1
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Hayakawa D, Videbæk TE, Grason GM, Rogers WB. Symmetry-Guided Inverse Design of Self-Assembling Multiscale DNA Origami Tilings. ACS NANO 2024; 18:19169-19178. [PMID: 38981100 PMCID: PMC11271658 DOI: 10.1021/acsnano.4c04515] [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: 04/05/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Recent advances enable the creation of nanoscale building blocks with complex geometries and interaction specificities for self-assembly. This nearly boundless design space necessitates design principles for defining the mutual interactions between multiple particle species to target a user-specified complex structure or pattern. In this article, we develop a symmetry-based method to generate the interaction matrices that specify the assembly of two-dimensional tilings, which we illustrate using equilateral triangles. By exploiting the allowed 2D symmetries, we develop an algorithmic approach by which any periodic 2D tiling can be generated from an arbitrarily large number of subunit species, notably addressing an unmet challenge of engineering 2D crystals with periodicities that can be arbitrarily larger than the subunit size. To demonstrate the utility of our design approach, we encode specific interactions between triangular subunits synthesized by DNA origami and show that we can guide their self-assembly into tilings with a wide variety of symmetries, using up to 12 unique species of triangles. By conjugating specific triangles with gold nanoparticles, we fabricate gold-nanoparticle supracrystals whose lattice parameter spans up to 300 nm. Finally, to generate economical design rules, we compare the design economy of various tilings. In particular, we show that (1) higher symmetries allow assembly of larger unit cells with fewer subunits and (2) linear supracrystals can be designed more economically using linear primitive unit cells. This work provides a simple algorithmic approach to designing periodic assemblies, aiding in the multiscale assembly of supracrystals of nanostructured "meta-atoms" with engineered plasmonic functions.
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Affiliation(s)
- Daichi Hayakawa
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Thomas E. Videbæk
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Gregory M. Grason
- Department
of Polymer Science and Engineering, University
of Massachusetts, Amherst, Massachusetts 01003, United States
| | - W. Benjamin Rogers
- Martin
A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
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2
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Wu Y, Luo L, Hao Z, Liu D. DNA-based nanostructures for RNA delivery. MEDICAL REVIEW (2021) 2024; 4:207-224. [PMID: 38919398 PMCID: PMC11195427 DOI: 10.1515/mr-2023-0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/28/2024] [Indexed: 06/27/2024]
Abstract
RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.
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Affiliation(s)
- Yuanyuan Wu
- Beijing SupraCirc Biotechnology Co., Ltd, Beijing, China
| | - Liangzhi Luo
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Ziyang Hao
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Dongsheng Liu
- Department of Chemistry, Engineering Research Center of Advanced Rare Earth Materials, (Ministry of Education), Tsinghua University, Beijing, China
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3
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Kang H, Yang Y, Wei B. Synthetic molecular switches driven by DNA-modifying enzymes. Nat Commun 2024; 15:3781. [PMID: 38710688 DOI: 10.1038/s41467-024-47742-2] [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: 08/08/2023] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Taking inspiration from natural systems, in which molecular switches are ubiquitous in the biochemistry regulatory network, we aim to design and construct synthetic molecular switches driven by DNA-modifying enzymes, such as DNA polymerase and nicking endonuclease. The enzymatic treatments on our synthetic DNA constructs controllably switch ON or OFF the sticky end cohesion and in turn cascade to the structural association or disassociation. Here we showcase the concept in multiple DNA nanostructure systems with robust assembly/disassembly performance. The switch mechanisms are first illustrated in minimalist systems with a few DNA strands. Then the ON/OFF switches are realized in complex DNA lattice and origami systems with designated morphological changes responsive to the specific enzymatic treatments.
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Affiliation(s)
- Hong Kang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuexuan Yang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
| | - Bryan Wei
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
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4
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Chau C, Mohanan G, Macaulay I, Actis P, Wälti C. Automated Purification of DNA Origami with SPRI Beads. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308776. [PMID: 38054620 DOI: 10.1002/smll.202308776] [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: 10/16/2023] [Indexed: 12/07/2023]
Abstract
DNA origami synthesis is a well-established technique with wide-ranging applications. In most cases, the synthesized origami must be purified to remove excess materials such as DNA oligos and other functional molecules. While several purification techniques are routinely used, all have limitations, and cannot be integrated with robotic systems. Here the use of solid-phase reversible immobilization (SPRI) beads as a scalable, high-throughput, and automatable method to purify DNA origami is demonstrated. Not only can this method remove unreacted oligos and biomolecules with yields comparable to existing methods while maintaining the high structural integrity of the origami, but it can also be integrated into an automated workflow to purify simultaneously large numbers and quantities of samples. It is envisioned that the SPRI beads purification method will improve the scalability of DNA nanostructures synthesis both for research and commercial applications.
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Affiliation(s)
- Chalmers Chau
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, NR1 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, NR4 7TJ, UK
| | - Paolo Actis
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Christoph Wälti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
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5
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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6
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Liu Y, Dai Z, Xie X, Li B, Jia S, Li Q, Li M, Fan C, Liu X. Spacer-Programmed Two-Dimensional DNA Origami Assembly. J Am Chem Soc 2024; 146:5461-5469. [PMID: 38355136 DOI: 10.1021/jacs.3c13180] [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: 02/16/2024]
Abstract
Two-dimensional (2D) DNA origami assembly represents a powerful approach to the programmable design and construction of advanced 2D materials. Within the context of hybridization-mediated 2D DNA origami assembly, DNA spacers play a pivotal role as essential connectors between sticky-end regions and DNA origami units. Here, we demonstrated that programming the spacer length, which determines the binding radius of DNA origami units, could effectively tune sticky-end hybridization reactions to produce distinct 2D DNA origami arrays. Using DNA-PAINT super-resolution imaging, we unveiled the significant impact of spacer length on the hybridization efficiency of sticky ends for assembling square DNA origami (SDO) units. We also found that the assembly efficiency and pattern diversity of 2D DNA origami assemblies were critically dependent on the spacer length. Remarkably, we realized a near-unity yield of ∼98% for the assembly of SDO trimers and tetramers via this spacer-programmed strategy. At last, we revealed that spacer lengths and thermodynamic fluctuations of SDO are positively correlated, using molecular dynamics simulations. Our study thus paves the way for the precision assembly of DNA nanostructures toward higher complexity.
