, Zhang T, Wu C, Ohayon YP, Sha R, Seeman NC, Wei B. Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control. Angew Chem Int Ed Engl 2021; 60:25781-25786. [PMID: 34596325 DOI: 10.1002/anie.202112487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/11/2022]
Abstract
Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson-Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chunyu Chen
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Simon Vecchioni
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Tianqing Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Chengxian Wu
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Yoel P Ohayon
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, New York, 10003, USA
| | - 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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30
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Baig MMFA, Dissanayaka WL, Zhang C. 2D DNA nanoporous scaffold promotes osteogenic differentiation of pre-osteoblasts. Int J Biol Macromol 2021; 188:657-669. [PMID: 34371047 DOI: 10.1016/j.ijbiomac.2021.07.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/23/2021] [Accepted: 07/31/2021] [Indexed: 01/06/2023]
Abstract
Biofunctional materials with nanomechanical parameters similar to bone tissue may promote the adherence, migration, proliferation, and differentiation of pre-osteoblasts. In this study, deoxyribonucleic acid (DNA) nanoporous scaffold (DNA-NPS) was synthesized by the polymerization of rectangular and double-crossover (DX) DNA tiles. The diagonally precise polymerization of nanometer-sized DNA tiles (A + B) through sticky end cohesion gave rise to a micrometer-sized porous giant-sheet material. The synthesized DNA-NPS exhibited a uniformly distributed porosity with a size of 25 ± 20 nm. The morphology, dimensions, sectional profiles, 2-dimensional (2D) layer height, texture, topology, pore size, and mechanical parameters of DNA-NPS have been characterized by atomic force microscopy (AFM). The size and zeta potential of DNA-NPS have been characterized by the zeta sizer. Cell biocompatibility, proliferation, and apoptosis have been evaluated by flow cytometry. The AFM results confirmed that the fabricated DNA-NPS was interconnected and uniformly porous, with a surface roughness of 0.125 ± 0.08035 nm. The elastic modulus of the DNA-NPS was 22.45 ± 8.65 GPa, which was comparable to that of native bone tissue. DNA-NPS facilitated pre-osteoblast adhesion, proliferation, and osteogenic differentiation. These findings indicated the potential of 2D DNA-NPS in promoting bone tissue regeneration.
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Affiliation(s)
| | - Waruna Lakmal Dissanayaka
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China
| | - Chengfei Zhang
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China.
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31
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Poppleton E, Romero R, Mallya A, Rovigatti L, Šulc P. OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures. Nucleic Acids Res 2021; 49:W491-W498. [PMID: 34009383 PMCID: PMC8265093 DOI: 10.1093/nar/gkab324] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an interactive visualization and analysis interface using the browser-based visualizer oxView to facilitate the understanding of simulation results for a user's specific structure. This online tool significantly lowers the entry barrier of integrating simulations in the nanostructure design pipeline for users who are not experts in the technical aspects of molecular simulation. The webserver is freely available at oxdna.org.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Roger Romero
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Lorenzo Rovigatti
- Department of Physics, Sapienza Università di Roma, P.le A. Moro 2 00185, Rome, Italy
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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32
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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33
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Wang ST, Minevich B, Liu J, Zhang H, Nykypanchuk D, Byrnes J, Liu W, Bershadsky L, Liu Q, Wang T, Ren G, Gang O. Designed and biologically active protein lattices. Nat Commun 2021; 12:3702. [PMID: 34140491 PMCID: PMC8211860 DOI: 10.1038/s41467-021-23966-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/13/2021] [Indexed: 01/13/2023] Open
Abstract
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.
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Affiliation(s)
- Shih-Ting Wang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York City, NY, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Honghu Zhang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Dmytro Nykypanchuk
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - James Byrnes
- Energy Sciences Directorate/Photon Science Division, NSLS II, Brookhaven National Laboratory, Upton, NY, USA
| | - Wu Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lev Bershadsky
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA
| | - Qun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Tong Wang
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York City, NY, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, USA.
- Department of Chemical Engineering, Columbia University, New York City, NY, USA.
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA.
