1
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DeLuca M, Sensale S, Lin PA, Arya G. Prediction and Control in DNA Nanotechnology. ACS APPLIED BIO MATERIALS 2024; 7:626-645. [PMID: 36880799 DOI: 10.1021/acsabm.2c01045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
DNA nanotechnology is a rapidly developing field that uses DNA as a building material for nanoscale structures. Key to the field's development has been the ability to accurately describe the behavior of DNA nanostructures using simulations and other modeling techniques. In this Review, we present various aspects of prediction and control in DNA nanotechnology, including the various scales of molecular simulation, statistical mechanics, kinetic modeling, continuum mechanics, and other prediction methods. We also address the current uses of artificial intelligence and machine learning in DNA nanotechnology. We discuss how experiments and modeling are synergistically combined to provide control over device behavior, allowing scientists to design molecular structures and dynamic devices with confidence that they will function as intended. Finally, we identify processes and scenarios where DNA nanotechnology lacks sufficient prediction ability and suggest possible solutions to these weak areas.
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Affiliation(s)
- Marcello DeLuca
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Po-An Lin
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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2
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Chen Z, Cao L, Yun K, Lu J. Dynamic Study of Kinetically Trapped Byproducts during DNA Assembly: Case Study on a Pathway-Dependent Assembly. ACS Macro Lett 2024; 13:94-98. [PMID: 38176070 DOI: 10.1021/acsmacrolett.3c00680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Despite 40 years of development of DNA nanotechnology, the fundamental knowledge of the process of DNA strand assembly into targeted nanostructures remains unclear. Study of the dynamic process, especially the competing hybridizations in kinetic traps, provides insight into DNA assembly. In this study, a system of middle-domain first assembly (MDFA) was proposed to enable oligonucleotides to assemble into a 2D DNA monolayer in a pathway-dependent approach. This system was an ideal case to study the dynamic interactions between competing hybridizations during oligonucleotide assembly. Dynamic study revealed the coexistence of the kinetically trapped dead-end byproduct and target product at the early stage of annealing, followed by transformation of the byproduct into the target product by reverse disassembly, due to the equilibrium of the competing hybridizations increasingly favoring the target product pathway. This study offered a better understanding of the assembly pathway of DNA nanostructures for future design.
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Affiliation(s)
- Zhe Chen
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Lingyan Cao
- Department of Prosthodontics, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai 200011, China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
- Key Laboratory of Forensic Toxicology of Ministry of Public Security, 98 University Street, Yuci District, Jinzhong, Shanxi 030600, China
| | - Jingxiong Lu
- Research Center for Intelligent Computing Platforms, Zhejiang Laboratory, Hangzhou 311100, China
- Institute of Medi-X, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 1088 Xueyuan Blvd., Nanshan District, Shenzhen, Guangdong 518055, China
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3
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Gambietz S, Stenke LJ, Saccà B. Sequence-dependent folding of monolayered DNA origami domains. NANOSCALE 2023; 15:13120-13132. [PMID: 37503690 DOI: 10.1039/d3nr02537c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Current models of DNA origami folding can explain the yield of the assembly process and the isomerization of the structure upon the application of mechanical forces. Nevertheless, the role of the sequence in this conformational transformation is still unclear. In this work, we address this question by performing a systematic thermodynamic study of three origami domains that have an identical design but different sequence contents. By comparing the thermal stability of the domains in various settings and measuring the extent of isomerization at equilibrium (both at the global and single-molecule levels), we extract the contribution to folding given by the sequence and propose thermal criton maps of the isomers to rationalize our findings. Our data contribute to a deeper understanding of DNA origami assembly by considering both the topological- and thermal-dependent properties of the sites of initial folding. While the former are responsible for the mechanical aspects of the process, the latter justify the observed sequence-dependent conformational preferences, which appear evident in simple origami structures but remain typically undisclosed in large and more intricate architectures.
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Affiliation(s)
- Sabrina Gambietz
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Lena J Stenke
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
| | - Barbara Saccà
- Center of Medical Biotechnology (ZMB) and Center for Nanointegration Duisburg Essen (CENIDE), University Duisburg-Essen, 45141 Essen, Germany.