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Affiliation(s)
- Yongjun Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zheze Dai
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bochen Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sisi Jia
- Zhangjiang Laboratory, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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7
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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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8
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Tang Y, Liu H, Wang Q, Qi X, Yu L, Šulc P, Zhang F, Yan H, Jiang S. DNA Origami Tessellations. J Am Chem Soc 2023. [PMID: 37329284 DOI: 10.1021/jacs.3c03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Molecular tessellation research aims to elucidate the underlying principles that govern intricate patterns in nature and to leverage these principles to create precise and ordered structures across multiple scales, thereby facilitating the emergence of novel functionalities. DNA origami nanostructures are excellent building blocks for constructing tessellation patterns. However, the size and complexity of DNA origami tessellation systems are currently limited by several unexplored factors relevant to the accuracy of essential design parameters, the applicability of design strategies, and the compatibility between different tiles. Here, we present a general method for creating DNA origami tiles that grow into tessellation patterns with micrometer-scale order and nanometer-scale precision. Interhelical distance (D) was identified as a critical design parameter determining tile conformation and tessellation outcome. Finely tuned D facilitated the accurate geometric design of monomer tiles with minimized curvature and improved tessellation capability, enabling the formation of single-crystalline lattices ranging from tens to hundreds of square micrometers. The general applicability of the design method was demonstrated by 9 tile geometries, 15 unique tile designs, and 12 tessellation patterns covering Platonic, Laves, and Archimedean tilings. Particularly, we took two strategies to increase the complexity of DNA origami tessellation, including reducing the symmetry of monomer tiles and coassembling tiles of different geometries. Both yielded various tiling patterns that rivaled Platonic tilings in size and quality, indicating the robustness of the optimized tessellation system. This study will promote DNA-templated, programmable molecular and material patterning and open up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
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Affiliation(s)
- Yue Tang
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Hao Liu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaodong Qi
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Lu Yu
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Fei Zhang
- Department of Chemistry, School of Arts & Sciences-Newark, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
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9
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Abstract
DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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10
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Sarraf N, Rodriguez KR, Qian L. Modular reconfiguration of DNA origami assemblies using tile displacement. Sci Robot 2023; 8:eadf1511. [PMID: 37099635 DOI: 10.1126/scirobotics.adf1511] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The power of natural evolution lies in the adaptability of biological organisms but is constrained by the time scale of genetics and reproduction. Engineeringartificial molecular machines should not only include adaptability as a core feature but also apply it within a larger design space and at a faster time scale. A lesson from engineering electromechanical robots is that modular robots can perform diverse functions through self-reconfiguration, a large-scale form of adaptation. Molecular machines made of modular, reconfigurable components may form the basis for dynamic self-reprogramming in future synthetic cells. To achieve modular reconfiguration in DNA origami assemblies, we previously developed a tile displacement mechanism in which an invader tile replaces another tile in an array with controlled kinetics. Here, we establish design principles for simultaneous reconfigurations in tile assemblies using complex invaders with distinct shapes. We present toehold and branch migration domain configurations that expand the design space of tile displacement reactions by two orders of magnitude. We demonstrate the construction of multitile invaders with fixed and variable sizes and controlled size distributions. We investigate the growth of three-dimensional (3D) barrel structures with variable cross sections and introduce a mechanism for reconfiguring them into 2D structures. Last, we show an example of a sword-shaped assembly transforming into a snake-shaped assembly, illustrating two independent tile displacement reactions occurring concurrently with minimum cross-talk. This work serves as a proof of concept that tile displacement could be a fundamental mechanism for modular reconfiguration robust to temperature and tile concentration.
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Affiliation(s)
- Namita Sarraf
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kellen R Rodriguez
- Business Economics and Management, California Institute of Technology, Pasadena, CA 91125, USA
- Astrophysics, California Institute of Technology, Pasadena, CA 91125, USA
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lulu Qian
- Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
- Computer Science, California Institute of Technology, Pasadena, CA 91125, USA
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11
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Benson E, Bath J. Reconfigurable self-assembled DNA devices. Sci Robot 2023; 8:eadh8148. [PMID: 37099637 DOI: 10.1126/scirobotics.adh8148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Modular reconfigurable systems can be achieved with DNA origami, demonstrating the potential to generate molecular robots.
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Affiliation(s)
- Erik Benson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
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12
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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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13
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Wang J, Yuan J, Liu J, Zou H, Yang L, Chen H, Qu X. Point-and-shoot Strategy based on Enzyme-assisted DNA "Paper-Cutting" to Construct Arbitrary Planar DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2207622. [PMID: 37021738 DOI: 10.1002/smll.202207622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/04/2023] [Indexed: 06/19/2023]
Abstract
DNA self-assembly provides a "bottom-up" route to fabricating complex shapes on the nanometer scale. However, each structure needs to be designed separately and carried out by professionally trained technicians, which seriously restricts its development and application. Herein, a point-and-shoot strategy based on enzyme-assisted DNA "paper-cutting" to construct planar DNA nanostructures using the same DNA origami as the template is reported. Precisely modeling the shapes with high precision in the strategy based on each staple strand of the desired shape structure hybridizes with its nearest neighbor fragments from the long scaffold strand. As a result, some planar DNA nanostructures by one-pot annealing the long scaffold strand and selected staple strands is constructed. The point-and-shoot strategy of avoiding DNA origami staple strands' re-designing based on different shapes breaks through the shape complexity limitation of the planar DNA nanostructures and enhances the simplicity of design and operation. Overall, the strategy's simple operability and great generality enable it to act as a candidate tool for manufacturing DNA nanostructures.