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34
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Kahn JS, Gang O. Designer Nanomaterials through Programmable Assembly. Angew Chem Int Ed Engl 2021; 61:e202105678. [PMID: 34128306 DOI: 10.1002/anie.202105678] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 11/08/2022]
Abstract
Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.
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Affiliation(s)
- Jason S Kahn
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.,Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY, 11973, USA
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35
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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36
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Wang Y, Dai L, Ding Z, Ji M, Liu J, Xing H, Liu X, Ke Y, Fan C, Wang P, Tian Y. DNA origami single crystals with Wulff shapes. Nat Commun 2021; 12:3011. [PMID: 34021131 PMCID: PMC8140131 DOI: 10.1038/s41467-021-23332-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
DNA origami technology has proven to be an excellent tool for precisely manipulating molecules and colloidal elements in a three-dimensional manner. However, fabrication of single crystals with well-defined facets from highly programmable, complex DNA origami units is a great challenge. Here, we report the successful fabrication of DNA origami single crystals with Wulff shapes and high yield. By regulating the symmetries and binding modes of the DNA origami building blocks, the crystalline shapes can be designed and well-controlled. The single crystals are then used to induce precise growth of an ultrathin layer of silica on the edges, resulting in mechanically reinforced silica-DNA hybrid structures that preserve the details of the single crystals without distortion. The silica-infused microcrystals can be directly observed in the dry state, which allows meticulous analysis of the crystal facets and tomographic 3D reconstruction of the single crystals by high-resolution electron microscopy.
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Affiliation(s)
- Yong Wang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Lizhi Dai
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Zhiyuan Ding
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China
| | - Min Ji
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China
| | - Jiliang Liu
- National Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, and Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Wang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China.
| | - Ye Tian
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, China.
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37
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Procyk J, Poppleton E, Šulc P. Coarse-grained nucleic acid-protein model for hybrid nanotechnology. SOFT MATTER 2021; 17:3586-3593. [PMID: 33398312 DOI: 10.1039/d0sm01639j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The emerging field of hybrid DNA-protein nanotechnology brings with it the potential for many novel materials which combine the addressability of DNA nanotechnology with the versatility of protein interactions. However, the design and computational study of these hybrid structures is difficult due to the system sizes involved. To aid in the design and in silico analysis process, we introduce here a coarse-grained DNA/RNA-protein model that extends the oxDNA/oxRNA models of DNA/RNA with a coarse-grained model of proteins based on an anisotropic network model representation. Fully equipped with analysis scripts and visualization, our model aims to facilitate hybrid nanomaterial design towards eventual experimental realization, as well as enabling study of biological complexes. We further demonstrate its usage by simulating DNA-protein nanocage, DNA wrapped around histones, and a nascent RNA in polymerase.
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Affiliation(s)
- Jonah Procyk
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, Arizona 85281, USA.
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38
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Dass M, Gür FN, Kołątaj K, Urban MJ, Liedl T. DNA Origami-Enabled Plasmonic Sensing. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:5969-5981. [PMID: 33828635 PMCID: PMC8016175 DOI: 10.1021/acs.jpcc.0c11238] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/31/2021] [Indexed: 05/02/2023]
Abstract
The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.