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4
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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: 63] [Impact Index Per Article: 63.0] [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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5
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Cumberworth A, Frenkel D, Reinhardt A. Simulations of DNA-Origami Self-Assembly Reveal Design-Dependent Nucleation Barriers. NANO LETTERS 2022; 22:6916-6922. [PMID: 36037484 PMCID: PMC9479157 DOI: 10.1021/acs.nanolett.2c01372] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding of the scaffold strand, is unclear. Here, using Monte Carlo simulations of a lattice model of DNA origami, we find that some, but not all, designs can have a nucleation barrier and that this barrier disappears at lower temperatures, rationalizing the success of isothermal assembly. We show that the height of the nucleation barrier depends primarily on the coaxial stacking of staples that are adjacent on the same helix, a parameter that can be modified with staple design. Creating a nucleation barrier to DNA-origami assembly could be useful in optimizing assembly times and yields, while eliminating the barrier may allow for fast molecular sensors that can assemble/disassemble without hysteresis in response to changes in the environment.
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Affiliation(s)
| | - Daan Frenkel
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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6
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Majikes JM, Zwolak M, Liddle JA. Best practice for improved accuracy: a critical reassessment of van't Hoff analysis of melt curves. Biophys J 2022; 121:1986-2001. [PMID: 35546781 DOI: 10.1016/j.bpj.2022.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Biomolecular thermodynamics, particularly for DNA, are frequently determined via van't Hoff analysis of optically-measured melt curves. Accurate and precise values of thermodynamic parameters are essential for the modelling of complex systems involving cooperative effects, such as RNA tertiary structure and DNA origami because the uncertainties associated with each motif in a folding energy landscape can compound, significantly reducing the power of predictive models. We follow the sources of uncertainty as they propagate through a typical van't Hoff analysis to derive best practices for melt experiments and subsequent data analysis, assuming perfect signal baseline correction. With appropriately designed experiments and analysis, a van't Hoff approach can provide surprisingly high precision, e.g., enthalpies may be determined with a precision as low as a 10-2 kJ∙mol-1 for an 8 base DNA oligomer.
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Affiliation(s)
- Jacob M Majikes
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland.
| | - Michael Zwolak
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland
| | - J Alexander Liddle
- Microsystem and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland.
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7
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Yang L, Cullin C, Elezgaray J. Detection of short DNA sequences with DNA nanopores. Chemphyschem 2022; 23:e202200021. [DOI: 10.1002/cphc.202200021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Luyan Yang
- UMR5031: Centre de Recherche Paul Pascal soft matter FRANCE
| | - Christophe Cullin
- CBMN: Chimie et Biologie des Membranes et des Nanoobjets Biology FRANCE
| | - Juan Elezgaray
- CBMN, UMR 5248, CNRS Allé Saint Hilaire, Batiment B14 33600 Pessac FRANCE
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8
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Majikes JM, Patrone PN, Kearsley AJ, Zwolak M, Liddle JA. Failure Mechanisms in DNA Self-Assembly: Barriers to Single-Fold Yield. ACS NANO 2021; 15:3284-3294. [PMID: 33565312 PMCID: PMC11005093 DOI: 10.1021/acsnano.0c10114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the folding process of DNA origami is a critical stepping stone to the broader implementation of nucleic acid nanofabrication technology but is notably nontrivial. Origami are formed by several hundred cooperative hybridization events-folds-between spatially separate domains of a scaffold, derived from a viral genome, and oligomeric staples. Individual events are difficult to detect. Here, we present a real-time probe of the unit operation of origami assembly, a single fold, across the scaffold as a function of hybridization domain separation-fold distance-and staple/scaffold ratio. This approach to the folding problem elucidates a predicted but previously unobserved blocked state that acts as a limit on yield for single folds, which may manifest as a barrier in whole origami assembly.
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Affiliation(s)
- Jacob M. Majikes
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Paul N. Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Anthony J. Kearsley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - J. Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
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9
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Insights into the Structure and Energy of DNA Nanoassemblies. Molecules 2020; 25:molecules25235466. [PMID: 33255286 PMCID: PMC7727707 DOI: 10.3390/molecules25235466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022] Open
Abstract
Since the pioneering work of Ned Seeman in the early 1980s, the use of the DNA molecule as a construction material experienced a rapid growth and led to the establishment of a new field of science, nowadays called structural DNA nanotechnology. Here, the self-recognition properties of DNA are employed to build micrometer-large molecular objects with nanometer-sized features, thus bridging the nano- to the microscopic world in a programmable fashion. Distinct design strategies and experimental procedures have been developed over the years, enabling the realization of extremely sophisticated structures with a level of control that approaches that of natural macromolecular assemblies. Nevertheless, our understanding of the building process, i.e., what defines the route that goes from the initial mixture of DNA strands to the final intertwined superstructure, is, in some cases, still limited. In this review, we describe the main structural and energetic features of DNA nanoconstructs, from the simple Holliday junction to more complicated DNA architectures, and present the theoretical frameworks that have been formulated until now to explain their self-assembly. Deeper insights into the underlying principles of DNA self-assembly may certainly help us to overcome current experimental challenges and foster the development of original strategies inspired to dissipative and evolutive assembly processes occurring in nature.