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Affiliation(s)
- Jingwen Wang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Guangdong, 518107, China
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, 361005, China
| | - Junjie Yuan
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Guangdong, 518107, China
| | - Jiajia Liu
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, 361005, China
| | - Haixia Zou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Guangdong, 518107, China
| | - Lin Yang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Guangdong, 518107, China
| | - Hong Chen
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, 361005, China
| | - Xiangmeng Qu
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Guangdong, 518107, China
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14
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Xie C, Chen Z, Chen K, Hu Y, Pan L. Regulating the Polymerization of DNA Structures via Allosteric Control of Monomers. ACS NANO 2023; 17:1505-1510. [PMID: 36633930 DOI: 10.1021/acsnano.2c10456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Regulation of self-assembly is crucial in constructing structural biomaterials, such as tunable DNA nanostructures. Traditional tuning of self-assembled DNA nanostructures was mainly conducted by introducing external stimuli after the assembly process. Here, we explored the allosteric assembly of DNA structures via introducing external stimuli during the assembly process to produce structurally heterogeneous polymerization products. We demonstrated that ethidium bromide (EB), a DNA intercalator, could increase the left-handed out-of-plane chirality of curved DNA structures. Then, EB and double strands were introduced as competing stimuli to transform monomers into allosteric conformations, leading to three different polymerization products. The steric trap between different polymerization products promoted the polymerized structures to keep their geometric properties, like chirality, under varying intensity of external stimuli. Our strategy harnesses allosteric effects for assembly of DNA-based materials and is expected to expand the design space for advanced control in synthetic materials.
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Affiliation(s)
- Chun Xie
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Zhekun Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Kuiting Chen
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, 050043 Hebei, China
| | - Linqiang Pan
- Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China, School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
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15
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Suzuki Y, Sugiyama H, Endo M. Two-Dimensional DNA Origami Lattices Assembled on Lipid Bilayer Membranes. Methods Mol Biol 2023; 2639:83-90. [PMID: 37166712 DOI: 10.1007/978-1-0716-3028-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Molecular self-assembly has attracted much attention as a method to create novel supramolecular architectures. The scaffolded DNA origami method has enabled the construction of almost arbitrarily shaped DNA nanostructures, which can be further used as components of higher-order architectures. Here, we describe a method to construct and visualize two-dimensional (2D) lattices self-assembled from DNA origami tiles on lipid bilayer membranes. The weak adsorption of DNA origami tiles onto the mica-supported lipid bilayer allows their lateral diffusion along the surface, facilitating interactions among the tiles to assemble and form large 2D lattices. Depending on the design (i.e., shape, size, and interactions with each other) of DNA origami tiles, a variety of 2D lattices made of DNA are constructed.
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Affiliation(s)
- Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aoba-ku, Sendai, Japan
- Department of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan.
- Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka, Japan.
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16
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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17
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Dreher Y, Fichtler J, Karfusehr C, Jahnke K, Xin Y, Keller A, Göpfrich K. Genotype-phenotype mapping with polyominos made from DNA origami tiles. Biophys J 2022; 121:4840-4848. [PMID: 36088535 PMCID: PMC9811662 DOI: 10.1016/j.bpj.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/18/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023] Open
Abstract
The correlation between genetic information and characteristics of a living cell-its genotype and its phenotype-constitutes the basis of genetics. Here, we experimentally realize a primitive form of genotype-phenotype mapping with DNA origami. The DNA origami can polymerize into two-dimensional lattices (phenotype) via blunt-end stacking facilitated by edge staples at the seam of the planar DNA origami. There are 80 binding positions for edge staples, which allow us to translate an 80-bit long binary code (genotype) onto the DNA origami. The presence of an edge staple thus corresponds to a "1" and its absence to a "0." The interactions of our DNA-based system can be reproduced by a polyomino model. Polyomino growth simulations qualitatively reproduce our experimental results. We show that not only the absolute number of base stacks but also their sequence position determine the cluster size and correlation length of the orientation of single DNA origami within the cluster. Importantly, the mutation of a few bits can result in major morphology changes of the DNA origami cluster, while more often, major sequence changes have no impact. Our experimental realization of a correlation between binary information ("genotype") and cluster morphology ("phenotype") thus reproduces key properties of genotype-phenotype maps known from living systems.
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Affiliation(s)
- Yannik Dreher
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Julius Fichtler
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany
| | - Christoph Karfusehr
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Max Planck School Matter to Life, Heidelberg University, Heidelberg, Germany
| | - Kevin Jahnke
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany
| | - Yang Xin
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Paderborn, Germany
| | - Kerstin Göpfrich
- Max Planck Institute for Medical Research, Biophysical Engineering Group, Heidelberg, Germany; Department of Physics and Astronomy, Heidelberg University, Heidelberg, Germany.
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18
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Geometrically programmed self-limited assembly of tubules using DNA origami colloids. Proc Natl Acad Sci U S A 2022; 119:e2207902119. [PMID: 36252043 PMCID: PMC9618141 DOI: 10.1073/pnas.2207902119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nature is replete with self-assembled materials that have one or more self-limited dimensions, including shells, tubules, and fibers. Despite significant advances in making nanometer- and micrometer-scale subunits, the programmable assembly of similar self-limiting architectures from synthetic components has remained largely out of reach. In this article, we create geometrically programmed subunits using DNA origami and study their assembly into tubules with a self-limited width. We show that the average self-limited dimension can be tuned by changing the local curvature encoded in a single subunit. Exploiting the programmability of our system, we further test the tradeoffs between fidelity and complexity embodied by two paradigms for self-limited assembly: self-closure through programmed curvature and addressable assembly through programmed specific interactions. Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the tradeoffs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and we study their assembly into tubules that have a self-limited width that is much larger than the size of an individual subunit. In the simplest case, the tubules are assembled from a single component by geometrically programming the dihedral angles between neighboring subunits. We show that the tubules can reach many micrometers in length and that their average width can be prescribed through the dihedral angles. We find that there is a distribution in the width and the chirality of the tubules, which we rationalize by developing a model that considers the finite bending rigidity of the assembled structure as well as the mechanism of self-closure. Finally, we demonstrate that the distributions of tubules can be further sculpted by increasing the number of subunit species, thereby increasing the assembly complexity, and demonstrate that using two subunit species successfully reduces the number of available end states by half. These results help to shed light on the roles of assembly complexity and geometry in self-limited assembly and could be extended to other self-limiting architectures, such as shells, toroids, or triply periodic frameworks.
