201
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Zhao Y, Zhao J, Zhang J, Sun Y, Li L, Li Z, Li M. Enzymatically Controlled Nanoflares for Specific Molecular Recognition and Biosensing. Anal Chem 2022; 94:8883-8889. [PMID: 35704434 DOI: 10.1021/acs.analchem.2c00166] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In situ sensing of physiological and pathological species in cancer cells is of great importance to unravel their molecular and cellular processes. However, the biosensing with conventional probes is often limited by the undesired on-target off-tumor interference. Here, we report a novel strategy to design enzymatically controlled nanoflares for sensing and imaging molecular targets in tumor cells. The triggerable nanoflare was designed via rational engineering of structure-switching aptamers with the incorporation of an enzyme-activatable site and further conjugation on gold nanoparticles. The nanoflare sensors did not respond to target molecules in normal cells, but they could be catalytically activated by specific enzymes in cancer cells, thereby enabling cancer-specific sensing and imaging in vitro and in vivo with improved tumor specificity. Considering that diverse aptamers were selected, we expect that this strategy would facilitate the precise detection of a broad range of targets in tumors and may promote the development of smart probes for cancer diagnosis.
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Affiliation(s)
- Ya Zhao
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jingfang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yan Sun
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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202
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Mathur D, Rogers KE, Díaz SA, Muroski ME, Klein WP, Nag OK, Lee K, Field LD, Delehanty JB, Medintz IL. Determining the Cytosolic Stability of Small DNA Nanostructures In Cellula. NANO LETTERS 2022; 22:5037-5045. [PMID: 35580267 PMCID: PMC9233082 DOI: 10.1021/acs.nanolett.2c00917] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
DNA nanostructures have proven potential in biomedicine. However, their intracellular interactions─especially cytosolic stability─remain mostly unknown and attempts to discern this are confounded by the complexities of endocytic uptake and entrapment. Here, we bypass the endocytic uptake and evaluate the DNA structural stability directly in live cells. Commonly used DNA structures─crosshairs and a tetrahedron─were labeled with a multistep Förster resonance energy transfer dye cascade and microinjected into the cytosol of transformed and primary cells. Energy transfer loss, as monitored by fluorescence microscopy, reported the structure's direct time-resolved breakdown in cellula. The results showed rapid degradation of the DNA crosshair within 20 min, while the tetrahedron remained consistently intact for at least 1 h postinjection. Nuclease assays in conjunction with a current understanding of the tetrahedron's torsional rigidity confirmed its higher stability. Such studies can inform design parameters for future DNA nanostructures where programmable degradation rates may be required.
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Affiliation(s)
- Divita Mathur
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Katherine E Rogers
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Megan E Muroski
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - William P Klein
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - Okhil K Nag
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Kwahun Lee
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- American Society of Engineering Education, Washington, DC 20036, United States
| | - Lauren D Field
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
- National Research Council, Washington, DC 20001, United States
| | - James B Delehanty
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, US Naval Research Laboratory, Washington, DC 20375, United States
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203
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Manero A, Crawford KE, Prock‐Gibbs H, Shah N, Gandhi D, Coathup MJ. Improving disease prevention, diagnosis, and treatment using novel bionic technologies. Bioeng Transl Med 2022; 8:e10359. [PMID: 36684104 PMCID: PMC9842045 DOI: 10.1002/btm2.10359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/09/2022] [Accepted: 05/30/2022] [Indexed: 01/25/2023] Open
Abstract
Increased human life expectancy, due in part to improvements in infant and childhood survival, more active lifestyles, in combination with higher patient expectations for better health outcomes, is leading to an extensive change in the number, type and manner in which health conditions are treated. Over the next decades as the global population rapidly progresses toward a super-aging society, meeting the long-term quality of care needs is forecast to present a major healthcare challenge. The goal is to ensure longer periods of good health, a sustained sense of well-being, with extended periods of activity, social engagement, and productivity. To accomplish these goals, multifunctionalized interfaces are an indispensable component of next generation medical technologies. The development of more sophisticated materials and devices as well as an improved understanding of human disease is forecast to revolutionize the diagnosis and treatment of conditions ranging from osteoarthritis to Alzheimer's disease and will impact disease prevention. This review examines emerging cutting-edge bionic materials, devices and technologies developed to advance disease prevention, and medical care and treatment in our elderly population including developments in smart bandages, cochlear implants, and the increasing role of artificial intelligence and nanorobotics in medicine.
