1
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Tosti Guerra F, Poppleton E, Šulc P, Rovigatti L. ANNaMo: Coarse-grained modeling for folding and assembly of RNA and DNA systems. J Chem Phys 2024; 160:205102. [PMID: 38814009 DOI: 10.1063/5.0202829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/04/2024] [Indexed: 05/31/2024] Open
Abstract
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales and system sizes involved. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents three nucleotides with a patchy particle and is parameterized using well-established nearest-neighbor models. Thanks to the reduction of degrees of freedom and to a bond-swapping mechanism, our model allows for simulations at timescales and length scales that are currently inaccessible to more detailed models. To validate the performance of our model, we conducted extensive simulations of various systems: We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions, the folding of an MMTV pseudoknot, which is a complex RNA structure involved in viral replication, and also explored the folding of an RNA tile containing a k-type pseudoknot. Finally, we evaluated the performance of the new model in reproducing the melting temperatures of oligomers and the dependence on the toehold length of the displacement rate in toehold-mediated displacement processes, a key reaction used in molecular computing. All in all, the successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of the new model.
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Affiliation(s)
- F Tosti Guerra
- Department of Physics, Sapienza University of Rome, Roma, Italy
| | - E Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - P Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
- Department of Bioscience, School of Natural Sciences, Technical University Munich, Munich, Germany
| | - L Rovigatti
- Department of Physics, Sapienza University of Rome, Roma, Italy
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2
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Cecconello A, Cencini A, Rilievo G, Tonolo F, Litti L, Vianello F, Willner I, Magro M. Chiroplasmonic DNA Scaffolded "Fusilli" Structures. NANO LETTERS 2024; 24:5944-5951. [PMID: 38588536 DOI: 10.1021/acs.nanolett.3c04943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
DNA is an ideal template for the design of nanoarchitectures with molecular-like features. Here, we present an optimized assembly strategy for the concatenation of DNA quasi-rings into long scaffolds. Ionic strength, which played a major role during self-assembly, produced the expected high quality only at 15 mM MgCl2. Atomic force microscopy (AFM) characterization showed several micrometer long tubular structures that were used as templates for the positioning of plasmonic nanoparticles (NPs) along a three-dimensional helical path using DNA tethers. As imaged by high-resolution scanning transmission electron microscopy (HR-STEM) and modeled by theoretical calculations, the NPs distributed into a "fusilli" fashion (i.e., a helical pasta shape), displaying chiroptical activity as revealed by a bisignated CD absorption, centered at the plasmon resonance wavelength. The present structures contribute to enrich the ever-developing arena of chiroplasmonic DNA-based nanomaterials and demonstrate that large assemblies are attainable for their future application to develop metamaterials.
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Affiliation(s)
- Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
| | - Aura Cencini
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
| | - Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
| | - Federica Tonolo
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
| | - Lucio Litti
- Department of Chemical Sciences, University of Padova, via marzolo 1, 35131 Padova, Italy
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padua, viale dell'Università 16, 35020 Legnaro, Italy
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3
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Aqib RM, Umer A, Li J, Liu J, Ding B. Light Responsive DNA Nanomaterials and Their Biomedical Applications. Chem Asian J 2024; 19:e202400226. [PMID: 38514391 DOI: 10.1002/asia.202400226] [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: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.
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Affiliation(s)
- Raja Muhammad Aqib
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arsalan Umer
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jialin Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Ge W, Wang Y, Xiao SJ. Three-Point-Star Deoxyribonucleic Acid Tiles with the Core Arm Length at Three Half-Turns for Two-Dimensional Archimedean Tilings and Beyond. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:10326-10333. [PMID: 38686650 DOI: 10.1021/acs.langmuir.4c00985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
2D Archimedean tiling and complex tessellation patterns assembled from soft materials including modular DNA tiles have attracted great interest because of their specific structures and potential applications in nanofabrication, nanoelectronics, nanophotonics, biomedical sensing, drug delivery, therapeutics, etc. Traditional three- and four-point-star DNA tiles with the core arm length at two half-turns (specified as three- and four-point-star-E previously and abbreviated as 3PSE and 4PSE tiles here) have been applied to assemble intricate tessellations through tuning the size of inserted nT (n = 1-7, T is thymine) loops on helper strands at the tile center. Following our recent findings using a new type of four-point-star tiles with the core arm length at three half-turns (specified as four-point-star-O previously and abbreviated as 4PSO tiles here) to assemble DNA tubes and flat 2D arrays, we report here the cross-hybridization weaving architectures at the tile center to construct three new 3PSO tiles with circular DNA oligonucleotides of 96-nt (nucleotides) serving as the scaffolds, further the monotonous and combinatory E- and O-tilings on one type of 3PSO tiles to create 2D Archimedean tiling patterns (6.6.6) and (4.8.8), and finally, the combination of 3PSO with 4PSO as well as 2PSO tiles to tile into complex tessellation patterns. The easy realization of regular and intricate DNA tessellations with 2-4PSO tiles not only richens the fundamental DNA modules and complex DNA nanostructures in types but also broadens the potential application scopes of DNA nanostructures in nanofabrication, DNA computing, biomedicine, etc.
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Affiliation(s)
- Wei Ge
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yantong Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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5
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Shapiro A, Joseph N, Mellul N, Abu-Horowitz A, Mizrahi B, Bachelet I. Folding molecular origami from ribosomal RNA. J Nanobiotechnology 2024; 22:218. [PMID: 38698435 PMCID: PMC11067225 DOI: 10.1186/s12951-024-02489-2] [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: 07/18/2023] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
Approximately 80 percent of the total RNA in cells is ribosomal RNA (rRNA), making it an abundant and inexpensive natural source of long, single-stranded nucleic acid, which could be used as raw material for the fabrication of molecular origami. In this study, we demonstrate efficient and robust construction of 2D and 3D origami nanostructures utilizing cellular rRNA as a scaffold and DNA oligonucleotide staples. We present calibrated protocols for the robust folding of contiguous shapes from one or two rRNA subunits that are efficient to allow folding using crude extracts of total RNA. We also show that RNA maintains stability within the folded structure. Lastly, we present a novel and comprehensive analysis and insights into the stability of RNA:DNA origami nanostructures and demonstrate their enhanced stability when coated with polylysine-polyethylene glycol in different temperatures, low Mg2+ concentrations, human serum, and in the presence of nucleases (DNase I or RNase H). Thus, laying the foundation for their potential implementation in emerging biomedical applications, where folding rRNA into stable structures outside and inside cells would be desired.
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Affiliation(s)
- Anastasia Shapiro
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
- Technion, Faculty of Biotechnology and Food Engineering, 32000, Haifa, Israel
| | - Noah Joseph
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
| | - Nadav Mellul
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel
| | | | - Boaz Mizrahi
- Technion, Faculty of Biotechnology and Food Engineering, 32000, Haifa, Israel
| | - Ido Bachelet
- Augmanity Nano Ltd., 8 Hamada St., 7670308, Rehovot, Israel.
