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Madhanagopal BR, Talbot H, Rodriguez A, Louis JM, Zeghal H, Vangaveti S, Reddy K, Chandrasekaran AR. The unusual structural properties and potential biological relevance of switchback DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.563609. [PMID: 38014227 PMCID: PMC10680705 DOI: 10.1101/2023.11.15.563609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Synthetic DNA motifs form the basis of nucleic acid nanotechnology, and their biochemical and biophysical properties determine their applications. Here, we present a detailed characterization of switchback DNA, a globally left-handed structure composed of two parallel DNA strands. Compared to a conventional duplex, switchback DNA shows lower thermodynamic stability and requires higher magnesium concentration for assembly but exhibits enhanced biostability against some nucleases. Strand competition and strand displacement experiments show that component sequences have an absolute preference for duplex complements instead of their switchback partners. Further, we hypothesize a potential role for switchback DNA as an alternate structure in sequences containing short tandem repeats. Together with small molecule binding experiments and cell studies, our results open new avenues for switchback DNA in biology and nanotechnology.
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Affiliation(s)
| | - Hannah Talbot
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Arlin Rodriguez
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Jiss Maria Louis
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Hana Zeghal
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, NY, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
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2
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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3
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Chandrasekaran AR. A DNA rotary nanodevice operated by enzyme-initiated strand resetting. Chem Commun (Camb) 2024; 60:534-537. [PMID: 38038977 PMCID: PMC10843534 DOI: 10.1039/d3cc05487j] [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] [Indexed: 12/02/2023]
Abstract
DNA nanostructures that respond to external stimuli have found applications in several areas such as biosensing, drug delivery and molecular computation. The use of different types of stimuli in a single operation provides another layer of control for the reconfiguration of nucleic acid nanostructures. This work demonstrates the use of a ribonuclease to "unset" a nucleic acid nanodevice based on the paranemic crossover (PX) DNA and specific DNA inputs to "reset" the structure into a juxtaposed DNA (JX2) configuration, resulting in a 180° rotation of the helical domains. Such operations would be useful in translational applications where DNA nanostructures can be designed to reconfigure on the basis of more than one stimulus.
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4
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Yang GQ, Cai W, Zhang Z, Wang Y. Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System. ACS APPLIED BIO MATERIALS 2023; 6:5125-5144. [PMID: 38011318 DOI: 10.1021/acsabm.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Every year cancer causes approximately 10 million deaths globally. Researchers have developed numerous targeted drug delivery systems (DDSs) with nanoparticles, polymers, and liposomes, but these synthetic materials have poor degradability and low biocompatibility. Because DNA nanostructures have good degradability and high biocompatibility, extensive studies have been performed to construct DDSs with DNA nanostructures as the molecular-layer master frame (MF) assembled via programmable DNA-aided self-assembly for targeted drug release. To learn the progressing trend of self-assembly techniques and keep pace with their recent rapid advancements, it is crucial to provide an overview of their past and recent progress. In this review article, we first present the techniques to assemble the MF of a DDS with solely DNA strands; to assemble MFs with one or more additional type of construction materials, e.g., polymers (including RNA and protein), inorganic nanoparticle, or metal ions, in addition to DNA strands; and to assemble the more complex DNA nanocomplexes. It is observed that both the techniques used and the MFs constructed have become increasingly complex and that the DDS constructed has an increasing number of advanced functions. From our focused review, we anticipate that DDSs with the MF of multiple building materials and DNA nanocomplexes will attract an increasing number of researchers' interests. On the basis of knowledge about materials and functional components (e.g., targeting aptamers/peptides/antibodies and stimuli for drug release) obtained from previously performed studies, researchers can combine more materials with DNA strands to assemble more powerful MFs and incorporate more components to endow DDSs with improved or additional properties/functions, thereby subsequently contributing to cancer prevention.
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Affiliation(s)
- Gary Q Yang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Weibin Cai
- School of Chemical and Environmental Engineering, China University of Mining and Technology, Beijing 100083, P. R. China
| | - Zhiwen Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. China
| | - Yujun Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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5
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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6
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Fochtman TJ, Oza JP. Established and Emerging Methods for Protecting Linear DNA in Cell-Free Expression Systems. Methods Protoc 2023; 6:mps6020036. [PMID: 37104018 PMCID: PMC10146267 DOI: 10.3390/mps6020036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
Cell-free protein synthesis (CFPS) is a method utilized for producing proteins without the limits of cell viability. The plug-and-play utility of CFPS is a key advantage over traditional plasmid-based expression systems and is foundational to the potential of this biotechnology. A key limitation of CFPS is the varying stability of DNA types, limiting the effectiveness of cell-free protein synthesis reactions. Researchers generally rely on plasmid DNA for its ability to support robust protein expression in vitro. However, the overhead required to clone, propagate, and purify plasmids reduces the potential of CFPS for rapid prototyping. While linear templates overcome the limits of plasmid DNA preparation, linear expression templates (LETs) were under-utilized due to their rapid degradation in extract based CFPS systems, limiting protein synthesis. To reach the potential of CFPS using LETs, researchers have made notable progress toward protection and stabilization of linear templates throughout the reaction. The current advancements range from modular solutions, such as supplementing nuclease inhibitors and genome engineering to produce strains lacking nuclease activity. Effective application of LET protection techniques improves expression yields of target proteins to match that of plasmid-based expression. The outcome of LET utilization in CFPS is rapid design–build–test–learn cycles to support synthetic biology applications. This review describes the various protection mechanisms for linear expression templates, methodological insights for implementation, and proposals for continued efforts that may further advance the field.
