1
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Abstract
DNA nanotechnology enables straightforward fabrication of user-defined and nanometer-precise templates for a cornucopia of different uses. To date, most of these DNA assemblies have been static, but dynamic structures are increasingly coming into view. The programmability of DNA not only allows for encoding of the DNA object shape but also it may be equally used in defining the mechanism of action and the type of stimuli-responsiveness of the dynamic structures. However, these "robotic" features of DNA nanostructures are usually demonstrated for only small, discrete, and device-like objects rather than for collectively behaving higher-order systems. Here, we show how a large-scale, two-dimensional (2D) and pH-responsive DNA origami-based lattice can be assembled into two different configurations ("open" and "closed" states) on a mica substrate and further switched from one to the other distinct state upon a pH change of the surrounding solution. The control over these two configurations is achieved by equipping the arms of the lattice-forming DNA origami units with "pH-latches" that form Hoogsteen-type triplexes at low pH. In short, we demonstrate how the electrostatic control over the adhesion and mobility of the DNA origami units on the surface can be used both in the large lattice formation (with the help of directed polymerization) and in the conformational switching of the whole lattice. To further emphasize the feasibility of the method, we also demonstrate the formation of pH-responsive 2D gold nanoparticle lattices. We believe this work can bridge the nanometer-precise DNA origami templates and higher-order large-scale systems with the stimuli-induced dynamicity.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
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2
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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3
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Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
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Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
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4
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Abstract
Hierarchical assembly of programmable DNA frameworks─such as DNA origami─paves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Adrian Keller
- Paderborn
University, Technical and Macromolecular
Chemistry, Warburger
Str. 100, 33098 Paderborn, Germany,
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland,LIBER
Center of Excellence, Aalto University, 00076 Aalto, Finland,
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5
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Piskunen P, Latham R, West CE, Castronovo M, Linko V. Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience 2022; 25:104389. [PMID: 35633938 PMCID: PMC9130510 DOI: 10.1016/j.isci.2022.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective.
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6
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Tseng CY, Wang WX, Douglas TR, Chou LYT. Engineering DNA Nanostructures to Manipulate Immune Receptor Signaling and Immune Cell Fates. Adv Healthc Mater 2022; 11:e2101844. [PMID: 34716686 DOI: 10.1002/adhm.202101844] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Immune cells sense, communicate, and logically integrate a multitude of environmental signals to make important cell-fate decisions and fulfill their effector functions. These processes are initiated and regulated by a diverse array of immune receptors and via their dynamic spatiotemporal organization upon ligand binding. Given the widespread relevance of the immune system to health and disease, there have been significant efforts toward understanding the biophysical principles governing immune receptor signaling and activation, as well as the development of biomaterials which exploit these principles for therapeutic immune engineering. Here, how advances in the field of DNA nanotechnology constitute a growing toolbox for further pursuit of these endeavors is discussed. Key cellular players involved in the induction of immunity against pathogens or diseased cells are first summarized. How the ability to design DNA nanostructures with custom shapes, dynamics, and with site-specific incorporation of diverse guests can be leveraged to manipulate the signaling pathways that regulate these processes is then presented. It is followed by highlighting emerging applications of DNA nanotechnology at the crossroads of immune engineering, such as in vitro reconstitution platforms, vaccines, and adjuvant delivery systems. Finally, outstanding questions that remain for further advancing immune-modulatory DNA nanodevices are outlined.
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Affiliation(s)
- Chung Yi Tseng
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Wendy Xueyi Wang
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Travis Robert Douglas
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
| | - Leo Y. T. Chou
- Institute of Biomedical Engineering University of Toronto Toronto Ontario M5S 3G9 Canada
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7
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Jergens E, Winter JO. Nanoparticles caged with DNA nanostructures. Curr Opin Biotechnol 2022; 74:278-284. [PMID: 35026622 DOI: 10.1016/j.copbio.2021.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 12/19/2021] [Indexed: 12/19/2022]
Abstract
Nanoparticles (NPs) offer many benefits in biotechnology because of their small size and unique properties. However, many applications require precise positioning of the NPs or biological targeting molecules on their surfaces. DNA cages constructed from DNA tile, origami, or wireframe nanostructures offer a promising path forward because of their simplicity and programmability that can be used to generate complex, dynamic 2D and 3D geometries. Such materials can be used to pattern DNA on NP surfaces and organize NPs into specific supramolecular structures. DNA-caged NPs can be implemented in biosensing and drug delivery applications with cavities precisely designed to encapsulate-specific biomolecules. Ultimately, such approaches provide a springboard for future DNA robot designs that will enable controlled interactions with biological systems.
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Affiliation(s)
- Elizabeth Jergens
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W Woodruff Ave., Columbus, OH 43210, USA
| | - Jessica O Winter
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W Woodruff Ave., Columbus, OH 43210, USA; Department of Biomedical Engineering, The Ohio State University, 140 W. 19th Ave., Columbus, OH 43210, USA.