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6
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Jiang Q, Shang Y, Xie Y, Ding B. DNA Origami: From Molecular Folding Art to Drug Delivery Technology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2301035. [PMID: 37715333 DOI: 10.1002/adma.202301035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/08/2023] [Indexed: 09/17/2023]
Abstract
DNA molecules that store genetic information in living creatures can be repurposed as building blocks to construct artificial architectures, ranging from the nanoscale to the microscale. The precise fabrication of self-assembled DNA nanomaterials and their various applications have greatly impacted nanoscience and nanotechnology. More specifically, the DNA origami technique has realized the assembly of various nanostructures featuring rationally predesigned geometries, precise addressability, and versatile programmability, as well as remarkable biocompatibility. These features have elevated DNA origami from academic interest to an emerging class of drug delivery platform for a wide range of diseases. In this minireview, the latest advances in the burgeoning field of DNA-origami-based innovative platforms for regulating biological functions and delivering versatile drugs are presented. Challenges regarding the novel drug vehicle's safety, stability, targeting strategy, and future clinical translation are also discussed.
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Affiliation(s)
- Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
| | - Yiming Xie
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, P. R. China
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7
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Adžić N, Jochum C, Likos CN, Stiakakis E. Engineering Ultrasoft Interactions in Stiff All-DNA Dendrimers by Site-Specific Control of Scaffold Flexibility. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308763. [PMID: 38183376 DOI: 10.1002/smll.202308763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/10/2023] [Indexed: 01/08/2024]
Abstract
A combined experimental and theoretical study of the structural correlations in moderately concentrated suspensions of all-DNA dendrimers of the second generation (G2) with controlled scaffold rigidity is reported here. Small-angle X-ray scattering experiments in concentrated aqueous saline solutions of stiff all-DNA G2 dendritic constructs reveal a novel anomalous liquid-like phase behavior which is reflected in the calculated structure factors as a two-step increase at low scattering wave vectors. By developing a new design strategy for adjusting the particle's internal flexibility based on site-selective incorporation of single-stranded DNA linkers into the dendritic scaffold, it is shown that this unconventional type of self-organization is strongly contingent on the dendrimer's stiffness. A comprehensive computer simulation study employing dendritic models with different levels of coarse-graining, and two theoretical approaches based on effective, pair-potential interactions, remarkably confirmed the origin of this unusual liquid-like behavior. The results demonstrate that the precise control of the internal structure of the dendritic scaffold conferred by the DNA can be potentially used to engineer a rich palette of novel ultrasoft interaction potentials that could offer a route for directed self-assembly of intriguing soft matter phases and experimental realizations of a host of unusual phenomena theoretically predicted for ultrasoft interacting systems.
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Affiliation(s)
- Nataša Adžić
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
- Institute of Physics Belgrade, University of Belgrade, Pregrevica 118, Belgrade, 11080, Serbia
| | - Clemens Jochum
- Institute for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10, Vienna, A-1040, Austria
| | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, A-1090, Austria
| | - Emmanuel Stiakakis
- Biomacromolecular Systems and Processes, Institute of Biological Information Processing (IBI-4), Forschungszentrum Jülich, D-52425, Jülich, Germany
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8
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Duque CM, Hall DM, Tyukodi B, Hagan MF, Santangelo CD, Grason GM. Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra. Proc Natl Acad Sci U S A 2024; 121:e2315648121. [PMID: 38669182 PMCID: PMC11067059 DOI: 10.1073/pnas.2315648121] [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: 09/08/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
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Affiliation(s)
- Carlos M. Duque
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Department of Physics, University of Massachusetts, Amherst, MA01003
| | - Douglas M. Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
| | - Botond Tyukodi
- Department of Physics, Babes-Bolyai University, Cluj-Napoca400084, Romania
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Christian D. Santangelo
- Department of Physics, University of Massachusetts, Amherst, MA01003
- Department of Physics, Syracuse University, Syracuse, NY13210
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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9
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Aqib RM, Wang Y, Liu J, Ding B. Efficient one-pot assembly of higher-order DNA nanostructures by chemically conjugated branched DNA. Chem Commun (Camb) 2024; 60:4715-4718. [PMID: 38596907 DOI: 10.1039/d4cc01097c] [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: 04/11/2024]
Abstract
Chemically conjugated branched DNA was successfully synthesized by a copper-free click reaction to construct sophisticated and higher-order polyhedral DNA nanostructures with pre-defined units in one pot, which can be used as an efficient nanoplatform to precisely organize multiple gold nanoparticles in predesigned patterns.
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Affiliation(s)
- Raja Muhammad Aqib
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Piantanida L, Liddle JA, Hughes WL, Majikes JM. DNA nanostructure decoration: a how-to tutorial. NANOTECHNOLOGY 2024; 35:273001. [PMID: 38373400 DOI: 10.1088/1361-6528/ad2ac5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 02/18/2024] [Indexed: 02/21/2024]
Abstract
DNA Nanotechnology is being applied to multiple research fields. The functionality of DNA nanostructures is significantly enhanced by decorating them with nanoscale moieties including: proteins, metallic nanoparticles, quantum dots, and chromophores. Decoration is a complex process and developing protocols for reliable attachment routinely requires extensive trial and error. Additionally, the granular nature of scientific communication makes it difficult to discern general principles in DNA nanostructure decoration. This tutorial is a guidebook designed to minimize experimental bottlenecks and avoid dead-ends for those wishing to decorate DNA nanostructures. We supplement the reference material on available technical tools and procedures with a conceptual framework required to make efficient and effective decisions in the lab. Together these resources should aid both the novice and the expert to develop and execute a rapid, reliable decoration protocols.
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Affiliation(s)
- Luca Piantanida
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
| | - William L Hughes
- Faculty of Applied Science, School of Engineering, University of British Columbia, Kelowna, B.C., V1V 1V7, Canada
| | - Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD, 20878, United States of America
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11
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Wang Y, Xiong Y, Shi K, Effah CY, Song L, He L, Liu J. DNA nanostructures for exploring cell-cell communication. Chem Soc Rev 2024; 53:4020-4044. [PMID: 38444346 DOI: 10.1039/d3cs00944k] [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: 03/07/2024]
Abstract
The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability. Herein, this review is dedicated to offering a new perspective on using DNA nanostructures to explore the progress of cell-cell communication. After briefly outlining the anchoring strategy of DNA nanostructures on cell membranes and the subsequent dynamic regulation of DNA nanostructures, this paper highlights the significant contribution of DNA nanostructures in monitoring cell-cell communication and regulating its interactions. Finally, we provide a quick overview of the current challenges and potential directions for the application of DNA nanostructures in cellular communication and interactions.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kangqi Shi
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Clement Yaw Effah
- The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou 450003, China
| | - Lulu Song
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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12
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Woo S, Saka SK, Xuan F, Yin P. Molecular robotic agents that survey molecular landscapes for information retrieval. Nat Commun 2024; 15:3293. [PMID: 38632239 PMCID: PMC11024175 DOI: 10.1038/s41467-024-46978-2] [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: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.