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Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
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Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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8
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Sampedro Vallina N, McRae EKS, Geary C, Andersen ES. An RNA Paranemic Crossover Triangle as A 3D Module for Cotranscriptional Nanoassembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204651. [PMID: 36526605 DOI: 10.1002/smll.202204651] [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: 07/29/2022] [Revised: 11/15/2022] [Indexed: 05/28/2023]
Abstract
RNA nanotechnology takes advantage of structural modularity to build self-assembling nano-architectures with applications in medicine and synthetic biology. The use of paranemic motifs, that form without unfolding existing secondary structure, allows for the creation of RNA nanostructures that are compatible with cotranscriptional folding in vitro and in vivo. In previous work, kissing-loop (KL) motifs have been widely used to design RNA nanostructures that fold cotranscriptionally. However, the paranemic crossover (PX) motif has not yet been explored for cotranscriptional RNA origami architectures and information about the structural geometry of the motif is unknown. Here, a six base pair-wide paranemic RNA interaction that arranges double helices in a perpendicular manner is introduced, allowing for the generation of a new and versatile building block: the paranemic-crossover triangle (PXT). The PXT is self-assembled by cotranscriptional folding and characterized by cryogenic electron microscopy, revealing for the first time an RNA PX interaction in high structural detail. The PXT is used as a building block for the construction of multimers that form filaments and rings and a duplicated PXT motif is used as a building block to self-assemble cubic structures, demonstrating the PXT as a rigid self-folding domain for the development of wireframe RNA origami architectures.
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Affiliation(s)
- Néstor Sampedro Vallina
- Interdisciplinary Nanoscience Center (iNANO); Gustav Wieds Vej 14, Aarhus University, Aarhus, DK-8000, Denmark
| | - Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO); Gustav Wieds Vej 14, Aarhus University, Aarhus, DK-8000, Denmark
| | - Cody Geary
- Interdisciplinary Nanoscience Center (iNANO); Gustav Wieds Vej 14, Aarhus University, Aarhus, DK-8000, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO); Gustav Wieds Vej 14, Aarhus University, Aarhus, DK-8000, Denmark
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9
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Chandrasekaran AR. DNA nanotechnology in the undergraduate laboratory: Electrophoretic analysis of DNA nanostructure biostability. JOURNAL OF CHEMICAL EDUCATION 2023; 100:316-320. [PMID: 37193549 PMCID: PMC10168010 DOI: 10.1021/acs.jchemed.2c00656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The field of DNA nanotechnology has grown rapidly in the last decade and has expanded to multiple laboratories. While lectures in DNA nanotechnology have been introduced in some institutions, laboratory components at the undergraduate level are still lacking. Undergraduate students predominantly learn about DNA nanotechnology through their involvement as interns in research laboratories. The DNA nanostructure biostability analysis experiment presented here can be used as a hands-on introductory laboratory exercise for discussing concepts in DNA nanotechnology in an undergraduate setting. This experiment discusses biostability, gel electrophoresis and quantitative analysis of nuclease degradation of a model DNA nanostructure, the paranemic crossover (PX) DNA motif. The experiment can be performed in a chemistry, biology or a biochemistry laboratory with minimal costs and can be adapted in undergraduate institutions using the instructor and student manuals provided here. Laboratory courses based on cutting edge research not only provide students a direct hands-on approach to the subject, but can also increase undergraduate student participation in research. Moreover, laboratory courses that reflect the increasingly multidisciplinary nature of research add value to undergraduate education.
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Yang M, Bakker D, Raghu D, Li ITS. A single strand: A simplified approach to DNA origami. Front Chem 2023; 11:1126177. [PMID: 36891219 PMCID: PMC9986268 DOI: 10.3389/fchem.2023.1126177] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Just as a single polypeptide strand can self-fold into a complex 3D structure, a single strand of DNA can self-fold into DNA origami. Most DNA origami structures (i.e., the scaffold-staple and DNA tiling systems) utilize hundreds of short single-stranded DNA. As such, these structures come with challenges inherent to intermolecular construction. Many assembly challenges involving intermolecular interactions can be resolved if the origami structure is constructed from one DNA strand, where folding is not concentration dependent, the folded structure is more resistant to nuclease degradation, and the synthesis can be achieved at an industrial scale at a thousandth of the cost. This review discusses the design principles and considerations employed in single-stranded DNA origami and its potential benefits and drawbacks.
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Affiliation(s)
- Micah Yang
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - David Bakker
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Dyuti Raghu
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
| | - Isaac T S Li
- Department of Chemistry, The University of British Columbia, Kelowna, BC, Canada
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11
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Poppleton E, Urbanek N, Chakraborty T, Griffo A, Monari L, Göpfrich K. RNA origami: design, simulation and application. RNA Biol 2023; 20:510-524. [PMID: 37498217 PMCID: PMC10376919 DOI: 10.1080/15476286.2023.2237719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/20/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023] Open
Abstract
Design strategies for DNA and RNA nanostructures have developed along parallel lines for the past 30 years, from small structural motifs derived from biology to large 'origami' structures with thousands to tens of thousands of bases. With the recent publication of numerous RNA origami structures and improved design methods-even permitting co-transcriptional folding of kilobase-sized structures - the RNA nanotechnolgy field is at an inflection point. Here, we review the key achievements which inspired and enabled RNA origami design and draw comparisons with the development and applications of DNA origami structures. We further present the available computational tools for the design and the simulation, which will be key to the growth of the RNA origami community. Finally, we portray the transition from RNA origami structure to function. Several functional RNA origami structures exist already, their expression in cells has been demonstrated and first applications in cell biology have already been realized. Overall, we foresee that the fast-paced RNA origami field will provide new molecular hardware for biophysics, synthetic biology and biomedicine, complementing the DNA origami toolbox.