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10
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Majikes JM, Patrone PN, Schiffels D, Zwolak M, Kearsley AJ, Forry SP, Liddle JA. Revealing thermodynamics of DNA origami folding via affine transformations. Nucleic Acids Res 2020; 48:5268-5280. [PMID: 32347943 PMCID: PMC7261180 DOI: 10.1093/nar/gkaa283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/07/2020] [Accepted: 04/28/2020] [Indexed: 01/25/2023] Open
Abstract
Structural DNA nanotechnology, as exemplified by DNA origami, has enabled the design and construction of molecularly-precise objects for a myriad of applications. However, limitations in imaging, and other characterization approaches, make a quantitative understanding of the folding process challenging. Such an understanding is necessary to determine the origins of structural defects, which constrain the practical use of these nanostructures. Here, we combine careful fluorescent reporter design with a novel affine transformation technique that, together, permit the rigorous measurement of folding thermodynamics. This method removes sources of systematic uncertainty and resolves problems with typical background-correction schemes. This in turn allows us to examine entropic corrections associated with folding and potential secondary and tertiary structure of the scaffold. Our approach also highlights the importance of heat-capacity changes during DNA melting. In addition to yielding insight into DNA origami folding, it is well-suited to probing fundamental processes in related self-assembling systems.
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Affiliation(s)
- Jacob M Majikes
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Paul N Patrone
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Daniel Schiffels
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Anthony J Kearsley
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - Samuel P Forry
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
| | - J Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, MD 20899-6203, USA
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11
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Sites of high local frustration in DNA origami. Nat Commun 2019; 10:1061. [PMID: 30837459 PMCID: PMC6400978 DOI: 10.1038/s41467-019-09002-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 12/30/2022] Open
Abstract
The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state. Self-assembly of DNA origami is a complex folding problem without a unified view of the energetic factors involved. Here the authors analyse identical structures that differ by nucleotide sequence and identify how mechanical stress at nucleation sites shapes the energy landscape.
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12
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Zhang B, Mei AR, Isbell MA, Wang D, Wang Y, Tan SF, Teo XL, Xu L, Yang Z, Heng JYY. DNA Origami as Seeds for Promoting Protein Crystallization. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44240-44246. [PMID: 30484631 DOI: 10.1021/acsami.8b15629] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study reports the first experimental evidence of DNA origami as a seed resulting in the increase in probability of protein crystallization. Using the DNA origami constructed from long single-stranded M13 DNA scaffolds folded with short single-stranded DNA staples, it was found that the addition of the DNA origami in concentrations of 2-6 nM to mixtures of a well-characterized protein (catalase) solution (1.0-7.0 mg/mL) resulted in a higher proportion of mixtures with successful crystallization, up to 11× greater. The improvement in crystallization is evident particularly for mixtures with low concentrations of catalase (<5 mg/mL). DNA origami in different conformations of a flat rectangular sheet and a tubular hollow cylinder were examined. Both conformations improved the crystallization as compared to control experiments without M13 DNA or nonfolded M13 DNA but exhibited little difference in the extent of protein crystallization improvement. This work confirms the predictions of the potential use of DNA origami to promote protein crystallization, with potential application to systems with limited protein availability or difficulty in crystallization.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry , Renmin University of China , Beijing 100872 , P. R. China
| | - Andy R Mei
- Surfaces and Particle Engineering Laboratory (SPEL), Department of Chemical Engineering , Imperial College London , South Kensington Campus , London SW7 2AZ , United Kingdom
| | - Mark Antonin Isbell
- Surfaces and Particle Engineering Laboratory (SPEL), Department of Chemical Engineering , Imperial College London , South Kensington Campus , London SW7 2AZ , United Kingdom
| | | | | | | | | | - Lijin Xu
- Department of Chemistry , Renmin University of China , Beijing 100872 , P. R. China
| | | | - Jerry Y Y Heng
- Surfaces and Particle Engineering Laboratory (SPEL), Department of Chemical Engineering , Imperial College London , South Kensington Campus , London SW7 2AZ , United Kingdom
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13
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Cumberworth A, Reinhardt A, Frenkel D. Lattice models and Monte Carlo methods for simulating DNA origami self-assembly. J Chem Phys 2018; 149:234905. [DOI: 10.1063/1.5051835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Alexander Cumberworth
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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14
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Lermusiaux L, Funston AM. Plasmonic isomers via DNA-based self-assembly of gold nanoparticles. NANOSCALE 2018; 10:19557-19567. [PMID: 30324955 DOI: 10.1039/c8nr05509b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Developments in DNA nanotechnology offer control of the self-assembly of materials into discrete nanostructures. Within this paradigm, pre-assembled DNA origami with hundreds of DNA strands allows for precise and programmable spatial positioning of functionalised nanoparticles. We propose an alternative approach to construct multiple, structurally different, nanoparticle assemblies from just a few complementary nanoparticle-functionalised DNA strands. The approach exploits local minima in the potential energy landscape of hybridised nanoparticle-DNA structures by employing kinetic control of the assembly. Using a four-strand DNA template, we synthesise five different 3D gold nanoparticle (plasmonic) tetrameric isomers, akin to molecular structural isomers. The number of different structures formed using this approach for a set of DNA strands represents a combinatorial library, which we summarise in a hybridisation pathway tree and use to achieve deposition of tetrahedral assemblies onto substrates in high yield. The ability to program nanoparticle self-assembly pathways gives unprecedented access to unique plasmonic nanostructures.