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Affiliation(s)
- Sungwook Woo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- European Molecular Biology Laboratory (EMBL), Heidelberg, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Feng Xuan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Spear Bio Inc., Woburn, MA, 01801, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
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13
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Iinuma R, Chen X, Masubuchi T, Ueda T, Tadakuma H. Size-Selective Capturing of Exosomes Using DNA Tripods. J Am Chem Soc 2024; 146:10293-10298. [PMID: 38569597 PMCID: PMC11027911 DOI: 10.1021/jacs.3c11067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024]
Abstract
Fractionating and characterizing target samples are fundamental to the analysis of biomolecules. Extracellular vesicles (EVs), containing information regarding the cellular birthplace, are promising targets for biology and medicine. However, the requirement for multiple-step purification in conventional methods hinders analysis of small samples. Here, we apply a DNA origami tripod with a defined aperture of binders (e.g., antibodies against EV biomarkers), which allows us to capture the target molecule. Using exosomes as a model, we show that our tripod nanodevice can capture a specific size range of EVs with cognate biomarkers from a broad distribution of crude EV mixtures. We further demonstrate that the size of captured EVs can be controlled by changing the aperture of the tripods. This simultaneous selection with the size and biomarker approach should simplify the EV purification process and contribute to the precise analysis of target biomolecules from small samples.
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Affiliation(s)
- Ryosuke Iinuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- JSR
Corporation, Ibaraki, 305-0841, Japan
| | - Xiaoxia Chen
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
| | - Takeya Masubuchi
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Department
of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Takuya Ueda
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- Graduate
School of Science and Engineering, Waseda
University, Tokyo 162-8480, Japan
| | - Hisashi Tadakuma
- Graduate
School of Frontier Science, The University
of Tokyo, Chiba 277-8562, Japan
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, People’s Republic of China
- Gene Editing
Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, People’s Republic
of China
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14
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Narayanan RP, Prasad A, Buchberger A, Zou L, Bernal-Chanchavac J, MacCulloch T, Fahmi NE, Yan H, Zhang F, Webber MJ, Stephanopoulos N. High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307585. [PMID: 37849034 PMCID: PMC10922742 DOI: 10.1002/smll.202307585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Indexed: 10/19/2023]
Abstract
The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. Here, efficient supramolecular polymerization of DNA origami nanostructures is demonstrated using a multivalent display of small molecule host-guest interactions. Modification of DNA strands with cucurbit[7]uril (CB[7]) and its adamantane guest, yielding a supramolecular complex with an affinity of order 1010 m-1 , directs hierarchical assembly of origami monomers into 1D nanofibers. This affinity regime enables efficient polymerization; a lower-affinity β-cyclodextrin-adamantane complex does not promote extended structures at a similar valency. Finally, the utility of the high-affinity CB[7]-adamantane interactions is exploited to enable responsive enzymatic actuation of origami nanofibers assembled using peptide linkers. This work demonstrates the power of high-affinity CB[7]-guest recognition as an orthogonal axis to drive self-assembly in DNA nanotechnology.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Alex Buchberger
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Lei Zou
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Julio Bernal-Chanchavac
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Nour Eddine Fahmi
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University-Newark, Newark, NJ, 07102, USA
| | - Matthew J Webber
- Chemical & Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, 85287, USA
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15
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Evans J, Šulc P. Designing 3D multicomponent self-assembling systems with signal-passing building blocks. J Chem Phys 2024; 160:084902. [PMID: 38385517 DOI: 10.1063/5.0191282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
We introduce an allostery-mimetic building block model for the self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can be irreversibly activated or deactivated by binding of the particle's other controlling patches to another particle. We show that these allostery-mimetic systems can be designed to increase yields of target structures by disallowing misassembled states and can further decrease the smallest number of distinct species needed to assemble a target structure. Next, we show applications to design a programmable nanoparticle swarm for multifarious assembly: a system of particles that stores multiple possible target structures and a particular structure is recalled by presenting an external trigger signal. Finally, we outline a possible pathway for realization of such structures at nanoscale using DNA nanotechnology devices.
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Affiliation(s)
- Joshua Evans
- 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
| | - Petr Šulc
- 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
- School of Natural Sciences, Department of Bioscience, Technical University Munich, 85748 Garching, Germany
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16
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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17
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Wang Y, Wang H, Li Y, Yang C, Tang Y, Lu X, Fan J, Tang W, Shang Y, Yan H, Liu J, Ding B. Chemically Conjugated Branched Staples for Super-DNA Origami. J Am Chem Soc 2024; 146:4178-4186. [PMID: 38301245 DOI: 10.1021/jacs.3c13331] [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: 02/03/2024]
Abstract
DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.
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Affiliation(s)
- Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yan Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Changping Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yue Tang
- Arizona State University, Tempe, Arizona 85281, United States
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jing Fan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Wantao Tang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hao Yan
- Arizona State University, Tempe, Arizona 85281, United States
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Wei WS, Trubiano A, Sigl C, Paquay S, Dietz H, Hagan MF, Fraden S. Hierarchical assembly is more robust than egalitarian assembly in synthetic capsids. Proc Natl Acad Sci U S A 2024; 121:e2312775121. [PMID: 38324570 PMCID: PMC10873614 DOI: 10.1073/pnas.2312775121] [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: 07/25/2023] [Accepted: 12/07/2023] [Indexed: 02/09/2024] Open
Abstract
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and concentrations of subunits. By contrast, we introduce an assembly paradigm that allows large error-tolerance in the subunit affinity and helps avoid kinetic traps. Our combined experimental and computational approach uses a model system of triangular subunits programmed to assemble into T = 3 icosahedral capsids comprising 60 units. The experimental platform uses DNA origami to create monodisperse colloids whose three-dimensional geometry is controlled to nanometer precision, with two distinct bonds whose affinities are controlled to kBT precision, quantified in situ by static light scattering. The computational model uses a coarse-grained representation of subunits, short-ranged potentials, and Langevin dynamics. Experimental observations and modeling reveal that when the bond affinities are unequal, two distinct hierarchical assembly pathways occur, in which the subunits first form dimers in one case and pentamers in another. These hierarchical pathways produce complete capsids faster and are more robust against affinity variation than egalitarian pathways, in which all binding sites have equal strengths. This finding suggests that hierarchical assembly may be a general engineering principle for optimizing self-assembly of complex target structures.
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Affiliation(s)
- Wei-Shao Wei
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Anthony Trubiano
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Christian Sigl
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Stefan Paquay
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Hendrik Dietz
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Garching85748, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Garching85748, Germany
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
| | - Seth Fraden
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
- Materials Research Science and Engineering Center, Brandeis University, Waltham, MA02453
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19
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Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y. DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. NANO LETTERS 2024; 24:1703-1709. [PMID: 38278134 PMCID: PMC10853956 DOI: 10.1021/acs.nanolett.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/20/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.