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19
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Liu J, Chen L, Zhai T, Li W, Liu Y, Gu H. Programmable Assembly of Amphiphilic DNA through Controlled Cholesterol Stacking. J Am Chem Soc 2022; 144:16598-16603. [PMID: 36040192 DOI: 10.1021/jacs.2c06610] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The excellent programmability and modifiability of DNA has enabled chemists to reproduce a series of specific molecular interactions in self-assembled synthetic systems. Among diverse modifications, cholesterol conjugation can turn DNA into an amphiphilic molecule (cholesterol-DNA), driving the formation of DNA assemblies through the cholesterol-endowed hydrophobic interaction. However, precise control of such an assembly process remains difficult because of the unbiased accumulation of cholesterol. Here, we report the serendipitous discovery of the favored tetramerization of cholesterol in cholesterol-DNA copolymers that carry the cholesterol modification at the blunt end of DNA. The discovery expands the repertoire of controllable molecular interactions by DNA and provides an effective way to precisely control the hydrophobic stacking of cholesterol for programmed cholesterol-DNA assembly.
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Affiliation(s)
- Jin Liu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Liman Chen
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Tingting Zhai
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Yuehua Liu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai 200433, China.,School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.,Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China
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20
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Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
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Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
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21
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Zhou Y, Dong J, Zhou C, Wang Q. Finite Assembly of Three-Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding. Angew Chem Int Ed Engl 2022; 61:e202116416. [PMID: 35147275 DOI: 10.1002/anie.202116416] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 01/01/2023]
Abstract
Reliable orthogonal bonding with precise and flexible orientation control would be ideal for building finite complex nanostructures via self-assembly. Employing a three-dimensional (3D) DNA origami, hexagonal prism DNA origami (HDO), as building block, we demonstrate it is practical to construct finite hierarchical nanoarchitectures with complicated conformations through orthogonal and directional bonding. The as-designed HDO building block has twelve prescribed directional valences in 3D space and each of them supports two opposite orientations, yielding the capability to generate abundant directional bonding. Meanwhile, we minimize the thorny non-specific interactions among HDOs and enable the orthogonal bonding between any two valences based on self-similar designing. Consequently, various hierarchical nanostructures are prepared at will simply by the combination of HDOs with appropriate valences. We believe this route towards hierarchically assembly is inspiring and hope it will facilitate the fabrication of functional superstructures.
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Affiliation(s)
- Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, China
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22
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Chang X, Yang Q, Lee J, Zhang F. Self-Assembled Nucleic Acid Nanostructures for Biomedical Applications. Curr Top Med Chem 2022; 22:652-667. [PMID: 35319373 DOI: 10.2174/1568026622666220321140729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Structural DNA nanotechnology has been developed into a powerful method for creating self-assembled nanomaterials. Their compatibility with biosystems, nanoscale addressability, and programmable dynamic features make them appealing candidates for biomedical research. This review paper focuses on DNA self-assembly strategies and designer nanostructures with custom functions for biomedical applications. Specifically, we review the development of DNA self-assembly methods, from simple DNA motifs consisting of a few DNA strands to complex DNA architectures assembled by DNA origami. Three advantages are discussed using structural DNA nanotechnology for biomedical applications: (1) precise spatial control, (2) molding and guiding other biomolecules, and (3) using reconfigurable DNA nanodevices to overcome biomedical challenges. Finally, we discuss the challenges and opportunities of employing DNA nanotechnology for biomedical applications, emphasizing diverse assembly strategies to create a custom DNA nanostructure with desired functions.
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Affiliation(s)
- Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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23
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Zhou Y, Dong J, Zhou C, Wang Q. Finite Assembly of Three‐Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
- College of Materials Sciences and Opto-Electronic Technology University of Chinese Academy of Sciences China
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24
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Chen C, Lin T, Ma M, Shi X, Li X. Programmable and scalable assembly of a flexible hexagonal DNA origami. NANOTECHNOLOGY 2021; 33:105606. [PMID: 34530415 DOI: 10.1088/1361-6528/ac2768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Nanoscale structures demonstrate considerable potential utility in the construction of nanorobots, nanomachines, and many other devices. In this study, a hexagonal DNA origami ring was assembled and visualized via atomic force microscopy. The DNA origami shape could be programmed into either a hexagonal or linear shape with an open or folded pattern. The flexible origami was robust and switchable for dynamic pattern recognition. Its edges were folded by six bundles of DNA helices, which could be opened or folded in a honeycomb shape. Additionally, the edges were programmed into a concave-convex pattern, which enabled linkage between the origami and dipolymers. Furthermore, biotin-streptavidin labels were embedded at each edge for nanoscale calibration. The atomic force microscopy results demonstrated the stability and high-yield of the flexible DNA origami ring. The polymorphous nanostructure is useful for dynamic nano-construction and calibration of structural probes or sensors.
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Affiliation(s)
- Congzhou Chen
- Key Laboratory of High Confidence Software Technologies, School of Computer Science, Peking University, Beijing 100871, People's Republic of China
| | - Tingting Lin
- Institute of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan 430074, People's Republic of China
| | - Mingyuan Ma
- Key Laboratory of High Confidence Software Technologies, School of Computer Science, Peking University, Beijing 100871, People's Republic of China
| | - Xiaolong Shi
- Institute of Computing Science & Technology, Guangzhou University, Guangzhou 510006, People's Republic of China
| | - Xin Li
- Department of Gynecology 2, Renmin Hospital of Wuhan University, Wuhan 430060, People's Republic of China
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25
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Qutbuddin Y, Krohn JH, Brüggenthies GA, Stein J, Gavrilovic S, Stehr F, Schwille P. Design Features to Accelerate the Higher-Order Assembly of DNA Origami on Membranes. J Phys Chem B 2021; 125:13181-13191. [PMID: 34818013 PMCID: PMC8667037 DOI: 10.1021/acs.jpcb.1c07694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanotechnology often exploits DNA origami nanostructures assembled into even larger superstructures up to micrometer sizes with nanometer shape precision. However, large-scale assembly of such structures is very time-consuming. Here, we investigated the efficiency of superstructure assembly on surfaces using indirect cross-linking through low-complexity connector strands binding staple strand extensions, instead of connector strands binding to scaffold loops. Using single-molecule imaging techniques, including fluorescence microscopy and atomic force microscopy, we show that low sequence complexity connector strands allow formation of DNA origami superstructures on lipid membranes, with an order-of-magnitude enhancement in the assembly speed of superstructures. A number of effects, including suppression of DNA hairpin formation, high local effective binding site concentration, and multivalency are proposed to contribute to the acceleration. Thus, the use of low-complexity sequences for DNA origami higher-order assembly offers a very simple but efficient way of improving throughput in DNA origami design.