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Affiliation(s)
- Mihir Dass
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Fatih N. Gür
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Karol Kołątaj
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Maximilian J. Urban
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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39
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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40
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Berengut JF, Wong CK, Berengut JC, Doye JPK, Ouldridge TE, Lee LK. Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation. ACS NANO 2020; 14:17428-17441. [PMID: 33232603 DOI: 10.1021/acsnano.0c07696] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biology demonstrates how a near infinite array of complex systems and structures at many scales can originate from the self-assembly of component parts on the nanoscale. But to fully exploit the benefits of self-assembly for nanotechnology, a crucial challenge remains: How do we rationally encode well-defined global architectures in subunits that are much smaller than their assemblies? Strain accumulation via geometric frustration is one mechanism that has been used to explain the self-assembly of global architectures in diverse and complex systems a posteriori. Here we take the next step and use strain accumulation as a rational design principle to control the length distributions of self-assembling polymers. We use the DNA origami method to design and synthesize a molecular subunit known as the PolyBrick, which perturbs its shape in response to local interactions via flexible allosteric blocking domains. These perturbations accumulate at the ends of polymers during growth, until the deformation becomes incompatible with further extension. We demonstrate that the key thermodynamic factors for controlling length distributions are the intersubunit binding free energy and the fundamental strain free energy, both which can be rationally encoded in a PolyBrick subunit. While passive polymerization yields geometrical distributions, which have the highest statistical length uncertainty for a given mean, the PolyBrick yields polymers that approach Gaussian length distributions whose variance is entirely determined by the strain free energy. We also show how strain accumulation can in principle yield length distributions that become tighter with increasing subunit affinity and approach distributions with uniform polymer lengths. Finally, coarse-grained molecular dynamics and Monte Carlo simulations delineate and quantify the dominant forces influencing strain accumulation in a molecular system. This study constitutes a fundamental investigation of the use of strain accumulation as a rational design principle in molecular self-assembly.
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Affiliation(s)
- Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
| | - Chak Kui Wong
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Julian C Berengut
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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41
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Ji M, Liu J, Dai L, Wang L, Tian Y. Programmable Cocrystallization of DNA Origami Shapes. J Am Chem Soc 2020; 142:21336-21343. [PMID: 33259193 DOI: 10.1021/jacs.0c08525] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Assembly of distinct types of species, particularly possessing anisotropic configurations, is the premise to broaden structural diversity and explore materials' collective properties. However, it remains a great challenge to programmably cocrystallize manifold anisotropic nanoparticles with the desired assembly mode, because it requires not only the complementarity of both sizes and shapes but also the control over their directional interactions. Here, by introducing DNA origami technique into lattice engineering, we synthesize two types of DNA nano-objects with different symmetries and program the heterogeneous functional patches precisely on their surfaces with nanometer-level precision, which could guide further assembly of these nano-objects. We show that these anisotropic DNA nano-objects could be cocrystallized along specified modes via modulating the combination of surface patches. The highly ordered DNA crystals were thoroughly evidenced by techniques including small-angle X-ray scattering and electron microscopy after careful encapsulation of a thin layer of silica on these DNA nano-objects. Our strategy endows distinct shapes of organic DNA origami structures with regulation features to control the sophisticated modes of cocrystallization of these diverse components, laying a foundation for designing and fabricating customized three-dimensional structures with given optical and mechanical properties.
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Affiliation(s)
- Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, 210023, China.,Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Jiliang Liu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, 210023, China.,Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
| | - Lei Wang
- Center for Analysis and Testing, Nanjing Normal University, Nanjing, 210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, 210023, China.,Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210023, China
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42
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A Matter of Size and Placement: Varying the Patch Size of Anisotropic Patchy Colloids. Int J Mol Sci 2020; 21:ijms21228621. [PMID: 33207624 PMCID: PMC7696828 DOI: 10.3390/ijms21228621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
Non-spherical colloids provided with well-defined bonding sites—often referred to as patches—are increasingly attracting the attention of materials scientists due to their ability to spontaneously assemble into tunable surface structures. The emergence of two-dimensional patterns with well-defined architectures is often controlled by the properties of the self-assembling building blocks, which can be either colloidal particles at the nano- and micro-scale or even molecules and macromolecules. In particular, the interplay between the particle shape and the patch topology gives rise to a plethora of tilings, from close-packed to porous monolayers with pores of tunable shapes and sizes. The control over the resulting surface structures is provided by the directionality of the bonding mechanism, which mostly relies on the selective nature of the patches. In the present contribution, we investigate the effect of the patch size on the assembly of a class of anisotropic patchy colloids—namely, rhombic platelets with four identical patches placed in different arrangements along the particle edges. Larger patches are expected to enhance the bond flexibility, while simultaneously reducing the bond selectivity as the single bond per patch condition—which would guarantee a straightforward mapping between local bonding arrangements and long-range pattern formation—is not always enforced. We find that the non-trivial interplay between the patch size and the patch position can either promote a parallel particle arrangement with respect to a non-parallel bonding scenario or give rise to a variety a bonded patterns, which destroy the order of the tilings. We rationalize the occurrence of these two different regimes in terms of single versus multiple bonds between pairs of particles and/or patches.