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Affiliation(s)
- Qinyi Lu
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Yang Xu
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Kun Zhou
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Petr Sulc
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- Biodesign
Center for Molecular Design and Biomimetics, Arizona State University, Tempe, Arizona 85287, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yonggang Ke
- Department
of Biomedical Engineering, Georgia Institute
of Technology and Emory University, Atlanta, Georgia 30322, United States
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20
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Fucetola CP, Wang JT, Bolonduro OA, Lieber CM, Timko BP. Single-Crystal Silicon Nanotubes, Hollow Nanocones, and Branched Nanotube Networks. ACS NANO 2024; 18:3775-3782. [PMID: 38227976 DOI: 10.1021/acsnano.3c11841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
We report a general approach for the synthesis of single-crystal silicon nanotubes, involving epitaxial deposition of silicon shells on germanium nanowire templates followed by removal of the germanium template by selective wet etching. By exploiting advances in the synthesis of germanium nanowires, we were able to rationally tune the nanotube internal diameters (5-80 nm), wall thicknesses (3-12 nm), and taper angles (0-9°) and additionally demonstrated branched silicon nanotube networks. Field effect transistors fabricated from p-type nanotubes exhibited a strong gate effect, and fluid transport experiments demonstrated that small molecules could be electrophoretically driven through the nanotubes. These results demonstrate the suitability of silicon nanotubes for the design of nanoelectrofluidic devices.
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Affiliation(s)
- Corey P Fucetola
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Justin T Wang
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Olurotimi A Bolonduro
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Charles M Lieber
- Lieber Research Group, Lexington, Massachusetts 02420, United States
| | - Brian P Timko
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
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21
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Kanzhigitova D, Abutalip M, Nazir F, Amze M, Askar P, Yeszhan Y, Pham TT, Rakhmetullayeva R, Adilov S, Nuraje N. Controlled Synthesis of Polyaniline-Based Nanomaterials with Self-Assembly and Interface Manipulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2183-2190. [PMID: 38236758 DOI: 10.1021/acs.langmuir.3c03167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Versatile nanostructures of conducting polymers are highly relevant based on unique properties, including electrical, optical, and thermal, with changes in morphology. This contribution reports a facile and reproducible synthesis approach for the design of conducting polymer nanostructures from zero- to three-dimensional composites. Two polymerization steps, namely, self-assembly-directed and interface thin layer-templated polymerizations in this synthesis, were kinetically controlled to fabricate such nanostructures directly. The uniquely designed bicontinuous nanoreactor offers an easy synthesis technique for fabricating 3D multifunctional conducting polymer composites. Self-assembly-directed polymerization could be controlled to form nanorods and further directed to form nanobowl/hollow spherical structures. The interface thin layer template process was tuned to produce hollow spherical and 2D film nanostructures. Kinetic control of polymerization was able to provide access to unprecedented nanostructures of the conducting polymers ranging from DNA origami to gecko-inspired nanostructures, with potential applications in drug delivery, energy storage, and adhesive materials. For example, this is the first conducting polymer material that can demonstrate similar adhesiveness (around 8 N/cm2) to gecko finger hairs.
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Affiliation(s)
- Dana Kanzhigitova
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
- Department of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Munziya Abutalip
- Lab of Renewable Energy, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Faisal Nazir
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
| | - Magzhan Amze
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
| | - Perizat Askar
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
| | - Yelriza Yeszhan
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
| | - Tri Thanh Pham
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Raikhan Rakhmetullayeva
- Department of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Salimgerey Adilov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana 010000, Kazakhstan
| | - Nurxat Nuraje
- Department of Chemical and Materials Engineering, School of Engineering and Digital Science, Nazarbayev University, Astana 010000, Kazakhstan
- Lab of Renewable Energy, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
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22
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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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23
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Wang DX, Liu B, Han GM, Li Q, Kong DM, Enderlein J, Chen T. Metal-Induced Energy Transfer (MIET) Imaging of Cell Surface Engineering with Multivalent DNA Nanobrushes. ACS NANO 2024. [PMID: 38231016 PMCID: PMC10883130 DOI: 10.1021/acsnano.3c10162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
The spacing between cells has a significant impact on cell-cell interactions, which are critical to the fate and function of both individual cells and multicellular organisms. However, accurately measuring the distance between cell membranes and the variations between different membranes has proven to be a challenging task. In this study, we employ metal-induced energy transfer (MIET) imaging/spectroscopy to determine and track the intermembrane distance and variations with nanometer precision. We have developed a DNA-based molecular adhesive called the DNA nanobrush, which serves as a cellular adhesive for connecting the plasma membranes of different cells. By manipulating the number of base pairs within the DNA nanobrush, we can modify various aspects of membrane-membrane interactions such as adhesive directionality, distance, and forces. We demonstrate that such nanometer-level changes can be detected with MIET imaging/spectroscopy. Moreover, we successfully employed MIET to measure distance variations between a cellular plasma membrane and a model membrane. This experiment not only showcases the effectiveness of MIET as a powerful tool for accurately quantifying membrane-membrane interactions but also validates the potential of DNA nanobrushes as cellular adhesives. This innovative method holds significant implications for advancing the study of multicellular interactions.
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Affiliation(s)
- Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
| | - Bo Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Gui-Mei Han
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Qingnan Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for Cell Responses, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Universitätsmedizin Göttingen, Robert-Koch-Strasse 40, Göttingen 37075, Germany
| | - Tao Chen
- III. Institute of Physics - Biophysics, Georg August University, 37077 Göttingen, Germany
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24
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Chen Z, Cao L, Yun K, Lu J. Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly. ACS Macro Lett 2024; 13:94-98. [PMID: 38176070 DOI: 10.1021/acsmacrolett.3c00680] [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: 01/06/2024]
Abstract
Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.
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Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Lingyan Cao
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Jingxiong Lu
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Institute of Medi-X, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, China
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25
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Kilwing L, Lill P, Nathwani B, Guerra R, Benson E, Liedl T, Shih WM. Multilayer DNA Origami with Terminal Interfaces That Are Flat and Wide-Area. ACS NANO 2024; 18:885-893. [PMID: 38109901 DOI: 10.1021/acsnano.3c09522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
DNA origami is a popular nanofabrication strategy that employs self-assembly of a long single scaffold strand, typically less than 10 kilobases in length, with hundreds of shorter staple strands into a desired shape. In particular, origami arranged as a single-layer rectangle has proven popular as flat pegboards that can display functionalities at staple-strand breakpoints, off the sides of the constituent double helices, with a ∼5.3 nm rhombic-lattice spacing. For applications that demand tighter spacing, functionalities can be displayed instead on the termini of helices of multilayer DNA origami. However, pegboards with the greatest addressable surface area are often found to be the most versatile. Given the practical limitations of the length of the scaffold that can be easily realized, designs that minimize the length of each helix would have advantages for maximizing the number of helices and therefore the number of addressable pixels on each terminal surface. Here we present an architecture for multilayer DNA origami displaying flush terminal interfaces from over 200 helices that each are only 5.3 turns in length. We characterize an example using cryo-EM imaging paired with single-particle analysis for further analysis of the global structure.