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Affiliation(s)
- Albert Manero
- Limbitless SolutionsUniversity of Central FloridaOrlandoFloridaUSA,Biionix ClusterUniversity of Central FloridaOrlandoFloridaUSA
| | - Kaitlyn E. Crawford
- Biionix ClusterUniversity of Central FloridaOrlandoFloridaUSA,Department of Materials Science and EngineeringUniversity of Central FloridaOrlandoFloridaUSA
| | | | - Neel Shah
- College of MedicineUniversity of Central FloridaOrlandoFloridaUSA
| | - Deep Gandhi
- College of MedicineUniversity of Central FloridaOrlandoFloridaUSA
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204
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Xu J, Chen C, Shi X. Graph Computation Using Algorithmic Self-Assembly of DNA Molecules. ACS Synth Biol 2022; 11:2456-2463. [PMID: 35703038 DOI: 10.1021/acssynbio.2c00120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA molecules have been used as novel computing tools, by which Synthetic DNA was designed to execute computing processes with a programmable sequence. Here, we proposed a parallel computing method using DNA origamis as agents to solve the three-color problem, an example of the graph problem. Each agent was fabricated with a DNA origami of ∼50 nm diameter and contained DNA probes with programmable sticky ends that execute preset computing processes. With the interaction of different nanoagents, DNA molecules self-assemble into spatial nanostructures, which embody the computation results of the three-color problem with polynomial numbers of computing nanoagents in a one-pot annealing step. The computing results were confirmed by atomic force microscopy. Our method is completely different from existing DNA computing methods in its computing algorithm, and it has an advantage in terms of computational complexity and results detection for solving graph problems.
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Affiliation(s)
- Jin Xu
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, School of Computer Science, Peking University, Beijing 100871, China
| | - Congzhou Chen
- Key Laboratory of High Confidence Software Technologies of Ministry of Education, School of Computer Science, Peking University, Beijing 100871, China
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou 510006, China
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205
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Chen K, Xu F, Hu Y, Yan H, Pan L. DNA Kirigami Driven by Polymerase-Triggered Strand Displacement. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201478. [PMID: 35561059 DOI: 10.1002/smll.202201478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
The precursors of functional biomolecules in living cells are synthesized in a bottom-up manner and subsequently activated by modification into a delicate structure with near-atomic precision. DNA origami technology provides a promising way to mimic the synthesis of precursors, although mimicking the modification process is a challenge. Herein, a DNA paper-cutting (DNA kirigami) method to trim origami into designer nanostructures is proposed, where the modification is implemented by a polymerase-triggered DNA strand displacement reaction. Six geometric shapes are created by cutting rectangular DNA origami. Gel electrophoresis and atomic force microscopy results demonstrate the feasibility and capability of the DNA paper-cutting method. The proposed DNA paper-cutting strategy can enrich the toolbox for dynamically transforming DNA origami and has potential applications in biomimetics. .
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Affiliation(s)
- Kuiting Chen
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fei Xu
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yingxin Hu
- College of Information Science and Technology, Shijiazhuang Tiedao University, Shijiazhuang, 050043, China
| | - Hao Yan
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ, 85287, USA
| | - Linqiang Pan
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, 430074, China
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206
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Shiu SCC, Whitehouse WL, Tanner JA. Designing aptamer-enabled DNA polyhedra using paper origami. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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207
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Cao S, Wang F, Wang L, Fan C, Li J. DNA nanotechnology-empowered finite state machines. NANOSCALE HORIZONS 2022; 7:578-588. [PMID: 35502877 DOI: 10.1039/d2nh00060a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A finite state machine (FSM, or automaton) is an abstract machine that can switch among a finite number of states in response to temporally ordered inputs, which allows storage and processing of information in an order-sensitive manner. In recent decades, DNA molecules have been actively exploited to develop information storage and nanoengineering materials, which hold great promise for smart nanodevices and nanorobotics under the framework of FSM. In this review, we summarize recent progress in utilizing DNA self-assembly and DNA nanostructures to implement FSMs. We describe basic principles for representative DNA FSM prototypes and highlight their advantages and potential in diverse applications. The challenges in this field and future directions have also been discussed.