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8
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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9
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Gangrade A, Stephanopoulos N, Bhatia D. Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. NANOSCALE 2021; 13:16834-16846. [PMID: 34622910 DOI: 10.1039/d1nr04475c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
DNA-based nanotechnology has evolved into an autonomous, highly innovative, and dynamic field of research at the nexus of supramolecular chemistry, nanotechnology, materials science, and biotechnology. DNA-based materials, including origami nanodevices, have started to emerge as an ideal scaffold for use in cellular programming, tissue engineering, and drug delivery applications. We cover herein the applications for DNA as a scaffold for interfacing with, and guiding, the activity of biological systems like cells and tissues. Although DNA is a highly programmable molecular building block, it suffers from a lack of functional capacity for guiding and modulating cells. Coupling DNA to biologically active molecules can bestow bioactivity to these nanodevices. The main goal of such nanodevices is to synthesize systems that can bind to cells and mimic the extracellular environment, and serve as a highly promising toolbox for multiple applications in cellular programming and tissue engineering. DNA-based programmable devices offer a highly promising approach for programming collections of cells, tissue engineering, and regenerative medicine applications.
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Affiliation(s)
- Ankit Gangrade
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, USA
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, USA
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, India.
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, India
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10
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Islam MS, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Chiral 3D DNA origami structures for ordered heterologous arrays. NANOSCALE ADVANCES 2021; 3:4685-4691. [PMID: 36134307 PMCID: PMC9418780 DOI: 10.1039/d1na00385b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/04/2021] [Indexed: 06/16/2023]
Abstract
The DNA origami technique allows the facile design and production of three-dimensional shapes from single template strands of DNA. These can act as functional devices with multiple potential applications but are constrained by practical limitations on size. Multi-functionality could be achieved by connecting together distinct DNA origami modules in an ordered manner. Arraying of non-identical, three-dimensional DNA origamis in an ordered manner is challenging due for example, to a lack of compatible rotational symmetries. Here we show that we can design and build ordered DNA structures using non-identical 3D building blocks by using DNA origami snub-cubes in left-handed and right-handed forms. These can be modified such that one form only binds to the opposite-handed form allowing regular arrays wherein building blocks demonstrate alternating chirality.
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Affiliation(s)
- Md Sirajul Islam
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
| | - Gerrit David Wilkens
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
- School of Molecular Medicine, Medical University of Warsaw Warszawa 02-091 Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 Kraków 30-387 Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 Kraków 30-387 Poland
| | - Jonathan Gardiner Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University Gronostajowa 7A Kraków 30-387 Poland
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11
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Ojasalo S, Piskunen P, Shen B, Kostiainen MA, Linko V. Hybrid Nanoassemblies from Viruses and DNA Nanostructures. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1413. [PMID: 34071795 PMCID: PMC8228324 DOI: 10.3390/nano11061413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 12/12/2022]
Abstract
Viruses are among the most intriguing nanostructures found in nature. Their atomically precise shapes and unique biological properties, especially in protecting and transferring genetic information, have enabled a plethora of biomedical applications. On the other hand, structural DNA nanotechnology has recently emerged as a highly useful tool to create programmable nanoscale structures. They can be extended to user defined devices to exhibit a wide range of static, as well as dynamic functions. In this review, we feature the recent development of virus-DNA hybrid materials. Such structures exhibit the best features of both worlds by combining the biological properties of viruses with the highly controlled assembly properties of DNA. We present how the DNA shapes can act as "structured" genomic material and direct the formation of virus capsid proteins or be encapsulated inside symmetrical capsids. Tobacco mosaic virus-DNA hybrids are discussed as the examples of dynamic systems and directed formation of conjugates. Finally, we highlight virus-mimicking approaches based on lipid- and protein-coated DNA structures that may elicit enhanced stability, immunocompatibility and delivery properties. This development also paves the way for DNA-based vaccines as the programmable nano-objects can be used for controlling immune cell activation.
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Affiliation(s)
- Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, P.O. Box 15100, 00076 Aalto, Finland
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12
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Chakraborty A, Ravi SP, Shamiya Y, Cui C, Paul A. Harnessing the physicochemical properties of DNA as a multifunctional biomaterial for biomedical and other applications. Chem Soc Rev 2021; 50:7779-7819. [PMID: 34036968 DOI: 10.1039/d0cs01387k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The biological purpose of DNA is to store, replicate, and convey genetic information in cells. Progress in molecular genetics have led to its widespread applications in gene editing, gene therapy, and forensic science. However, in addition to its role as a genetic material, DNA has also emerged as a nongenetic, generic material for diverse biomedical applications. DNA is essentially a natural biopolymer that can be precisely programed by simple chemical modifications to construct materials with desired mechanical, biological, and structural properties. This review critically deciphers the chemical tools and strategies that are currently being employed to harness the nongenetic functions of DNA. Here, the primary product of interest has been crosslinked, hydrated polymers, or hydrogels. State-of-the-art applications of macroscopic, DNA-based hydrogels in the fields of environment, electrochemistry, biologics delivery, and regenerative therapy have been extensively reviewed. Additionally, the review encompasses the status of DNA as a clinically and commercially viable material and provides insight into future possibilities.