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Affiliation(s)
- Yusuf Qutbuddin
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Jan-Hagen Krohn
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.,Exzellenzcluster ORIGINS, Boltzmannstrasse 2, D-85748 Garching, Germany
| | - Gereon A Brüggenthies
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Johannes Stein
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Svetozar Gavrilovic
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Florian Stehr
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Kong G, Xiong M, Liu L, Hu L, Meng HM, Ke G, Zhang XB, Tan W. DNA origami-based protein networks: from basic construction to emerging applications. Chem Soc Rev 2021; 50:1846-1873. [PMID: 33306073 DOI: 10.1039/d0cs00255k] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.
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Affiliation(s)
- Gezhi Kong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Mengyi Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Lu Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Ling Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Hong-Min Meng
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou 450001, China
| | - Guoliang Ke
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China.
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28
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Constructing Large 2D Lattices Out of DNA-Tiles. Molecules 2021; 26:molecules26061502. [PMID: 33801952 PMCID: PMC8000633 DOI: 10.3390/molecules26061502] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
The predictable nature of deoxyribonucleic acid (DNA) interactions enables assembly of DNA into almost any arbitrary shape with programmable features of nanometer precision. The recent progress of DNA nanotechnology has allowed production of an even wider gamut of possible shapes with high-yield and error-free assembly processes. Most of these structures are, however, limited in size to a nanometer scale. To overcome this limitation, a plethora of studies has been carried out to form larger structures using DNA assemblies as building blocks or tiles. Therefore, DNA tiles have become one of the most widely used building blocks for engineering large, intricate structures with nanometer precision. To create even larger assemblies with highly organized patterns, scientists have developed a variety of structural design principles and assembly methods. This review first summarizes currently available DNA tile toolboxes and the basic principles of lattice formation and hierarchical self-assembly using DNA tiles. Special emphasis is given to the forces involved in the assembly process in liquid-liquid and at solid-liquid interfaces, and how to master them to reach the optimum balance between the involved interactions for successful self-assembly. In addition, we focus on the recent approaches that have shown great potential for the controlled immobilization and positioning of DNA nanostructures on different surfaces. The ability to position DNA objects in a controllable manner on technologically relevant surfaces is one step forward towards the integration of DNA-based materials into nanoelectronic and sensor devices.
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29
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Liu C, Liu Y, Zhu E, Zhang Q, Wei X, Wang B. Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement. Nucleic Acids Res 2020; 48:10691-10701. [PMID: 33045746 PMCID: PMC7641751 DOI: 10.1093/nar/gkaa835] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 01/19/2023] Open
Abstract
Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.
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Affiliation(s)
- Chanjuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Enqiang Zhu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China
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30
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31
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Lin Z, Emamy H, Minevich B, Xiong Y, Xiang S, Kumar S, Ke Y, Gang O. Engineering Organization of DNA Nano-Chambers through Dimensionally Controlled and Multi-Sequence Encoded Differentiated Bonds. J Am Chem Soc 2020; 142:17531-17542. [PMID: 32902966 DOI: 10.1021/jacs.0c07263] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Engineering the assembly of nanoscale objects into complex and prescribed structures requires control over their binding properties. Such control might benefit from a well-defined bond directionality, the ability to designate their engagements through specific encodings, and the capability to coordinate local orientations. Although much progress has been achieved in our ability to design complex nano-objects, the challenges in creating such nano-objects with fully controlled binding modes and understanding their fundamental properties are still outstanding. Here, we report a facile strategy for creating a DNA nanochamber (DNC), a hollow cuboid nano-object, whose bonds can be fully prescribed and complexly encoded along its three orthogonal axes, giving rise to addressable and differentiated bonds. The DNC can host nanoscale cargoes, which allows for the integration with functional nano-objects and their organization in larger-scale systems. We explore the relationship between the design of differentiated bonds and a formation of one-(1D), two-(2D), and three-(3D) dimensional organized arrays. Through the realization of different binding modes, we demonstrate sequence encoded nanoscale heteropolymers, helical polymers, 2D lattices, and mesoscale 3D nanostructures with internal order, and show that this assembly strategy can be applied for the organization of nanoparticles. We combine experimental investigations with computational simulation to understand the mechanism of structural formation for different types of ordered arrays, and to correlate the bonds design with assembly processes.
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Affiliation(s)
- Zhiwei Lin
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Hamed Emamy
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Yan Xiong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Shuting Xiang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Sanat Kumar
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States.,Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States.,Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
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32
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Chen C, Xu J, Shi X. Multiform DNA origami arrays using minimal logic control. NANOSCALE 2020; 12:15066-15071. [PMID: 32458902 DOI: 10.1039/d0nr00783h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Self-assembled DNA nanostructures significantly contribute to DNA nanotechnology. Algorithmic guiding of the assembly of DNA arrays remains a challenge in nanoarchitecture. Usually, the more sophisticated a DNA nanoarchitecture, the more DNA connections with specific sequences are required. This study aimed to investigate the feasibility of using the minimum pairs of DNA connection strands to implement algorithm-based self-assembly with finite DNA origamis. We found that the DNA origami linking complexity was markedly reduced. By rotating and turning the origami tile in different linking directions, we obtained 2 × 2 arrays of DNA origamis using a pair of DNA connections, 2 × 4 arrays using two pairs of DNA connections, and 4 × 4 arrays using three pairs of connection strands. We further analysed the effects of distortion on array formation. Overall, this study presents a hierarchical assembly strategy with minimal connections to generate multi-scale DNA arrays.