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Affiliation(s)
- Erik Poppleton
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Molecular Biomechanics, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Niklas Urbanek
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Taniya Chakraborty
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Luca Monari
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
- Institut de Science Et D’ingénierie Supramoléculaires (ISIS), Université de Strasbourg, Strasbourg, France
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
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12
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Lee JY, Yang Q, Chang X, Wisniewski H, Olivera TR, Saji M, Kim S, Perumal D, Zhang F. Nucleic acid paranemic structures: a promising building block for functional nanomaterials in biomedical and bionanotechnological applications. J Mater Chem B 2022; 10:7460-7472. [PMID: 35912570 DOI: 10.1039/d2tb00605g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the past few decades, DNA has been recognized as a powerful self-assembling material capable of crafting supramolecular nanoarchitectures with quasi-angstrom precision, which promises various applications in the fields of materials science, nanoengineering, and biomedical science. Notable structural features include biocompatibility, biodegradability, high digital encodability by Watson-Crick base pairing, nanoscale dimension, and surface addressability. Bottom-up fabrication of complex DNA nanostructures relies on the design of fundamental DNA motifs, including parallel (PX) and antiparallel (AX) crossovers. However, paranemic or PX motifs have not been thoroughly explored for the construction of DNA-based nanostructures compared to AX motifs. In this review, we summarize the developments of PX-based DNA nanostructures, highlight the advantages as well as challenges of PX-based assemblies, and give an overview of the structural and chemical features that lend their utilization in a variety of applications. The works presented cover PX-based DNA nanostructures in biological systems, dynamic systems, and biomedical contexts. The possible future advances of PX structures and applications are also summarized, discussed, and postulated.
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Affiliation(s)
- Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Henry Wisniewski
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | - Suchan Kim
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
| | | | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA.
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13
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Obtaining Precise Molecular Information via DNA Nanotechnology. MEMBRANES 2021; 11:membranes11090683. [PMID: 34564500 PMCID: PMC8466356 DOI: 10.3390/membranes11090683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022]
Abstract
Precise characterization of biomolecular information such as molecular structures or intermolecular interactions provides essential mechanistic insights into the understanding of biochemical processes. As the resolution of imaging-based measurement techniques improves, so does the quantity of molecular information obtained using these methodologies. DNA (deoxyribonucleic acid) molecule have been used to build a variety of structures and dynamic devices on the nanoscale over the past 20 years, which has provided an accessible platform to manipulate molecules and resolve molecular information with unprecedented precision. In this review, we summarize recent progress related to obtaining precise molecular information using DNA nanotechnology. After a brief introduction to the development and features of structural and dynamic DNA nanotechnology, we outline some of the promising applications of DNA nanotechnology in structural biochemistry and in molecular biophysics. In particular, we highlight the use of DNA nanotechnology in determination of protein structures, protein-protein interactions, and molecular force.
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14
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Wang DX, Wang J, Wang YX, Du YC, Huang Y, Tang AN, Cui YX, Kong DM. DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem Sci 2021; 12:7602-7622. [PMID: 34168817 PMCID: PMC8188511 DOI: 10.1039/d1sc00587a] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022] Open
Abstract
In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.
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Affiliation(s)
- Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yan Huang
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
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15
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Mao S, Chang Z, Ying Zheng Y, Shekhtman A, Sheng J. DNA Functionality with Photoswitchable Hydrazone Cytidine*. Chemistry 2021; 27:8372-8379. [PMID: 33872432 DOI: 10.1002/chem.202100742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 12/18/2022]
Abstract
A new family of hydrazone modified cytidine phosphoramidite building block was synthesized and incorporated into oligodeoxynucleotides to construct photoswitchable DNA strands. The E-Z isomerization triggered by the irradiation of blue light with a wavelength of 450 nm was investigated and confirmed by 1 H NMR spectroscopy and HPLC in the contexts of both nucleoside and oligodeoxynucleotide. The light activated Z form isomer of this hydrazone-cytidine with a six-member intramolecular hydrogen bond was found to inhibit DNA synthesis in the primer extension model by using Bst DNA polymerase. In addition, the hydrazone modification caused the misincorporation of dATP together with dGTP into the growing DNA strand with similar selectivity, highlighting a potential G to A mutation. This work provides a novel functional DNA building block and an additional molecular tool that has potential chemical biology and biomedicinal applications to control DNA synthesis and DNA-enzyme interactions using the cell friendly blue light irradiation.
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Affiliation(s)
- Song Mao
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA.,The RNA Institute, University at Albany State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA
| | - Zhihua Chang
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA.,The RNA Institute, University at Albany State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA
| | - Ya Ying Zheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA.,The RNA Institute, University at Albany State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA.,The RNA Institute, University at Albany State University of New York, 1400 Washington Ave., Albany, NY, 1222, USA
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16
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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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17
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Chandrasekaran AR, Halvorsen K. Nuclease Degradation Analysis of DNA Nanostructures Using Gel Electrophoresis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2020; 82:e115. [PMID: 32931657 PMCID: PMC8034824 DOI: 10.1002/cpnc.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Custom-built DNA nanostructures are now used in applications such as biosensing, molecular computation, biomolecular analysis, and drug delivery. While the functionality and biocompatibility of DNA makes DNA nanostructures useful in such applications, the field faces a challenge in making biostable DNA nanostructures. Being a natural material, DNA is most suited for biological applications, but is also easily degraded by nucleases. Several methods have been employed to study the nuclease degradation rates and enhancement of nuclease resistance. This protocol describes the use of gel electrophoresis to analyze the extent of nuclease degradation of DNA nanostructures and to report degradation times, kinetics of nuclease digestion, and evaluation of biostability enhancement factors. © 2020 Wiley Periodicals LLC. Basic Protocol: Timed analysis of nuclease degradation of DNA nanostructures Support Protocol: Calculating biostability enhancement factors.
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Affiliation(s)
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York
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18
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Ding T, Yang J, Pan V, Zhao N, Lu Z, Ke Y, Zhang C. DNA nanotechnology assisted nanopore-based analysis. Nucleic Acids Res 2020; 48:2791-2806. [PMID: 32083656 PMCID: PMC7102975 DOI: 10.1093/nar/gkaa095] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/29/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.