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Affiliation(s)
- Laurent Lermusiaux
- ARC Centre of Excellence in Exciton Science and School of Chemistry, Monash University, Clayton, VIC 3800, Australia.
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15
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Majikes JM, Nash JA, LaBean TH. Search for effective chemical quenching to arrest molecular assembly and directly monitor DNA nanostructure formation. NANOSCALE 2017; 9:1637-1644. [PMID: 28074960 DOI: 10.1039/c6nr08433h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural DNA nanotechnology has demonstrated both versatility and potential as a molecular manufacturing tool; the formation and processing of DNA nanostructures has therefore been subject to much interest. Characterization of the formation process itself is vital to understanding the role of design in production yield. We present our search for a robust new technique, chemical quenching, to arrest molecular folding in DNA systems for subsequent characterization. Toward this end we will introduce two miniM13 origami designs based on a 2.4 kb scaffold, each with diametrically opposed scaffold routing strategies (maximized scaffold crossovers versus maximized staple crossovers) to examine the relevance of design in the folding process. By chemically rendering single strand DNA inert and unable to hybridize, we probe the folding pathway of several scaffolded DNA origami structures.
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Affiliation(s)
- J M Majikes
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - J A Nash
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
| | - T H LaBean
- Department of Materials Science & Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA.
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16
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Wah JLT, David C, Rudiuk S, Baigl D, Estevez-Torres A. Observing and Controlling the Folding Pathway of DNA Origami at the Nanoscale. ACS NANO 2016; 10:1978-87. [PMID: 26795025 DOI: 10.1021/acsnano.5b05972] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA origami is a powerful method to fold DNA into rationally designed nanostructures that holds great promise for bionanotechnology. However, the folding mechanism has yet to be fully resolved, principally due to a lack of data with single molecule resolution. To address this issue, we have investigated in detail, using atomic force microscopy, the morphological evolution of hundreds of individual rectangular origamis in solution as a function of temperature. Significant structural changes were observed between 65 and 55 °C both for folding and melting, and six structural intermediates were identified. Under standard conditions, folding was initiated at the edges of the rectangle and progressed toward the center. Melting occurred through the reverse pathway until the structures were significantly disrupted but ended through a different pathway involving out-of-equilibrium chainlike structures. Increasing the relative concentration of center to edge staples dramatically modified the folding pathway to a mechanism progressing from the center toward the edges. These results indicate that the folding pathway is determined by thermodynamics and suggest a way of controlling it.
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Affiliation(s)
- Jonathan Lee Tin Wah
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
| | - Christophe David
- Laboratoire de photonique et de nanostructures, CNRS, route de Nozay, 91460 Marcoussis, France
| | - Sergii Rudiuk
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - Damien Baigl
- Department of Chemistry, Ecole Normale Supérieure-PSL Research University , 24 Rue Lhomond, 75005 Paris, France
- Sorbonne Universités , UPMC Univ Paris 06, PASTEUR, 75005 Paris, France
- CNRS, UMR 8640 PASTEUR, 75005 Paris, France
| | - André Estevez-Torres
- Laboratoire Jean Perrin, Université Pierre et Marie Curie , 4 place Jussieu, 75005 Paris, France
- CNRS, UMR 8237, 75005 Paris, France
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17
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Affiliation(s)
- A. Subha Mahadevi
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
| | - G. Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad, India 500607
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18
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Dannenberg F, Dunn KE, Bath J, Kwiatkowska M, Turberfield AJ, Ouldridge TE. Modelling DNA origami self-assembly at the domain level. J Chem Phys 2015; 143:165102. [DOI: 10.1063/1.4933426] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frits Dannenberg
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom
| | - Katherine E. Dunn
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
- Department of Electronics, University of York, York YO10 5DD, United Kingdom
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Marta Kwiatkowska
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom
| | - Andrew J. Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas E. Ouldridge
- Department of Physics, University of Oxford, Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
- Department of Mathematics, Imperial College, 180 Queen’s Gate, London SW7 2AZ, United Kingdom
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19
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Abstract
DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its rapid development and become a reliable manufacturing technology.