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Affiliation(s)
- Congzhou Chen
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China.
| | - Jin Xu
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China.
| | - Xiaolong Shi
- Institute of Computing Science & Technology, Guangzhou University, Guangzhou 510006, China.
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33
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Aghebat Rafat A, Sagredo S, Thalhammer M, Simmel FC. Barcoded DNA origami structures for multiplexed optimization and enrichment of DNA-based protein-binding cavities. Nat Chem 2020; 12:852-859. [PMID: 32661410 DOI: 10.1038/s41557-020-0504-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/05/2020] [Indexed: 01/15/2023]
Abstract
Simultaneous binding of molecules by multiple binding partners is known to strongly reduce the apparent dissociation constant of the corresponding molecular complexes, and can be used to achieve strong, non-covalent molecular interactions. Based on this principle, efficient binding of proteins to DNA nanostructures has been achieved previously by placing several aptamers in close proximity to each other onto DNA scaffolds. Here, we develop an approach for exploring design parameters, such as the geometric arrangement or the nanomechanical properties of the binding sites, that use two-dimensional DNA origami-based nanocavities that bear aptamers with known mechanical properties at defined distances and orientations. The origami structures are labelled with barcodes, which enables large numbers of binding cavities to be investigated in parallel and under identical conditions, and facilitates a direct and reliable quantitative comparison of their binding yields. We demonstrate that binding geometry and mechanical properties have a dramatic effect on origami-based multivalent binding sites, and that optimization of linker spacings and flexibilities can improve the effective binding strength of the sites substantially.
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Affiliation(s)
- Ali Aghebat Rafat
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Sandra Sagredo
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Melissa Thalhammer
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany
| | - Friedrich C Simmel
- Physics Department E14 and ZNN, Technical University Munich, Garching, Germany.
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34
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020; 59:12991-12997. [PMID: 32304157 DOI: 10.1002/anie.202003823] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 01/26/2023]
Abstract
DNA nanostructures with programmable nanoscale patterns has been achieved in the past decades, and molecular information coding (MIC) on those designed nanostructures has gained increasing attention for information security. However, achieving steganography and cryptography synchronously on DNA nanostructures remains a challenge. Herein, we demonstrated MIC in a reconfigurable DNA origami domino array (DODA), which can reconfigure intrinsic patterns but keep the DODA outline the same for steganography. When a set of keys (DNA strands) are added, the cryptographic data can be translated into visible patterns within DODA. More complex cryptography with the ASCII code within a programmable 6×6 lattice is demonstrated to demosntrate the versatility of MIC in the DODA. Furthermore, an anti-counterfeiting approach based on conformational transformation-mediated toehold strand displacement reaction is designed to protect MIC from decoding and falsification.
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Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
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35
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Fan S, Wang D, Cheng J, Liu Y, Luo T, Cui D, Ke Y, Song J. Information Coding in a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Tao Luo
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
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36
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Abstract
Recent advances in structural DNA nanotechnology, including DNA origami and DNA bricks, have enabled arbitrarily complexed nanopatterns. However, most of these DNA structures are limited with sub-100 nm dimensions because of the limits from the length of scaffold strand, as well as the sequence library. This review will focus on different strategies for scaling-up DNA self-assembly, including the hierarchical assembly of the preformed DNA building blocks both in solution and on surface, the scaffolded assembly of finite sized DNA structures, the nonhierarchical assembly of single-stranded DNA bricks, and the seed-mediated algorithmic assembly. The design criteria, the building blocks, and the key assembly conditions for each assembly strategy are described. In addition, the future challenges, as well as application potentials of large-area DNA structures, are discussed.
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Affiliation(s)
- Yahong Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices, Department of Electronics, Peking University, Beijing 100871, 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, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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37
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38
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Chen C, Xu J, Shi X. Adjusting Linking Strands to Form Size-Controllable DNA Origami Rings. IEEE Trans Nanobioscience 2020; 19:167-172. [PMID: 31905142 DOI: 10.1109/tnb.2020.2964061] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA origami is a powerful tool in nanotechnology that can be used to construct arbitrary structures for several nanoengineering applications. Generally, the more complex and sophisticated the construction, the greater is the number of origamis and connection strands that will be needed. Therefore, developing an effective and low-cost method for multiform DNA architecture is important in nanoengineering. Here, we adopted an oblique linking strategy to connect cross-shaped DNA origami with a controlled curing angle. The size of the DNA rings ranged from four blocks of approximately 200 nm to eleven blocks of c.a. 600 nm. We observed that the minimum size of the DNA ring structure was limited by the width of a single block. The largest rings were negatively affected by thermodynamic randomness, and thus, DNA rings consisting of more than eleven blocks were not observed. This strategy facilitates the generation of various DNA origami rings, whose size can be controlled by adjusting the length of the connection strands.
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39
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Abstract
Extended DNA nanostructures have already been constructed in a repetitive arrangement from millions of building blocks, many more than currently feasible with even the gold standard of addressable self-assembled structures. In order to construct addressable DNA nanostructures with more building blocks, it is desirable to arrange the addressable components repetitively. Accordingly, the overall size of the structure can be multiplied by the level of repetition in the addressable strands. In this study, we present a nanotube system that combines two seemingly conflicting features: addressability and repetitiveness. Based on an understanding of the tubulation resulting from the intrinsic curvature of the components, we produce DNA nanotubes with addressability available along the axial direction of the self-assembled tubes, which are also programmably repetitive along the lateral direction.