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Affiliation(s)
- Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Pascal Lill
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Richard Guerra
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Erik Benson
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford OX1 3PU, United Kingdom
- The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford OX1 3PU, United Kingdom
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539 Munich, Germany
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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26
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Evans CG, O'Brien J, Winfree E, Murugan A. Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly. Nature 2024; 625:500-507. [PMID: 38233621 PMCID: PMC10794147 DOI: 10.1038/s41586-023-06890-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/22/2023] [Indexed: 01/19/2024]
Abstract
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles1-3. Analogous high-dimensional, highly interconnected computational architectures also arise within information-processing molecular systems inside living cells, such as signal transduction cascades and genetic regulatory networks4-7. Might collective modes analogous to neural computation be found more broadly in other physical and chemical processes, even those that ostensibly play non-information-processing roles? Here we examine nucleation during self-assembly of multicomponent structures, showing that high-dimensional patterns of concentrations can be discriminated and classified in a manner similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends sensitively on the extent of colocalization of high-concentration tiles within the three structures. The system was trained in silico to classify a set of 18 grayscale 30 × 30 pixel images into three categories. Experimentally, fluorescence and atomic force microscopy measurements during and after a 150 hour anneal established that all trained images were correctly classified, whereas a test set of image variations probed the robustness of the results. Although slow compared to previous biochemical neural networks, our approach is compact, robust and scalable. Our findings suggest that ubiquitous physical phenomena, such as nucleation, may hold powerful information-processing capabilities when they occur within high-dimensional multicomponent systems.
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Affiliation(s)
- Constantine Glen Evans
- California Institute of Technology, Pasadena, CA, USA.
- Evans Foundation for Molecular Medicine, Pasadena, CA, USA.
- Maynooth University, Maynooth, Ireland.
| | | | - Erik Winfree
- California Institute of Technology, Pasadena, CA, USA.
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27
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Chen K, Jiang M, Liu J, Huang D, Yang YR. DNA nanostructures as biomolecular scaffolds for antigen display. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1921. [PMID: 37562787 DOI: 10.1002/wnan.1921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Nanoparticle-based vaccines offer a multivalent approach for antigen display, efficiently activating T and B cells in the lymph nodes. Among various nanoparticle design strategies, DNA nanotechnology offers an innovative alternative platform, featuring high modularity, spatial addressing, nanoscale regulation, high functional group density, and lower self-antigenicity. This review delves into the potential of DNA nanostructures as biomolecular scaffolds for antigen display, addressing: (1) immunological mechanisms behind nanovaccines and commonly used nanoparticles in their design, (2) techniques for characterizing protein NP-antigen complexes, (3) advancements in DNA nanotechnology and DNA-protein assembly approach, (4) strategies for precise antigen presentation on DNA scaffolds, and (5) current applications and future possibilities of DNA scaffolds in antigen display. This analysis aims to highlight the transformative potential of DNA nanoscaffolds in immunology and vaccinology. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Ming Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Jin Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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28
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Demir Gİ, Tekin A. NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond. J Chem Phys 2023; 159:244117. [PMID: 38153156 DOI: 10.1063/5.0176641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
A new non-empirical ab initio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary ab initio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level ab initio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.
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Affiliation(s)
- Gözde İniş Demir
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
| | - Adem Tekin
- Informatics Institute, Istanbul Technical University, 34469 Maslak, Istanbul, Türkiye
- Research Institute for Fundamental Sciences (TÜBİTAK-TBAE), Kocaeli, Türkiye
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29
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Sun X, Yao D, Liang H. pH-Controlled Resettable Modular DNA Strand-Displacement Circuits. NANO LETTERS 2023; 23:11540-11547. [PMID: 38085915 DOI: 10.1021/acs.nanolett.3c03265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Sophisticated dynamic molecular systems with diverse functions have been fabricated by using the fundamental tool of toehold-mediated strand displacement (TMSD) in the field of dynamic DNA nanotechnology. However, simple approaches to reset these TMSD-based dynamic systems are lacking due to the difficulty in creating kinetically favored pathways to implement the backward resetting reactions. Here, we develop a facile proton-driven strategy to achieve complete resetting of a modular DNA circuit by integrating a pH-responsive intermolecular CG-C+ triplex DNA and an i-motif DNA into the conventional DNA substrate. The pH-programmed strategy allows modular DNA components to specifically associate/dissociate to promote the forward/backward TMSD reactions, thereby enabling the modular DNA circuit to be repeatedly operated at a constant temperature without generating any DNA waste products. Leveraging this tractable approach, we further constructed two resettable DNA logic gates used for logical computation and two resettable catalytic DNA systems with good performance in signal transduction and amplification.
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Affiliation(s)
- Xiaoyun Sun
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Dongbao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Haojun Liang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Polymer Science and Engineering, School of Chemistry and Materials Science, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), University of Science and Technology of China, Hefei, Anhui 230026, China
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30
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Tang W, Tong T, Wang H, Lu X, Yang C, Wu Y, Wang Y, Liu J, Ding B. A DNA Origami-Based Gene Editing System for Efficient Gene Therapy in Vivo. Angew Chem Int Ed Engl 2023; 62:e202315093. [PMID: 37906116 DOI: 10.1002/anie.202315093] [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: 10/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
DNA nanostructures have played an important role in the development of novel drug delivery systems. Herein, we report a DNA origami-based CRISPR/Cas9 gene editing system for efficient gene therapy in vivo. In our design, a PAM-rich region precisely organized on the surface of DNA origami can easily recruit and load sgRNA/Cas9 complex by PAM-guided assembly and pre-designed DNA/RNA hybridization. After loading the sgRNA/Cas9 complex, the DNA origami can be further rolled up by the locking strands with a disulfide bond. With the incorporation of DNA aptamer and influenza hemagglutinin (HA) peptide, the cargo-loaded DNA origami can realize the targeted delivery and effective endosomal escape. After reduction by GSH, the opened DNA origami can release the sgRNA/Cas9 complex by RNase H cleavage to achieve a pronounced gene editing of a tumor-associated gene for gene therapy in vivo. This rationally developed DNA origami-based gene editing system presents a new avenue for the development of gene therapy.
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Affiliation(s)
- Wantao Tang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ting Tong
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Changping Yang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yushuai Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Yang GQ, Cai W, Zhang Z, Wang Y. Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System. ACS APPLIED BIO MATERIALS 2023; 6:5125-5144. [PMID: 38011318 DOI: 10.1021/acsabm.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.
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Affiliation(s)
- Gary Q Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Weibin Cai
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083, P. R. China
| | - Zhiwen Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Yujun Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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32
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Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nat Commun 2023; 14:8328. [PMID: 38097568 PMCID: PMC10721878 DOI: 10.1038/s41467-023-43168-4] [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: 12/31/2022] [Accepted: 11/02/2023] [Indexed: 12/17/2023] Open
Abstract
The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.
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Affiliation(s)
- Agnese I Curatolo
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Ofer Kimchi
- Lewis-Sigler Institute, Princeton University, Princeton, NJ, 08544, USA
| | - Carl P Goodrich
- Institute of Science and Technology Austria, A-3400, Klosterneuburg, Austria
| | - Ryan K Krueger
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
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33
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Zhou F, Ni H, Zhu G, Bershadsky L, Sha R, Seeman NC, Chaikin PM. Toward three-dimensional DNA industrial nanorobots. Sci Robot 2023; 8:eadf1274. [PMID: 38055806 DOI: 10.1126/scirobotics.adf1274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Nanoscale industrial robots have potential as manufacturing platforms and are capable of automatically performing repetitive tasks to handle and produce nanomaterials with consistent precision and accuracy. We demonstrate a DNA industrial nanorobot that fabricates a three-dimensional (3D), optically active chiral structure from optically inactive parts. By making use of externally controlled temperature and ultraviolet (UV) light, our programmable robot, ~100 nanometers in size, grabs different parts, positions and aligns them so that they can be welded, releases the construct, and returns to its original configuration ready for its next operation. Our robot can also self-replicate its 3D structure and functions, surpassing single-step templating (restricted to two dimensions) by using folding to access the third dimension and more degrees of freedom. Our introduction of multiple-axis precise folding and positioning as a tool/technology for nanomanufacturing will open the door to more complex and useful nano- and microdevices.