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20
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Shapiro A, Hozeh A, Girshevitz O, Abu-Horowitz A, Bachelet I. Cooperativity-based modeling of heterotypic DNA nanostructure assembly. Nucleic Acids Res 2015; 43:6587-95. [PMID: 26071955 PMCID: PMC4513873 DOI: 10.1093/nar/gkv602] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/28/2015] [Indexed: 01/28/2023] Open
Abstract
DNA origami is a robust method for the fabrication of nanoscale 2D and 3D objects with complex features and geometries. The process of DNA origami folding has been recently studied, however quantitative understanding of it is still elusive. Here, we describe a systematic quantification of the assembly process of DNA nanostructures, focusing on the heterotypic DNA junction—in which arms are unequal—as their basic building block. Using bulk fluorescence studies we tracked this process and identified multiple levels of cooperativity from the arms in a single junction to neighboring junctions in a large DNA origami object, demonstrating that cooperativity is a central underlying mechanism in the process of DNA nanostructure assembly. We show that the assembly of junctions in which the arms are consecutively ordered is more efficient than junctions with randomly-ordered components, with the latter showing assembly through several alternative trajectories as a potential mechanism explaining the lower efficiency. This highlights consecutiveness as a new design consideration that could be implemented in DNA nanotechnology CAD tools to produce more efficient and high-yield designs. Altogether, our experimental findings allowed us to devise a quantitative, cooperativity-based heuristic model for the assembly of DNA nanostructures, which is highly consistent with experimental observations.
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Affiliation(s)
- Anastasia Shapiro
- Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Avital Hozeh
- Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Olga Girshevitz
- Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Almogit Abu-Horowitz
- Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ido Bachelet
- Faculty of Life Sciences and Institute of Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat Gan 52900, Israel
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21
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Closa F, Gosse C, Jullien L, Lemarchand A. Identification of two-step chemical mechanisms and determination of thermokinetic parameters using frequency responses to small temperature oscillations. J Chem Phys 2014; 138:244109. [PMID: 23822229 DOI: 10.1063/1.4811288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Increased focus on kinetic signatures in biology, coupled with the lack of simple tools for chemical dynamics characterization, lead us to develop an efficient method for mechanism identification. A small thermal modulation is used to reveal chemical dynamics, which makes the technique compatible with in cellulo imaging. Then, the detection of concentration oscillations in an appropriate frequency range followed by a judicious analytical treatment of the data is sufficient to determine the number of chemical characteristic times, the reaction mechanism, and the full set of associated rate constants and enthalpies of reaction. To illustrate the scope of the method, dimeric protein folding is chosen as a biologically relevant example of nonlinear mechanism with one or two characteristic times.
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Affiliation(s)
- F Closa
- Université Pierre et Marie Curie-Paris 6, Laboratoire de Physique Théorique de la Matière Condensée, UMR 7600 LPTMC, 4 place Jussieu, case courrier 121, 75252 Paris cedex 05, France
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22
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Genot AJ, Fujii T, Rondelez Y. Scaling down DNA circuits with competitive neural networks. J R Soc Interface 2013; 10:20130212. [PMID: 23760296 DOI: 10.1098/rsif.2013.0212] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
DNA has proved to be an exquisite substrate to compute at the molecular scale. However, nonlinear computations (such as amplification, comparison or restoration of signals) remain costly in term of strands and are prone to leak. Kim et al. showed how competition for an enzymatic resource could be exploited in hybrid DNA/enzyme circuits to compute a powerful nonlinear primitive: the winner-take-all (WTA) effect. Here, we first show theoretically how the nonlinearity of the WTA effect allows the robust and compact classification of four patterns with only 16 strands and three enzymes. We then generalize this WTA effect to DNA-only circuits and demonstrate similar classification capabilities with only 23 strands.
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