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Affiliation(s)
- Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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40
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Programming DNA origami patterning with non-canonical DNA-based metallization reactions. Nat Commun 2019; 10:5597. [PMID: 31811136 PMCID: PMC6897912 DOI: 10.1038/s41467-019-13507-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/13/2019] [Indexed: 01/15/2023] Open
Abstract
The inherent specificity of DNA sequence hybridization has been extensively exploited to develop bioengineering applications. Nevertheless, the structural potential of DNA has been far less explored for creating non-canonical DNA-based reactions. Here we develop a DNA origami-enabled highly localized metallization reaction for intrinsic metallization patterning with 10-nm resolution. Both theoretical and experimental studies reveal that low-valence metal ions (Cu2+ and Ag+) strongly coordinate with DNA bases in protruding clustered DNA (pcDNA) prescribed on two-dimensional DNA origami, which results in effective attraction within flexible pcDNA strands for site-specific pcDNA condensation. We find that the metallization reactions occur selectively on prescribed sites while not on origami substrates. This strategy is generically applicable for free-style metal painting of alphabet letters, digits and geometric shapes on all−DNA substrates with near-unity efficiency. We have further fabricated single- and double-layer nanoscale printed circuit board (nano-PCB) mimics, shedding light on bio-inspired fabrication for nanoelectronic and nanophotonic applications. DNA origami has gained great interest for the creation of precise nanostructures. Here, the authors report on the creation of metalized DNA origami structured formed by metal condensation of DNA and nucleated metal growth on the formed DNA nanostructures.
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41
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Sheheade B, Liber M, Popov M, Berger Y, Khara DC, Jopp J, Nir E. Self-Assembly of DNA Origami Heterodimers in High Yields and Analysis of the Involved Mechanisms. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902979. [PMID: 31755230 DOI: 10.1002/smll.201902979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Efficient fabrication of structurally and functionally diverse nanomolecular devices and machines by organizing separately prepared DNA origami building blocks into a larger structure is limited by origami attachment yields. A general method that enables attachment of origami building blocks using 'sticky ends' at very high yields is demonstrated. Two different rectangular origami monomers are purified using agarose gel electrophoresis conducted in solute containing 100 × 10-3 m NaCl, a treatment that facilitates the dissociation of most of the incorrectly hybridized origami structures that form through blunt-end interactions during the thermal annealing process and removes these structures as well as excess strands that otherwise interfere with the desired heterodimerization reaction. Heterodimerization yields of gel-purified monomers are between 98.6% and 99.6%, considerably higher than that of monomers purified using the polyethylene glycol (PEG) method (88.7-96.7%). Depending on the number of PEG purification rounds, these results correspond to about 4- to 25-fold reduction in the number of incorrect structures observed by atomic force microscopy. Furthermore, the analyses of the incorrect structures observed before and after the heterodimerization reactions and comparison of the purification methods provide valuable information on the reaction mechanisms that interfere with heterodimerization.
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Affiliation(s)
- Breveruos Sheheade
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Miran Liber
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Mary Popov
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Yaron Berger
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Dinesh C Khara
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Jürgen Jopp
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Eyal Nir
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
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42
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Lee AJ, Wälti C. DNA nanostructures: A versatile lab-bench for interrogating biological reactions. Comput Struct Biotechnol J 2019; 17:832-842. [PMID: 31316727 PMCID: PMC6611922 DOI: 10.1016/j.csbj.2019.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 01/10/2023] Open
Abstract
At its inception DNA nanotechnology was conceived as a tool for spatially arranging biological molecules in a programmable and deterministic way to improve their interrogation. To date, DNA nanotechnology has provided a versatile toolset of nanostructures and functional devices to augment traditional single molecule investigation approaches - including atomic force microscopy - by isolating, arranging and contextualising biological systems at the single molecule level. This review explores the state-of-the-art of DNA-based nanoscale tools employed to enhance and tune the interrogation of biological reactions, the study of spatially distributed pathways, the visualisation of enzyme interactions, the application and detection of forces to biological systems, and biosensing platforms.
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Affiliation(s)
- Andrew J. Lee
- Bioelectronics, The Pollard Institute, School of Electronic & Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
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Seo J, Kim S, Park HH, Nam JM. Biocomputing with Nanostructures on Lipid Bilayers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900998. [PMID: 31026121 DOI: 10.1002/smll.201900998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/13/2019] [Indexed: 06/09/2023]
Abstract
Biocomputation is the algorithmic manipulation of biomolecules. Nanostructures, most notably DNA nanostructures and nanoparticles, become active substrates for biocomputation when modified with stimuli-responsive, programmable biomolecular ligands. This approach-biocomputing with nanostructures ("nano-bio computing")-allows autonomous control of matter and information at the nanoscale; their dynamic assemblies and beneficial properties can be directed without human intervention. Recently, lipid bilayers interfaced with nanostructures have emerged as a new biocomputing platform. This new nano-bio interface, which exploits lipid bilayers as a chemical circuit board for information processing, offers a unique reaction space for realizing nanostructure-based computation at a previously unexplored dimension. In this Concept, recent advances in nano-bio computing are briefly reviewed and the newly emerging concept of biocomputing with nanostructures on lipid bilayers is introduced.
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Affiliation(s)
- Jinyoung Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Sungi Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Ha H Park
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
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44
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Fan S, Wang D, Kenaan A, Cheng J, Cui D, Song J. Create Nanoscale Patterns with DNA Origami. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805554. [PMID: 31018040 DOI: 10.1002/smll.201805554] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/16/2019] [Indexed: 05/21/2023]
Abstract
Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
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Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ahmad Kenaan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
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Kim J, Narayana A, Patel S, Sahay G. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides. Theranostics 2019; 9:3191-3212. [PMID: 31244949 PMCID: PMC6567962 DOI: 10.7150/thno.33921] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Cells utilize natural supramolecular assemblies to maintain homeostasis and biological functions. Naturally inspired modular assembly of biomaterials are now being exploited for understanding or manipulating cell biology for treatment, diagnosis, and detection of diseases. Supramolecular biomaterials, in particular peptides and oligonucleotides, can be precisely tuned to have diverse structural, mechanical, physicochemical and biological properties. These merits of oligonucleotides and peptides as building blocks have given rise to the evolution of numerous nucleic acid- and peptide-based self-assembling nanomaterials for various medical applications, including drug delivery, tissue engineering, regenerative medicine, and immunotherapy. In this review, we provide an extensive overview of the intracellular delivery approaches using supramolecular self-assembly of DNA, RNA, and peptides. Furthermore, we discuss the current challenges related to subcellular delivery and provide future perspectives of the application of supramolecular biomaterials for intracellular delivery in theranostics.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Ashwanikumar Narayana
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Robertson Life Sciences Building, Oregon State University, Portland, OR
- Department of Biomedical Engineering, Robertson Life Sciences Building, Oregon Health Science University, Portland, OR
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46
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Chen Z, Johnson MC, Chen J, Bick MJ, Boyken SE, Lin B, De Yoreo JJ, Kollman JM, Baker D, DiMaio F. Self-Assembling 2D Arrays with de Novo Protein Building Blocks. J Am Chem Soc 2019; 141:8891-8895. [PMID: 31050411 DOI: 10.1021/jacs.9b01978] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Modular self-assembly of biomolecules in two dimensions (2D) is straightforward with DNA but has been difficult to realize with proteins, due to the lack of modular specificity similar to Watson-Crick base pairing. Here we describe a general approach to design 2D arrays using de novo designed pseudosymmetric protein building blocks. A homodimeric helical bundle was reconnected into a monomeric building block, and the surface was redesigned in Rosetta to enable self-assembly into a 2D array in the C12 layer symmetry group. Two out of ten designed arrays assembled to micrometer scale under negative stain electron microscopy, and displayed the designed lattice geometry with assembly size up to 100 nm under atomic force microscopy. The design of 2D arrays with pseudosymmetric building blocks is an important step toward the design of programmable protein self-assembly via pseudosymmetric patterning of orthogonal binding interfaces.