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Affiliation(s)
- Feng Zhou
- Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, China
- Ningbo Cixi Institute of Biomedical Engineering, Ningbo, China
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, New York University, New York, NY, USA
| | - Heng Ni
- Department of Physics, New York University, New York, NY, USA
| | - Guolong Zhu
- Department of Physics, New York University, New York, NY, USA
- Department of Chemistry, Biochemistry, and Physics, Fairleigh Dickinson University, Madison, NJ, USA
| | - Lev Bershadsky
- Department of Physics, New York University, New York, NY, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, USA
| | | | - Paul M Chaikin
- Department of Physics, New York University, New York, NY, USA
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34
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Kim JE, Kang JH, Kwon WH, Lee I, Park SJ, Kim CH, Jeong WJ, Choi JS, Kim K. Self-assembling biomolecules for biosensor applications. Biomater Res 2023; 27:127. [PMID: 38053161 PMCID: PMC10696764 DOI: 10.1186/s40824-023-00466-8] [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: 10/01/2023] [Accepted: 11/22/2023] [Indexed: 12/07/2023] Open
Abstract
Molecular self-assembly has received considerable attention in biomedical fields as a simple and effective method for developing biomolecular nanostructures. Self-assembled nanostructures can exhibit high binding affinity and selectivity by displaying multiple ligands/receptors on their surface. In addition, the use of supramolecular structure change upon binding is an intriguing approach to generate binding signal. Therefore, many self-assembled nanostructure-based biosensors have been developed over the past decades, using various biomolecules (e.g., peptides, DNA, RNA, lipids) and their combinations with non-biological substances. In this review, we provide an overview of recent developments in the design and fabrication of self-assembling biomolecules for biosensing. Furthermore, we discuss representative electrochemical biosensing platforms which convert the biochemical reactions of those biomolecules into electrical signals (e.g., voltage, ampere, potential difference, impedance) to contribute to detect targets. This paper also highlights the successful outcomes of self-assembling biomolecules in biosensor applications and discusses the challenges that this promising technology needs to overcome for more widespread use.
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Affiliation(s)
- Ji-Eun Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea
| | - Jeon Hyeong Kang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Woo Hyun Kwon
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
- Department of Materials Science and Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Inseo Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | - Sang Jun Park
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Chun-Ho Kim
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea
| | - Woo-Jin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
- Department of Biological Engineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Jun Shik Choi
- Laboratory of Tissue Engineering, Korea Institute of Radiological and Medical Sciences, Seoul, 01812, Republic of Korea.
| | - Kyobum Kim
- Department of Chemical & Biochemical Engineering, Dongguk University, Seoul, 04620, Republic of Korea.
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35
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Martynenko IV, Erber E, Ruider V, Dass M, Posnjak G, Yin X, Altpeter P, Liedl T. Site-directed placement of three-dimensional DNA origami. NATURE NANOTECHNOLOGY 2023; 18:1456-1462. [PMID: 37640908 DOI: 10.1038/s41565-023-01487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.
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Affiliation(s)
- Irina V Martynenko
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| | - Elisabeth Erber
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Xin Yin
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Altpeter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
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36
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Yang Y, Lu Q, Chen Y, DeLuca M, Arya G, Ke Y, Zauscher S. Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures. Angew Chem Int Ed Engl 2023; 62:e202311727. [PMID: 37820028 DOI: 10.1002/anie.202311727] [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: 08/24/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to "smart" functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.
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Affiliation(s)
- Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qinyi Lu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Yu Chen
- University Program in Materials Science and Engineering, Duke University, Durham, NC 27708, USA
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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37
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Feng F, Xiao SJ. Structural Description of Chiral E-Tiling DNA Nanotubes with the Chiral Indices (n,m) and Handedness Defined by Microscopic Imaging. Chembiochem 2023; 24:e202300460. [PMID: 37675822 DOI: 10.1002/cbic.202300460] [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: 06/28/2023] [Revised: 08/22/2023] [Indexed: 09/08/2023]
Abstract
In structural DNA nanotechnology, E-tiling DNA nanotubes are evidenced to be homogeneous in diameter and thus have great potential in biomedical applications such as cellular transport and communication, transmembrane ion/molecule channeling, and drug delivery. However, a precise structural description of chiral DNA nanotubes with chiral parameters was lacking, thus greatly hindering their application breadth and depth, until we recently raised and partly solved this problem. In this perspective, we summarize recent progress in defining the chiral indices and handedness of E-tiling DNA nanotubes by microscopic imaging, especially atomic force microscopy (AFM) imaging. Such a detailed understanding of the chiral structures of E-tiling DNA nanotubes will be very helpful in the future, on the one hand for engineering DNA nanostructures precisely, and, on the other, for realizing specific physicochemical properties and biological functions successfully.
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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, 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
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38
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Alarcón-Correa M, Kilwing L, Peter F, Liedl T, Fischer P. Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide. Chemphyschem 2023; 24:e202300294. [PMID: 37640688 DOI: 10.1002/cphc.202300294] [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: 04/24/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.
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Affiliation(s)
- Mariana Alarcón-Correa
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Florian Peter
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Peer Fischer
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
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39
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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Wu T, Wang H, Tian R, Guo S, Liao Y, Liu J, Ding B. A DNA Origami-based Bactericide for Efficient Healing of Infected Wounds. Angew Chem Int Ed Engl 2023; 62:e202311698. [PMID: 37755438 DOI: 10.1002/anie.202311698] [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: 08/11/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
Bacteria infection is a significant obstacle in the clinical treatment of exposed wounds facing widespread pathogens. Herein, we report a DNA origami-based bactericide for efficient anti-infection therapy of infected wounds in vivo. In our design, abundant DNAzymes (G4/hemin) can be precisely organized on the DNA origami for controllable generation of reactive oxygen species (ROS) to break bacterial membranes. After the destruction of the membrane, broad-spectrum antibiotic levofloxacin (LEV, loaded in the DNA origami through interaction with DNA duplex) can be easily delivered into the bacteria for successful sterilization. With the incorporation of DNA aptamer targeting bacterial peptidoglycan, the DNA origami-based bactericide can achieve targeted and combined antibacterial therapy for efficiently promoting the healing of infected wounds. This tailored DNA origami-based nanoplatform provides a new strategy for the treatment of infectious diseases in vivo.