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Affiliation(s)
- Taoli Ding
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China.,Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Nan Zhao
- School of Control and Computer Engineering, North China Electric Power University, Beijing 102206, China
| | - Zuhong Lu
- Department of Biomedical Engineering, College of engineering, Peking University, Beijing 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Cheng Zhang
- Department of Computer Science and Technology, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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19
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Chandrasekaran AR, Vilcapoma J, Dey P, Wong-Deyrup SW, Dey BK, Halvorsen K. Exceptional Nuclease Resistance of Paranemic Crossover (PX) DNA and Crossover-Dependent Biostability of DNA Motifs. J Am Chem Soc 2020; 142:6814-6821. [PMID: 32208657 DOI: 10.1021/jacs.0c02211] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanometer-sized features and molecular recognition properties make DNA a useful material for nanoscale construction, but degradation in biological fluids poses a considerable roadblock to biomedical applications of DNA nanotechnology. Here, we report the remarkable biostability of a multistranded motif called paranemic crossover (PX) DNA. Compared to double stranded DNA, PX DNA has dramatically enhanced (sometimes >1000 fold) resistance to degradation by four different nucleases, bovine and human serum, and human urine. We trace the cause of PX's biostability to DNA crossovers, showing a continuum of protection that scales with the number of crossovers. These results suggest that enhanced biostability can be engineered into DNA nanostructures by adopting PX-based architectures or by strategic crossover placement.
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Affiliation(s)
- Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Javier Vilcapoma
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States.,Department of Biological Sciences, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Siu Wah Wong-Deyrup
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States.,Department of Biological Sciences, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States.,Department of Biological Sciences, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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20
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Huang J, Ma W, Sun H, Wang H, He X, Cheng H, Huang M, Lei Y, Wang K. Self-Assembled DNA Nanostructures-Based Nanocarriers Enabled Functional Nucleic Acids Delivery. ACS APPLIED BIO MATERIALS 2020; 3:2779-2795. [DOI: 10.1021/acsabm.9b01197] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jin Huang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Wenjie Ma
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Huanhuan Sun
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Huizhen Wang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Xiaoxiao He
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Hong Cheng
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Mingmin Huang
- College of Biology, Hunan University, Changsha 410082, China
| | - Yanli Lei
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
| | - Kemin Wang
- College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- College of Biology, Hunan University, Changsha 410082, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410082, China
- Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China
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21
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22
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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23
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Graczyk A, Pawlowska R, Jedrzejczyk D, Chworos A. Gold Nanoparticles in Conjunction with Nucleic Acids as a Modern Molecular System for Cellular Delivery. Molecules 2020; 25:E204. [PMID: 31947834 PMCID: PMC6982881 DOI: 10.3390/molecules25010204] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
Development of nanotechnology has become prominent in many fields, such as medicine, electronics, production of materials, and modern drugs. Nanomaterials and nanoparticles have gained recognition owing to the unique biochemical and physical properties. Considering cellular application, it is speculated that nanoparticles can transfer through cell membranes following different routes exclusively owing to their size (up to 100 nm) and surface functionalities. Nanoparticles have capacity to enter cells by themselves but also to carry other molecules through the lipid bilayer. This quality has been utilized in cellular delivery of substances like small chemical drugs or nucleic acids. Different nanoparticles including lipids, silica, and metal nanoparticles have been exploited in conjugation with nucleic acids. However, the noble metal nanoparticles create an alternative, out of which gold nanoparticles (AuNP) are the most common. The hybrids of DNA or RNA and metal nanoparticles can be employed for functional assemblies for variety of applications in medicine, diagnostics or nano-electronics by means of biomarkers, specific imaging probes, or gene expression regulatory function. In this review, we focus on the conjugates of gold nanoparticles and nucleic acids in the view of their potential application for cellular delivery and biomedicine. This review covers the current advances in the nanotechnology of DNA and RNA-AuNP conjugates and their potential applications. We emphasize the crucial role of metal nanoparticles in the nanotechnology of nucleic acids and explore the role of such conjugates in the biological systems. Finally, mechanisms guiding the process of cellular intake, essential for delivery of modern therapeutics, will be discussed.
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Affiliation(s)
| | | | | | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (A.G.); (R.P.); (D.J.)
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24
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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25
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Design, assembly, characterization, and operation of double-stranded interlocked DNA nanostructures. Nat Protoc 2019; 14:2818-2855. [DOI: 10.1038/s41596-019-0198-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/16/2019] [Indexed: 01/03/2023]
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26
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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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27
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Complex wireframe DNA nanostructures from simple building blocks. Nat Commun 2019; 10:1067. [PMID: 30842408 PMCID: PMC6403373 DOI: 10.1038/s41467-019-08647-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 01/18/2019] [Indexed: 11/08/2022] Open
Abstract
DNA nanostructures with increasing complexity have showcased the power of programmable self-assembly from DNA strands. At the nascent stage of the field, a variety of small branched objects consisting of a few DNA strands were created. Since then, a quantum leap of complexity has been achieved by a scaffolded 'origami' approach and a scaffold-free approach using single-stranded tiles/bricks-creating fully addressable two-dimensional and three-dimensional DNA nanostructures designed on densely packed lattices. Recently, wireframe architectures have been applied to the DNA origami method to construct complex structures. Here, revisiting the original wireframe framework entirely made of short synthetic strands, we demonstrate a design paradigm that circumvents the sophisticated routing and size limitations intrinsic to the scaffold strand in DNA origami. Under this highly versatile self-assembly framework, we produce a myriad of wireframe structures, including 2D arrays, tubes, polyhedra, and multi-layer 3D arrays.