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Affiliation(s)
| | | | - Jiajun Chen
- Physical Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | | | | | | | - James J De Yoreo
- Physical Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
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Yang ZZ, Wen ZB, Peng X, Chai YQ, Liang WB, Yuan R. A novel fluorescent assay for the ultrasensitive detection of miRNA-21 with the use of G-quadruplex structures as an immobilization material for a signal indicator. Chem Commun (Camb) 2019; 55:6453-6456. [DOI: 10.1039/c9cc01850f] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A fluorescent assay for the ultrasensitive detection of miRNA-21 is based on immobilization of PPIX as signal indicators in massive G-quadruplex structures obtained by target recycling, three-dimensional DNA walker and RCA coupled cascade nucleic acid amplification.
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Affiliation(s)
- Ze-Zhou Yang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Zhi-Bin Wen
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xin Peng
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ya-Qin Chai
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Wen-Bin Liang
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescence and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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Petersen P, Tikhomirov G, Qian L. Information-based autonomous reconfiguration in systems of interacting DNA nanostructures. Nat Commun 2018; 9:5362. [PMID: 30560865 PMCID: PMC6299139 DOI: 10.1038/s41467-018-07805-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
The dynamic interactions between complex molecular structures underlie a wide range of sophisticated behaviors in biological systems. In building artificial molecular machines out of DNA, an outstanding challenge is to develop mechanisms that can control the kinetics of interacting DNA nanostructures and that can compose the interactions together to carry out system-level functions. Here we show a mechanism of DNA tile displacement that follows the principles of toehold binding and branch migration similar to DNA strand displacement, but occurs at a larger scale between interacting DNA origami structures. Utilizing this mechanism, we show controlled reaction kinetics over five orders of magnitude and programmed cascades of reactions in multi-structure systems. Furthermore, we demonstrate the generality of tile displacement for occurring at any location in an array in any order, illustrated as a tic-tac-toe game. Our results suggest that tile displacement is a simple-yet-powerful mechanism that opens up the possibility for complex structural components in artificial molecular machines to undergo information-based reconfiguration in response to their environments.
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Affiliation(s)
- Philip Petersen
- Biology, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Grigory Tikhomirov
- Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lulu Qian
- Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA. .,Computer Science, California Institute of Technology, Pasadena, CA, 91125, USA.
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49
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Li Y, Yang S, Zheng J, Zou Z, Yang R, Tan W. "Trojan Horse" DNA Nanostructure for Personalized Theranostics: Can It Knock on the Door of Preclinical Practice? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15028-15044. [PMID: 30295491 DOI: 10.1021/acs.langmuir.8b02008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanotheranostics, combing diagnostic and therapeutic components in an all-in-one nanomaterial, possess exciting potentials for precision nanomedicine. However, a major obstacle for current nanotheranostics to enter preclinical and/or clinical trials is the intrinsic toxicities of these nanomaterials. As an emerging biomaterial, the bioinspired DNA nanostructure shows advantages for constructing better nanotheranostics due to its excellent features, including native biocompatibility, full programmability, and ready accessibility. In this feature article, we highlight recent advances in the design of DNA-nanostructure-based diagnostics and/or therapeutics capable of specifically responding to biological stimuli in a dynamic way, with a particular focus on the design mechanism, responsive performance, and potential for preclinical and/or clinical trials in personalized theranostics.
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Affiliation(s)
- Yuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Sheng Yang
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Zhen Zou
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
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50
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Abstract
DNA origami tilings provide methods for creating complex molecular patterns and shapes using flat DNA origami structures as building blocks. Square tiles have been developed to construct micrometer-scale arrays and to generate patterns using stochastic or deterministic strategies. Here we show triangular tiles as a complementary approach for enriching the design space of DNA tilings and for extending the shape of the self-assembled arrays from 2D to 3D. We introduce a computational approach for maximizing binding specificity in a fully symmetric tile design, with which we construct a 20-tile structure resembling a rhombic triacontahedron. We demonstrate controlled transition between 3D and 2D structures using simple methods including tile concentration, magnesium, and fold symmetry in tile edge design. Using these approaches, we construct 2D arrays with unbounded and designed sizes. The programmability of the edge design and the flexibility of the structure make the triangular DNA origami tile an ideal building block for complex self-assembly and reconfiguration in artificial molecular machines and fabricated nanodevices.
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Affiliation(s)
- Grigory Tikhomirov
- Bioengineering , California Institute of Technology , Pasadena , California 91125 , United States
| | - Philip Petersen
- Biology , California Institute of Technology , Pasadena , California 91125 , United States
| | - Lulu Qian
- Bioengineering , California Institute of Technology , Pasadena , California 91125 , United States.,Computer Science , California Institute of Technology , Pasadena , California 91125 , United States
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