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Affiliation(s)
- Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, 100190, Beijing, China
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, 510091, Guangzhou, China
- School of Pharmaceutical Sciences, Hainan Medical University, 570228, Haikou, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, 100190, Beijing, China
| | - Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shuang Guo
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, 510091, Guangzhou, China
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, 510091, Guangzhou, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, 100190, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
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41
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Habteyes TG, Westphal ER, Plackowski KM, Kotula PG, Meyerson ML, White SL, Corbin WC, Ghosh K, Grey JK. Hierarchical Self-Assembly of Carbon Dots into High-Aspect-Ratio Nanowires. NANO LETTERS 2023; 23:9474-9481. [PMID: 37831934 DOI: 10.1021/acs.nanolett.3c02977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
We report a spontaneous and hierarchical self-assembly mechanism of carbon dots prepared from citric acid and urea into nanowire structures with large aspect ratios (>50). Scattering-type scanning near-field optical microscopy (s-SNOM) with broadly tunable mid-IR excitation was used to interrogate details of the self-assembly process by generating nanoscopic chemical maps of local wire morphology and composition. s-SNOM images capture the evolution of wire formation and the complex interplay between different chemical constituents directing assembly over the nano- to microscopic length scales. We propose that residual citrate promotes tautomerization of melamine surface functionalities to produce supramolecular shape synthons comprised of melamine-cyanurate adducts capable of forming long-range and highly directional hydrogen-bonding networks. This intrinsic, heterogeneity-driven self-assembly mechanism reflects synergistic combinations of high chemical specificity and long-range cooperativity that may be harnessed to reproducibly fabricate functional structures on arbitrary surfaces.
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Affiliation(s)
- Terefe G Habteyes
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Eric R Westphal
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - Kenneth M Plackowski
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
- Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Paul G Kotula
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - Melissa L Meyerson
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - Stephanie L White
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - W Cody Corbin
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - Koushik Ghosh
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
| | - John K Grey
- Sandia National Laboratories, 1515 Eubank Drive SE, Albuquerque, New Mexico 87185, United States
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42
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Shrivastava A, Du Y, Adepu HK, Li R, Madhvacharyula AS, Swett AA, Choi JH. Motility of Synthetic Cells from Engineered Lipids. ACS Synth Biol 2023; 12:2789-2801. [PMID: 37729546 DOI: 10.1021/acssynbio.3c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Synthetic cells are artificial systems that resemble natural cells. Significant efforts have been made over the years to construct synthetic protocells that can mimic biological mechanisms and perform various complex processes. These include compartmentalization, metabolism, energy supply, communication, and gene reproduction. Cell motility is also of great importance, as nature uses elegant mechanisms for intracellular trafficking, immune response, and embryogenesis. In this review, we discuss the motility of synthetic cells made from lipid vesicles and relevant molecular mechanisms. Synthetic cell motion may be classified into surface-based or solution-based depending on whether it involves interactions with surfaces or movement in fluids. Collective migration behaviors have also been demonstrated. The swarm motion requires additional mechanisms for intercellular signaling and directional motility that enable communication and coordination among the synthetic vesicles. In addition, intracellular trafficking for molecular transport has been reconstituted in minimal cells with the help of DNA nanotechnology. These efforts demonstrate synthetic cells that can move, detect, respond, and interact. We envision that new developments in protocell motility will enhance our understanding of biological processes and be instrumental in bioengineering and therapeutic applications.
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Affiliation(s)
- Aishwary Shrivastava
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Ruixin Li
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Alexander A Swett
- School of Mechanical Engineering, Purdue University, Neil Armstrong Hall of Engineering, 701 W. Stadium Avenue, West Lafayette, Indiana 47907, United States
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, 585 Purdue Mall, West Lafayette, Indiana 47907, United States
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43
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Tobiason M, Yurke B, Hughes WL. Generation of DNA oligomers with similar chemical kinetics via in-silico optimization. Commun Chem 2023; 6:226. [PMID: 37853171 PMCID: PMC10584830 DOI: 10.1038/s42004-023-01026-w] [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: 02/22/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023] Open
Abstract
Networks of interacting DNA oligomers are useful for applications such as biomarker detection, targeted drug delivery, information storage, and photonic information processing. However, differences in the chemical kinetics of hybridization reactions, referred to as kinetic dispersion, can be problematic for some applications. Here, it is found that limiting unnecessary stretches of Watson-Crick base pairing, referred to as unnecessary duplexes, can yield exceptionally low kinetic dispersions. Hybridization kinetics can be affected by unnecessary intra-oligomer duplexes containing only 2 base-pairs, and such duplexes explain up to 94% of previously reported kinetic dispersion. As a general design rule, it is recommended that unnecessary intra-oligomer duplexes larger than 2 base-pairs and unnecessary inter-oligomer duplexes larger than 7 base-pairs be avoided. Unnecessary duplexes typically scale exponentially with network size, and nearly all networks contain unnecessary duplexes substantial enough to affect hybridization kinetics. A new method for generating networks which utilizes in-silico optimization to mitigate unnecessary duplexes is proposed and demonstrated to reduce in-vitro kinetic dispersions as much as 96%. The limitations of the new design rule and generation method are evaluated in-silico by creating new oligomers for several designs, including three previously programmed reactions and one previously engineered structure.
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Affiliation(s)
- Michael Tobiason
- Department of Computer Science, Boise State University, Boise, ID, USA.
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID, USA
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID, USA
| | - William L Hughes
- School of Engineering, University of British Columbia Okanagan Campus, Kelowna, BC, Canada.
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44
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Chen Y, Zhao M, Ouyang Y, Zhang S, Liu Z, Wang K, Zhang Z, Liu Y, Yang C, Sun W, Shen J, Zhu Z. Biotemplated precise assembly approach toward ultra-scaled high-performance electronics. Nat Protoc 2023; 18:2975-2997. [PMID: 37670036 DOI: 10.1038/s41596-023-00870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/08/2023] [Indexed: 09/07/2023]
Abstract
Structural DNA nanotechnology can be programmed into complex designer structures with molecular precision for directing a wide range of inorganic and biological materials. However, the use of DNA-templated approaches for the fabrication and performance requirements of ultra-scaled semiconductor electronics is limited by its assembly disorder and destructive interface composition. In this protocol, using carbon nanotubes (CNTs) as model semiconductors, we provide a stepwise process to build ultra-scaled, high-performance field-effect transistors (FETs) from micron-scale three-dimensional DNA templates. We apply the approach to assemble CNT arrays with uniform pitches scaled between 24.1 and 10.4 nm with yields of more than 95%, which exceeds the resolution limits of conventional lithography. To achieve highly clean CNT interfaces, we detail a rinsing-after-fixing step to remove residual DNA template and salt contaminations present around the contact and the channel regions, without modifying the alignment of the CNT arrays. The DNA-templated CNT FETs display both high on-state current (4-15 μA per CNT) and small subthreshold swing (60-100 mV per decade), which are superior to previous examples of biotemplated electronics and match the performance metrics of high-performance, silicon-based electronics. The scalable assembly of defect-free three-dimensional DNA templates requires 1 week and the CNT arrays can be synthesized within half a day. The interface engineering requires 1-2 d, while the fabrication of high-performance FET and logic gate circuits requires 2-4 d. The structural and performance characterizations of molecular-precise DNA self-assembly and high-performance electronics requires 1-2 d. The protocol is suited for users with expertise in DNA nanotechnology and semiconductor electronics.