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28
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Kizer M, Huntress ID, Walcott BD, Fraser K, Bystroff C, Wang X. Complex between a Multicrossover DNA Nanostructure, PX-DNA, and T7 Endonuclease I. Biochemistry 2019; 58:1332-1342. [PMID: 30794750 DOI: 10.1021/acs.biochem.9b00057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Paranemic crossover DNA (PX-DNA) is a four-stranded multicrossover structure that has been implicated in recombination-independent recognition of homology. Although existing evidence has suggested that PX is the DNA motif in homologous pairing (HP), this conclusion remains ambiguous. Further investigation is needed but will require development of new tools. Here, we report characterization of the complex between PX-DNA and T7 endonuclease I (T7endoI), a junction-resolving protein that could serve as the prototype of an anti-PX ligand (a critical prerequisite for the future development of such tools). Specifically, nuclease-inactive T7endoI was produced and its ability to bind to PX-DNA was analyzed using a gel retardation assay. The molar ratio of PX to T7endoI was determined using gel electrophoresis and confirmed by the Hill equation. Hydroxyl radical footprinting of T7endoI on PX-DNA is used to verify the positive interaction between PX and T7endoI and to provide insight into the binding region. Cleavage of PX-DNA by wild-type T7endoI produces DNA fragments, which were used to identify the interacting sites on PX for T7endoI and led to a computational model of their interaction. Altogether, this study has identified a stable complex of PX-DNA and T7endoI and lays the foundation for engineering an anti-PX ligand, which can potentially assist in the study of molecular mechanisms for HP at an advanced level.
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Affiliation(s)
- Megan Kizer
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ian D Huntress
- Programs of Bioinformatics and Molecular Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Benjamin D Walcott
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Keith Fraser
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Christopher Bystroff
- Department of Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Xing Wang
- Department of Chemistry and Chemical Biology , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States.,Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
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Gao X, Gethers M, Han SP, Goddard WA, Sha R, Cunningham RP, Seeman NC. The PX Motif of DNA Binds Specifically to Escherichia coli DNA Polymerase I. Biochemistry 2018; 58:575-581. [PMID: 30557012 DOI: 10.1021/acs.biochem.8b01148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PX motif of DNA is a four-stranded structure in which two parallel juxtaposed double-helical domains are fused by crossovers at every point where the strands approach each other. Consequently, its twist and writhe are approximately half of those of conventional DNA. This property has been shown to relax supercoiled plasmid DNA under circumstances in which head-to-head homology exists within the plasmid; the homology can be either complete homology or every-other-half-turn homology, known as PX homology. It is clearly of interest to establish whether the cell contains proteins that interact with this unusual and possibly functional motif. We have examined Escherichia coli extracts to seek such a protein. We find by gel mobility studies that the PX motif is apparently bound by a cellular component. Fractionation of this binding activity reveals that the component is DNA polymerase I (Pol I). Although the PX motif binds to Pol I, we find that PX-DNA is not able to serve as a substrate for the extension of a shortened strand. We cannot say at this time whether the binding is a coincidence or whether it represents an activity of Pol I that is currently unknown. We have modeled the interaction of Pol I and PX-DNA using symmetry considerations and molecular dynamics.
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Affiliation(s)
- Xiang Gao
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Matthew Gethers
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - Si-Ping Han
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - William A Goddard
- Materials and Process Simulation Center , MC139-74 California Institute of Technology , Pasadena , California 91125 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10003 , United States
| | - Richard P Cunningham
- Department of Biological Sciences , State University of New York at Albany , Albany , New York 12222 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10003 , United States
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30
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Shen W, Liu Q, Ding B, Shen Z, Zhu C, Mao C. The study of the paranemic crossover (PX) motif in the context of self-assembly of DNA 2D crystals. Org Biomol Chem 2018; 14:7187-90. [PMID: 27404049 DOI: 10.1039/c6ob01146b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This manuscript systematically studies the self-assembly behavior of the paranemic crossover (PX) motif in the context of DNA 2D crystallization. The PX structure is a class of DNA nanomotifs that has been suggested as a model for DNA homologous recognition in cells and, more importantly, used as a cohesion mechanism/building block (tile) for DNA nanoconstruction. However, there is no vigorous examination on the relationship between structural variation and assembly behavior. The lack of this essential information prevents us from applying the PX motif to complex nanoconstruction. In this study, we have devised a system that allows us to systematically examine this relationship and found the best PX motif that best suits the assembly of 2D crystals.
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Affiliation(s)
- Weili Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Qing Liu
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Baoquan Ding
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Zhiyong Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Changqing Zhu
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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31
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Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
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32
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Hooper WF, Walcott BD, Wang X, Bystroff C. Fast design of arbitrary length loops in proteins using InteractiveRosetta. BMC Bioinformatics 2018; 19:337. [PMID: 30249181 PMCID: PMC6154894 DOI: 10.1186/s12859-018-2345-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/29/2018] [Indexed: 11/10/2022] Open
Abstract
Background With increasing interest in ab initio protein design, there is a desire to be able to fully explore the design space of insertions and deletions. Nature inserts and deletes residues to optimize energy and function, but allowing variable length indels in the context of an interactive protein design session presents challenges with regard to speed and accuracy. Results Here we present a new module (INDEL) for InteractiveRosetta which allows the user to specify a range of lengths for a desired indel, and which returns a set of low energy backbones in a matter of seconds. To make the loop search fast, loop anchor points are geometrically hashed using C α-C α and C β-C β distances, and the hash is mapped to start and end points in a pre-compiled random access file of non-redundant, protein backbone coordinates. Loops with superposable anchors are filtered for collisions and returned to InteractiveRosetta as poly-alanine for display and selective incorporation into the design template. Sidechains can then be added using RosettaDesign tools. Conclusions INDEL was able to find viable loops in 100% of 500 attempts for all lengths from 3 to 20 residues. INDEL has been applied to the task of designing a domain-swapping loop for T7-endonuclease I, changing its specificity from Holliday junctions to paranemic crossover (PX) DNA. Electronic supplementary material The online version of this article (10.1186/s12859-018-2345-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William F Hooper
- Emmes Corporation, Rockville, Washington, MD, USA.,Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | | | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Christopher Bystroff
- Department of Biology, Rensselaer Polytechnic Institute, Troy, NY, USA. .,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY, USA.