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Affiliation(s)
- Aishik Chakraborty
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada.
| | - Shruthi Polla Ravi
- School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Yasmeen Shamiya
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Caroline Cui
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada. and School of Biomedical Engineering, The University of Western Ontario, London, ON N6A 5B9, Canada and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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13
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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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14
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Wang H, Luo D, Wang H, Wang F, Liu X. Construction of Smart Stimuli-Responsive DNA Nanostructures for Biomedical Applications. Chemistry 2021; 27:3929-3943. [PMID: 32830363 DOI: 10.1002/chem.202003145] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/12/2020] [Indexed: 12/13/2022]
Abstract
DNA nanostructures have recently attracted increasing interest in biological and biomedical applications by virtue of their unique properties, such as structural programmability, multi-functionality, stimuli-responsive behaviors, and excellent biocompatibility. In particular, the intelligent responsiveness of smart DNA nanostructures to specific stimuli has facilitated their extensive development in the field of high-performance biosensing and controllable drug delivery. This minireview begins with different self-assembly strategies for the construction of various DNA nanostructures, followed by the introduction of a variety of stimuli-responsive functional DNA nanostructures for assembling metastable soft materials and for facilitating amplified biosensing. The recent achievements of smart DNA nanostructures for controllable drug delivery are highlighted. Finally, the current challenges and possible developments of this promising research are discussed in the fields of intelligent nanomedicine.
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Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China.,College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, Hubei, 443002, P. R. China
| | - Dan Luo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, 430000, P. R. China
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Abstract
Over the past decade, DNA nanotechnology has spawned a broad variety of functional nanostructures tailored toward the enabled state at which applications are coming increasingly in view. One of the branches of these applications is in synthetic biology, where the intrinsic programmability of the DNA nanostructures may pave the way for smart task-specific molecular robotics. In brief, the synthesis of the user-defined artificial DNA nano-objects is based on employing DNA molecules with custom lengths and sequences as building materials that predictably assemble together by obeying Watson-Crick base pairing rules. The general workflow of creating DNA nanoshapes is getting more and more straightforward, and some objects can be designed automatically from the top down. The versatile DNA nano-objects can serve as synthetic tools at the interface with biology, for example, in therapeutics and diagnostics as dynamic logic-gated nanopills, light-, pH-, and thermally driven devices. Such diverse apparatuses can also serve as optical polarizers, sensors and capsules, autonomous cargo-sorting robots, rotary machines, precision measurement tools, as well as electric and magnetic-field directed robotic arms. In this review, we summarize the recent progress in robotic DNA nanostructures, mechanics, and their various implementations.
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Affiliation(s)
- Sami Nummelin
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Centre, Department of Applied Physics, Aalto
University, 00076 Aalto, Finland
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16
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Shen B, Piskunen P, Nummelin S, Liu Q, Kostiainen MA, Linko V. Advanced DNA Nanopore Technologies. ACS APPLIED BIO MATERIALS 2020; 3:5606-5619. [DOI: 10.1021/acsabm.0c00879] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Qing Liu
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
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17
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Synthesis of DNA Origami Scaffolds: Current and Emerging Strategies. Molecules 2020; 25:molecules25153386. [PMID: 32722650 PMCID: PMC7435391 DOI: 10.3390/molecules25153386] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/20/2022] Open
Abstract
DNA origami nanocarriers have emerged as a promising tool for many biomedical applications, such as biosensing, targeted drug delivery, and cancer immunotherapy. These highly programmable nanoarchitectures are assembled into any shape or size with nanoscale precision by folding a single-stranded DNA scaffold with short complementary oligonucleotides. The standard scaffold strand used to fold DNA origami nanocarriers is usually the M13mp18 bacteriophage’s circular single-stranded DNA genome with limited design flexibility in terms of the sequence and size of the final objects. However, with the recent progress in automated DNA origami design—allowing for increasing structural complexity—and the growing number of applications, the need for scalable methods to produce custom scaffolds has become crucial to overcome the limitations of traditional methods for scaffold production. Improved scaffold synthesis strategies will help to broaden the use of DNA origami for more biomedical applications. To this end, several techniques have been developed in recent years for the scalable synthesis of single stranded DNA scaffolds with custom lengths and sequences. This review focuses on these methods and the progress that has been made to address the challenges confronting custom scaffold production for large-scale DNA origami assembly.
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