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Affiliation(s)
- Yahong Chen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Mengyu Zhao
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yifan Ouyang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Suhui Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zhihan Liu
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Zhaoxuan Zhang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China
| | - Yingxia Liu
- Department of Systems Engineering, City University of Hong Kong, Hong Kong, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
- Zhangjiang Laboratory, Shanghai, China.
| | - Jie Shen
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, School of Materials Science and Engineering, Peking University, Beijing, China.
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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45
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Mohammad H, Anantram MP. Charge transport through DNA with energy-dependent decoherence. Phys Rev E 2023; 108:044403. [PMID: 37978586 DOI: 10.1103/physreve.108.044403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.
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Affiliation(s)
- Hashem Mohammad
- Department of Electrical Engineering, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98195, USA
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46
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Ye T, Liu X, Zhong X, Yan R, Shi P. Nongenetic surface engineering of mesenchymal stromal cells with polyvalent antibodies to enhance targeting efficiency. Nat Commun 2023; 14:5806. [PMID: 37726299 PMCID: PMC10509227 DOI: 10.1038/s41467-023-41609-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023] Open
Abstract
Systemic infusion is a prevalent administration method for mesenchymal stromal cells (MSCs) in clinical trials. However, the inability to deliver a large number of therapeutic cells to diseased tissue is a substantial barrier. Here, we demonstrate that surface engineering of MSCs with polyvalent antibodies can effectively improve the targeting efficiency of MSCs to diseased tissue. The polyvalent antibody is directly synthesized on the cell surface via DNA template-directed biomolecule assembly. The data show that engineered MSCs exhibit superior adhesion to inflamed endothelium in vitro and in vivo. In female mouse models of acute inflammation and inflammatory bowel disease, engineered MSCs show enhanced targeting efficiency and therapeutic efficacy in damaged tissues. Notably, the entire procedure for polyvalent functionalization only requires the simple mixing of cells and solutions under physiological conditions within a few hours, which significantly reduces preparation processes and manufacturing costs and minimizes the impact on the cells. Thus, our study provides a strategy for improved MSC-based regenerative medicine.
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Affiliation(s)
- Tenghui Ye
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Xi Liu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Xianghua Zhong
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Ran Yan
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China
| | - Peng Shi
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, 511442, PR China.
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, PR China.
- Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou, 510006, PR China.
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, 510006, PR China.
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Zhang Z, Jin J, Paluzzi VE, Jin Z, Wen Y, Huang CZ, Li CM, Mao C, Zuo H. AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing. J Am Chem Soc 2023; 145:19503-19507. [PMID: 37638713 DOI: 10.1021/jacs.3c06260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jin Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuoer Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuandong Wen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | | | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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Lee H, Noh H. Advancements in Nanogels for Enhanced Ocular Drug Delivery: Cutting-Edge Strategies to Overcome Eye Barriers. Gels 2023; 9:718. [PMID: 37754399 PMCID: PMC10529109 DOI: 10.3390/gels9090718] [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: 08/14/2023] [Revised: 08/29/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023] Open
Abstract
Nanomedicine in gel or particle formation holds considerable potential for enhancing passive and active targeting within ocular drug delivery systems. The complex barriers of the eye, exemplified by the intricate network of closely connected tissue structures, pose significant challenges for drug administration. Leveraging the capability of engineered nanomedicine offers a promising approach to enhance drug penetration, particularly through active targeting agents such as protein peptides and aptamers, which facilitate targeted release and heightened bioavailability. Simultaneously, DNA carriers have emerged as a cutting-edge class of active-targeting structures, connecting active targeting agents and illustrating their potential in ocular drug delivery applications. This review aims to consolidate recent findings regarding the optimization of various nanoparticles, i.e., hydrogel-based systems, incorporating both passive and active targeting agents for ocular drug delivery, thereby identifying novel mechanisms and strategies. Furthermore, the review delves into the potential application of DNA nanostructures, exploring their role in the development of targeted drug delivery approaches within the field of ocular therapy.
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Affiliation(s)
| | - Hyeran Noh
- Department of Optometry, Seoul National University of Science and Technology, Gongnung-ro 232, Nowon-gu, Seoul 01811, Republic of Korea;
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He L, Charron M, Mensing P, Briggs K, Adams J, de Haan H, Tabard-Cossa V. DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield. NANOSCALE 2023; 15:14043-14054. [PMID: 37580994 DOI: 10.1039/d3nr01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Due to their programmability via specific base pairing, self-assembled DNA origami structures have proven to be useful for a wide variety of applications, including diagnostics, molecular computation, drug delivery, and therapeutics. Measuring and characterizing these structures is therefore of great interest and an important part of quality control. Here, we show the extent to which DNA nanostructures can be characterized by a solid-state nanopore; a non-destructive, label-free, single-molecule sensor capable of electrically detecting and characterizing charged biomolecules. We demonstrate that in addition to geometrical dimensions, nanopore sensing can provide information on the mechanical properties, assembly yield, and stability of DNA nanostructures. For this work, we use a model structure consisting of a 3 helix-bundle (3HB), i.e. three interconnected DNA double helices using a M13 scaffold folded twice on itself by short DNA staple strands, and translocate it through solid-state nanopores fabricated by controlled breakdown. We present detailed analysis of the passage characteristics of 3HB structures through nanopores under different experimental conditions which suggest that segments of locally higher flexibility are present along the nanostructure contour that allow for the otherwise rigid 3HB to fold inside nanopores. By characterizing partially melted 3HB structures, we find that locally flexible segments are likely due to short staple oligomers missing from the fully assembled structure. The 3HB used herein is a prototypical example to establish nanopores as a sensitive, non-destructive, and label-free alternative to conventional techniques such as gel electrophoresis with which to characterize DNA nanostructures.
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Affiliation(s)
- Liqun He
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Martin Charron
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Philipp Mensing
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
| | - Jonathan Adams
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
| | - Hendrick de Haan
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, Canada
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Wang J, Li P, Wang C, Liu N, Xing D. Molecularly or atomically precise nanostructures for bio-applications: how far have we come? MATERIALS HORIZONS 2023; 10:3304-3324. [PMID: 37365977 DOI: 10.1039/d3mh00574g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
A huge variety of nanostructures are promising for biomedical applications, but only a few have been practically applied. Among the various reasons, the limited structural preciseness is a critical one, as it increases the difficulty in product quality control, accurate dosing, and ensuring the repeatability of material performance. Constructing nanoparticles with molecule-like preciseness is becoming a new research field. In this review, we focus on the artificial nanomaterials that can currently be molecularly or atomically precise, including DNA nanostructures, some metallic nanoclusters, dendrimer nanoparticles and carbon nanostructures, describing their syntheses, bio-applications and limitations, in view of up-to-date studies. A perspective on their potential for clinical translation is also given. This review is expected to provide a particular rationale for the future design of nanomedicines.
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Affiliation(s)
- Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ping Li
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ning Liu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
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