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33
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Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
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Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
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34
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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35
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Shen W, Liu Q, Ding B, Zhu C, Shen Z, Seeman NC. Facilitation of DNA self-assembly by relieving the torsional strains between building blocks. Org Biomol Chem 2018; 15:465-469. [PMID: 27924995 DOI: 10.1039/c6ob02281b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Paranemic crossover (PX) DNA motifs were designed and used for self-assembly of two dimensional lattices. The PX motifs tested include overwound and underwound ones, and different forms of self-assembled two-dimensional (2D) lattices were generated, demonstrating the correlation between the helical torsional strain within the system and the quality of the lattice formed. Relief of the torsional strain by adjusting the number of base pairs in the JX region adjacent to the PX motifs, facilitates and optimizes DNA self-assembly, which leads to 2D lattices of greater uniformity and higher yield. This study demonstrated that the helical relationship among DNA building blocks is a critical factor for the tile-based self-assembly of large nanostructures.
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Affiliation(s)
- Weili Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Qing Liu
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Baoquan Ding
- National Center for NanoScience and Technology, ZhongGuanCun, Beijing 100190, China
| | - Changqing Zhu
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Zhiyong Shen
- College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241000, China.
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York 10003, USA.
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36
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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37
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Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P. Single-stranded DNA and RNA origami. Science 2017; 358:eaao2648. [PMID: 29242318 PMCID: PMC6384012 DOI: 10.1126/science.aao2648] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/27/2017] [Indexed: 12/22/2022]
Abstract
Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology.
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Affiliation(s)
- Dongran Han
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xiaodong Qi
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Cameron Myhrvold
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bei Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Mingjie Dai
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Shuoxing Jiang
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Maxwell Bates
- BioNano Research Group, Autodesk Life Sciences, Pier 9, San Francisco, CA 94111, USA
| | - Yan Liu
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Byoungkwon An
- BioNano Research Group, Autodesk Life Sciences, Pier 9, San Francisco, CA 94111, USA.
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics Biodesign Institute, Tempe, AZ 85287, USA.
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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38
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Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component. Cell Chem Biol 2017; 24:1401-1406.e2. [DOI: 10.1016/j.chembiol.2017.08.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/06/2017] [Accepted: 08/18/2017] [Indexed: 11/15/2022]
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39
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Pan K, Bricker WP, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Res 2017; 45:6284-6298. [PMID: 28482032 PMCID: PMC5499760 DOI: 10.1093/nar/gkx378] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/25/2017] [Indexed: 12/22/2022] Open
Abstract
Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson–Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5–100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone.
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Affiliation(s)
- Keyao Pan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sakul Ratanalert
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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40
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Jiang S, Hong F, Hu H, Yan H, Liu Y. Understanding the Elementary Steps in DNA Tile-Based Self-Assembly. ACS NANO 2017; 11:9370-9381. [PMID: 28813590 DOI: 10.1021/acsnano.7b04845] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although many models have been developed to guide the design and implementation of DNA tile-based self-assembly systems with increasing complexity, the fundamental assumptions of the models have not been thoroughly tested. To expand the quantitative understanding of DNA tile-based self-assembly and to test the fundamental assumptions of self-assembly models, we investigated DNA tile attachment to preformed "multi-tile" arrays in real time and obtained the thermodynamic and kinetic parameters of single tile attachment in various sticky end association scenarios. With more sticky ends, tile attachment becomes more thermostable with an approximately linear decrease in the free energy change (more negative). The total binding free energy of sticky ends is partially compromised by a sequence-independent energy penalty when tile attachment forms a constrained configuration: "loop". The minimal loop is a 2 × 2 tetramer (Loop4). The energy penalty of loops of 4, 6, and 8 tiles was analyzed with the independent loop model assuming no interloop tension, which is generalizable to arbitrary tile configurations. More sticky ends also contribute to a faster on-rate under isothermal conditions when nucleation is the rate-limiting step. Incorrect sticky end contributes to neither the thermostability nor the kinetics. The thermodynamic and kinetic parameters of DNA tile attachment elucidated here will contribute to the future improvement and optimization of tile assembly modeling, precise control of experimental conditions, and structural design for error-free self-assembly.
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Affiliation(s)
- Shuoxing Jiang
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Fan Hong
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Huiyu Hu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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41
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Yang D, Tan Z, Mi Y, Wei B. DNA nanostructures constructed with multi-stranded motifs. Nucleic Acids Res 2017; 45:3606-3611. [PMID: 28334880 PMCID: PMC5389474 DOI: 10.1093/nar/gkx121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 02/09/2017] [Indexed: 11/25/2022] Open
Abstract
Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices. The extended set of motifs is used for self-assembly of complex one dimensional, two dimensional and three dimensional structures.