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43
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail. Angew Chem Int Ed Engl 2020; 59:18619-18626. [PMID: 32533629 DOI: 10.1002/anie.202005505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 11/08/2022]
Abstract
DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson-Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.
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Affiliation(s)
- Chad R Simmons
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA.,School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
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45
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Simmons CR, MacCulloch T, Zhang F, Liu Y, Stephanopoulos N, Yan H. A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chad R. Simmons
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Tara MacCulloch
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Nicholas Stephanopoulos
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Arizona State University USA
- School of Molecular Sciences Arizona State University Tempe AZ 85287 USA
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46
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Baig MMFA, Lai WF, Akhtar MF, Saleem A, Mikrani R, Farooq MA, Ahmed SA, Tahir A, Naveed M, Abbas M, Ansari MT. Targeting folate receptors (α1) to internalize the bleomycin loaded DNA-nanotubes into prostate cancer xenograft CWR22R cells. J Mol Liq 2020; 316:113785. [DOI: 10.1016/j.molliq.2020.113785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Lv J, Dong Y, Gu Z, Yang D. Programmable DNA Nanoflowers for Biosensing, Bioimaging, and Therapeutics. Chemistry 2020; 26:14512-14524. [DOI: 10.1002/chem.202002242] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/02/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Jigang Lv
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Yuhang Dong
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
| | - Zi Gu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Dayong Yang
- Frontier Science Center for Synthetic Biology Key Laboratory of, Systems Bioengineering (MOE) School of Chemical Engineering and Technology Tianjin University Tianjin 300350 P. R. China
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48
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Li C, Chen Z, Zhang Y, He J, Yuan R, Xu W. Guanine-Lighting-Up Fluorescence Biosensing of Silver Nanoclusters Populated in Functional DNA Constructs by a pH-Triggered Switch. Anal Chem 2020; 92:13369-13377. [PMID: 32900187 DOI: 10.1021/acs.analchem.0c02744] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Dark or weak-emissive DNA-harbored silver nanoclusters (AgNCs) can be remarkably lighted up when approaching to guanine bases. The resultant bright AgNCs acting as a fluorescent reporter are fascinating in biosensing. To explore the applicable guanine-enhanced emission of AgNCs for biosensing microRNA-155 (miR-155) as a model, here we designed a unique stem-loop hairpin beacon (HB) encoding with an miR-155-recognizable sequence and a AgNCs-nucleable template, as well as a hairpin helper tethering a partially locked guanine-rich (15-nt) tail (G15H), while two identical cytosine-rich segments were inserted in HB and G15H to merge for folding/unfolding of i-motif at changed pHs. Initially, the intact clusters populated in HB (HB/AgNCs) were almost nonfluorescent in a buffer (pH 7.0). Then, miR-155 was introduced to trigger a repeated hairpin assembly of HB and G15H by competitive strand displacement reactions at decreased pH 5.0 within 10 min, consequently generating numerous duplex DNA constructs (DDCs). With the resultant template of pH-responsive i-motifs incorporated in DDCs, their folding at pH 5.0 brought the proximity of unlocked G15 overhang to the clusters in a crowded environment, remarkably lighting up the red-emitting fluorescence of HB/AgNCs (λem = 628 ± 5 nm) for amplified signal readout. About 3.5-fold enhancement of quantum yield was achievable using different variants of i-motif length and G15 position. Simply by adding OH-, the configuration fluctuation of i-motifs was implemented for switchable fluorescence biosensing to variable miR-155. Based on a one-step amplification and signaling scheme, this subtle strategy was rapid, low-cost, and specific for miR-155 with high sensitivity down to 67 pM.
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Affiliation(s)
- Chong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Zehui Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yuxuan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Jiayang He
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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49
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 313] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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50
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Ribbon of DNA Lattice on Gold Nanoparticles for Selective Drug Delivery to Cancer Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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