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Affiliation(s)
- Donglei Yang
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhenyu Tan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongli Mi
- School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China.,Department of Chemical and Biomolecular Engineering, the Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - 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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42
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Valero J, Lohmann F, Famulok M. Interlocked DNA topologies for nanotechnology. Curr Opin Biotechnol 2017; 48:159-167. [PMID: 28505598 DOI: 10.1016/j.copbio.2017.04.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 11/19/2022]
Abstract
Interlocked molecular architectures are well known in supramolecular chemistry and are widely used for various applications like sensors, molecular machines and logic gates. The use of DNA for constructing these interlocked structures has increased significantly within the current decade. Because of Watson-Crick base pairing rules, DNA is an excellent material for the self-assembly of well-defined interlocked nanoarchitectures. These DNA nanostructures exhibit sufficient stability, good solubility in aqueous media, biocompatibility, and can be easily combined with other biomolecules in bio-hybrid nano-assemblies. Therefore, the study of novel DNA-based interlocked systems is of interest for nanotechnology, synthetic biology, supramolecular chemistry, biotechnology, and for sensing purposes. Here we summarize recent developments and applications of interlocked supramolecular architectures made of DNA. Examples illustrating that these systems can be precisely controlled by switching on and off the molecular motion of its mechanically trapped components are discussed. Introducing different triggers into such systems creates molecular assemblies capable of performing logic gate operations and/or catalytic activity control. Interlocked DNA-based nanostructures thus represent promising frameworks for building increasingly complex and dynamic nanomachines with highly controllable functionality.
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Affiliation(s)
- Julián Valero
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Finn Lohmann
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Michael Famulok
- Life and Medical Sciences (LIMES) Institute, Chemical Biology and Medicinal Chemistry Unit, c/o Kekulé Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany; Center of Advanced European Studies and Research (CASEAR), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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43
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Joshi H, Kaushik A, Seeman NC, Maiti PK. Nanoscale Structure and Elasticity of Pillared DNA Nanotubes. ACS NANO 2016; 10:7780-91. [PMID: 27400249 DOI: 10.1021/acsnano.6b03360] [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: 05/26/2023]
Abstract
We present an atomistic model of pillared DNA nanotubes (DNTs) and their elastic properties which will facilitate further studies of these nanotubes in several important nanotechnological and biological applications. In particular, we introduce a computational design to create an atomistic model of a 6-helix DNT (6HB) along with its two variants, 6HB flanked symmetrically with two double helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation trajectories in the presence of explicit water and ions shows that these structures are stable and well behaved in all three geometries. Hydrogen bonding is well maintained for all variants of 6HB DNTs. From the equilibrium bending angle distribution, we calculate the persistence lengths of these tubes. The measured persistence lengths of these nanotubes are ∼10 μm, which is 2 orders of magnitude larger than that of dsDNA. We also find a gradual increase of persistence length with an increasing number of pillars, in quantitative agreement with previous experimental findings. To have a quantitative understanding of the stretch modulus of these tubes, we carried out nonequilibrium steered molecular dynamics (SMD). The linear part of the force-extension plot gives a stretch modulus in the range 6500 pN for 6HB without pillars, which increases to 11 000 pN for tubes with three pillars. The values of the stretch modulus calculated using contour length distribution obtained from equilibrium MD simulations are similar to those obtained from nonequilibrium SMD simulations. The addition of pillars makes these DNTs very rigid.
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Affiliation(s)
- Himanshu Joshi
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India
| | - Atul Kaushik
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600 036, India
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science , Bangalore 560012, India
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44
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Shi X, Wu X, Song T, Li X. Construction of DNA nanotubes with controllable diameters and patterns using hierarchical DNA sub-tiles. NANOSCALE 2016; 8:14785-14792. [PMID: 27444699 DOI: 10.1039/c6nr02695h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The design of DNA nanotubes is a promising and hot research branch in structural DNA nanotechnology, which is rapidly developing as a versatile method for achieving subtle nanometer scale materials and molecular diagnostic/curative devices. Multifarious methods have been proposed to achieve varied DNA nanotubes, such as using square tiles and single-stranded tiles, but it is still a challenge to develop a bottom-up assembly way to build DNA nanotubes with different diameters and patterns using certain universal DNA nanostructures. This work addresses the challenge by assembling three types of spatial DNA nanotubes with different diameters and patterns from the so-called "basic bricks", i.e., hierarchical DNA sub-tiles. A high processing rate and throughput synthesis of DNA nanotubes are observed and analyzed by atomic force microscopy. Experimental observations and data analysis suggests the stability and controllability of DNA nanotubes assembled by hierarchical DNA sub-tiles.
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Affiliation(s)
- Xiaolong Shi
- Key Laboratory of Image Information Processing and Intelligent Control, School of Automation, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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45
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Alves C, Iacovelli F, Falconi M, Cardamone F, Morozzo Della Rocca B, de Oliveira CLP, Desideri A. A Simple and Fast Semiautomatic Procedure for the Atomistic Modeling of Complex DNA Polyhedra. J Chem Inf Model 2016; 56:941-9. [PMID: 27050675 DOI: 10.1021/acs.jcim.5b00586] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A semiautomatic procedure to build complex atomistic covalently linked DNA nanocages has been implemented in a user-friendly, free, and fast program. As a test set, seven different truncated DNA polyhedra, composed by B-DNA double helices connected through short single-stranded linkers, have been generated. The atomistic structures, including a tetrahedron, a cube, an octahedron, a dodecahedron, a triangular prism, a pentagonal prism, and a hexagonal prism, have been probed through classical molecular dynamics and analyzed to evaluate their structural and dynamical properties and to highlight possible building faults. The analysis of the simulated trajectories also allows us to investigate the role of the different geometries in defining nanocages stability and flexibility. The data indicate that the cages are stable and that their structural and dynamical parameters measured along the trajectories are slightly affected by the different geometries. These results demonstrate that the constraints imposed by the covalent links induce an almost identical conformational variability independently of the three-dimensional geometry and that the program presented here is a reliable and valid tool to engineer DNA nanostructures.
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Affiliation(s)
- Cassio Alves
- Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil.,Department of Engineering and Sciences, Federal University of Paraná , 85950-000 Palotina, Paraná, Brazil
| | - Federico Iacovelli
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Mattia Falconi
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Francesca Cardamone
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Blasco Morozzo Della Rocca
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Cristiano L P de Oliveira
- Instituto de Fisica, Grupo de Fluidos Complexos, Universidade de São Paulo , Caixa Postal 66318, 05314-970 Sao Paulo, Brazil
| | - Alessandro Desideri
- Department of Biology, University of Rome "Tor Vergata" , Via della Ricerca Scientifica, 00133 Rome, Italy
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46
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Mazur AK. Homologous Pairing between Long DNA Double Helices. PHYSICAL REVIEW LETTERS 2016; 116:158101. [PMID: 27127987 DOI: 10.1103/physrevlett.116.158101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments, I show here that direct recognition between homologous dsDNA is possible through the formation of short quadruplexes due to direct complementary hydrogen bonding of major-groove surfaces in parallel alignment. The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism and concomitant predictions agree with the available experimental data and shed light upon the sequence effects and the possible involvement of topoisomerase II in the recognition.
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Affiliation(s)
- Alexey K Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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47
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Ohayon YP, Sha R, Flint O, Chandrasekaran AR, Abdallah HO, Wang T, Wang X, Zhang X, Seeman NC. Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion. ACS NANO 2015; 9:10296-10303. [PMID: 26364680 DOI: 10.1021/acsnano.5b04333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
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Affiliation(s)
- Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ortho Flint
- Department of Mathematics, University of Western Ontario , London, ON N6A 3K7, Canada
| | | | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Tong Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xing Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xiaoping Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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48
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Ohayon YP, Sha R, Flint O, Liu W, Chakraborty B, Subramanian HKK, Zheng J, Chandrasekaran AR, Abdallah HO, Wang X, Zhang X, Seeman NC. Covalent Linkage of One-Dimensional DNA Arrays Bonded by Paranemic Cohesion. ACS NANO 2015; 9:10304-10312. [PMID: 26343906 DOI: 10.1021/acsnano.5b04335] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The construction of DNA nanostructures from branched DNA motifs, or tiles, typically relies on the use of sticky-ended cohesion, owing to the specificity and programmability of DNA sequences. The stability of such constructs when unligated is restricted to a specific range of temperatures, owing to the disruption of base pairing at elevated temperatures. Paranemic (PX) cohesion was developed as an alternative to sticky ends for the cohesion of large topologically closed species that could be purified reliably on denaturing gels. However, PX cohesion is also of limited stability. In this work, we added sticky-ended interactions to PX-cohesive complexes to create interlocked complexes by functionalizing the sticky ends with psoralen, which can form cross-links between the two strands of a double helix. We were able to reinforce the stability of the constructs by creating covalent linkages between the 3'-ends and 5'-ends of the sticky ends; the sticky ends were added to double crossover domains via 3'-3' and 5'-5' linkages. Catenated arrays were obtained either by enzymatic ligation or by UV cross-linking. We have constructed finite-length one-dimensional arrays linked by interlocking loops and have positioned streptavidin-gold particles on these constructs.
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Affiliation(s)
- Yoel P Ohayon
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ruojie Sha
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Ortho Flint
- Department of Mathematics, University of Western Ontario , London, ON N6A 5B7, Canada
| | - Wenyan Liu
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Banani Chakraborty
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Hari K K Subramanian
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Jianping Zheng
- Department of Chemistry, New York University , New York, New York 10003, United States
| | | | - Hatem O Abdallah
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xing Wang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Xiaoping Zhang
- Department of Chemistry, New York University , New York, New York 10003, United States
| | - Nadrian C Seeman
- Department of Chemistry, New York University , New York, New York 10003, United States
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49
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Zhang F, Jiang S, Wu S, Li Y, Mao C, Liu Y, Yan H. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. NATURE NANOTECHNOLOGY 2015; 10:779-84. [PMID: 26192207 DOI: 10.1038/nnano.2015.162] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/23/2015] [Indexed: 05/20/2023]
Abstract
Structural DNA nanotechnology and the DNA origami technique, in particular, have provided a range of spatially addressable two- and three-dimensional nanostructures. These structures are, however, typically formed of tightly packed parallel helices. The development of wireframe structures should allow the creation of novel designs with unique functionalities, but engineering complex wireframe architectures with arbitrarily designed connections between selected vertices in three-dimensional space remains a challenge. Here, we report a design strategy for fabricating finite-size wireframe DNA nanostructures with high complexity and programmability. In our approach, the vertices are represented by n × 4 multi-arm junctions (n = 2-10) with controlled angles, and the lines are represented by antiparallel DNA crossover tiles of variable lengths. Scaffold strands are used to integrate the vertices and lines into fully assembled structures displaying intricate architectures. To demonstrate the versatility of the technique, a series of two-dimensional designs including quasi-crystalline patterns and curvilinear arrays or variable curvatures, and three-dimensional designs including a complex snub cube and a reconfigurable Archimedean solid were constructed.
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Affiliation(s)
- Fei Zhang
- Center for Molecular Design and Biomimetics, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Siyu Wu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yulin Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yan Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute and the Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA
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50
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Niu D, Jiang H, Sha R, Canary JW, Seeman NC. The unusual and dynamic character of PX-DNA. Nucleic Acids Res 2015; 43:7201-6. [PMID: 26184876 PMCID: PMC4551946 DOI: 10.1093/nar/gkv739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/08/2015] [Indexed: 11/13/2022] Open
Abstract
PX-DNA is a four-stranded DNA structure that has been implicated in the recognition of homology, either continuously, or in an every-other-half-turn fashion. Some of the structural features of the molecule have been noted previously, but the structure requires further characterization. Here, we report atomic force microscopic characterization of PX molecules that contain periodically placed biotin groups, enabling the molecule to be labeled by streptavidin molecules at these sites. In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure. Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure. Circular dichroism spectroscopy indicates unusual features in the PX molecule that are absent in both the molecules to which it is compared.
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Affiliation(s)
- Dong Niu
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Hualin Jiang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Nadrian C Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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