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Affiliation(s)
- Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Jiang Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China.
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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208
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Fil J, Dalchau N, Chu D. Programming Molecular Systems To Emulate a Learning Spiking Neuron. ACS Synth Biol 2022; 11:2055-2069. [PMID: 35622431 PMCID: PMC9208023 DOI: 10.1021/acssynbio.1c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Hebbian theory seeks
to explain how the neurons in the brain adapt
to stimuli to enable learning. An interesting feature of Hebbian learning
is that it is an unsupervised method and, as such, does not require
feedback, making it suitable in contexts where systems have to learn
autonomously. This paper explores how molecular systems can be designed
to show such protointelligent behaviors and proposes the first chemical
reaction network (CRN) that can exhibit autonomous Hebbian learning
across arbitrarily many input channels. The system emulates a spiking
neuron, and we demonstrate that it can learn statistical biases of
incoming inputs. The basic CRN is a minimal, thermodynamically plausible
set of microreversible chemical equations that can be analyzed with
respect to their energy requirements. However, to explore how such
chemical systems might be engineered de novo, we also propose an extended
version based on enzyme-driven compartmentalized reactions. Finally,
we show how a purely DNA system, built upon the paradigm of DNA strand
displacement, can realize neuronal dynamics. Our analysis provides
a compelling blueprint for exploring autonomous learning in biological
settings, bringing us closer to realizing real synthetic biological
intelligence.
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Affiliation(s)
- Jakub Fil
- APT Group, School of Computer Science, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Neil Dalchau
- Microsoft Research, Cambridge CB1 2FB, United Kingdom
| | - Dominique Chu
- CEMS, School of Computing, University of Kent, Canterbury CT2 7NF, United Kingdom
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209
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Zarubiieva I, Spaccasassi C, Kulkarni V, Phillips A. Automated Leak Analysis of Nucleic Acid Circuits. ACS Synth Biol 2022; 11:1931-1948. [PMID: 35544754 DOI: 10.1021/acssynbio.2c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acids are a powerful engineering material that can be used to implement a broad range of computational circuits at the nanoscale, with potential applications in high-precision biosensing, diagnostics, and therapeutics. However, nucleic acid circuits are prone to leaks, which result from unintended displacement interactions between nucleic acid strands. Such leaks can grow combinatorially with circuit size, are challenging to mitigate, and can significantly compromise circuit behavior. While several techniques have been proposed to partially mitigate leaks, computational methods for designing new leak mitigation strategies and comparing their effectiveness on circuit behavior are limited. Here we present a general method for the automated leak analysis of nucleic acid circuits, referred to as DSD Leaks. Our method extends the logic programming functionality of the Visual DSD language, developed for the design and analysis of nucleic acid circuits, with predicates for leak generation, a leak reaction enumeration algorithm, and predicates to exclude low probability leak reactions. We use our method to identify the critical leak reactions affecting the performance of control circuits, and to analyze leak mitigation strategies by automatically generating leak reactions. Finally, we design new control circuits with substantially reduced leakage including a sophisticated proportional-integral controller circuit, which can in turn serve as building blocks for future circuits. By integrating our method within an open-source nucleic acid circuit design tool, we enable the leak analysis of a broad range of circuits, as an important step toward facilitating robust and scalable nucleic acid circuit design.
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210
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Ji C, Yu C, Song M, Pei H, Fu P, Lin Y, Wang J. Construction of Molecular Transporter Based on DNA Structure Regulation. ACS APPLIED BIO MATERIALS 2022; 5:2122-2129. [PMID: 35481744 DOI: 10.1021/acsabm.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This study aims to build a molecular transporter machine that is based on the microstructure regulation of DNA triplets, which can automatically search, load, target delivery, and unload target protein molecules. The design of the molecular transporter includes: (1) a DNA triplet, which can recognize and load of the target protein; (2) a similar DNA triplet realizing the target transport; and (3) the signal-indicating DNA, which is connected at the target destination to achieve fixation of the target protein at the target destination. The molecular transporter machine would provide research practice and theoretical guidance for the development of DNA-based molecular machines.
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Affiliation(s)
- Chengdong Ji
- Zybio Inc, Chongqing, 400082, China.,Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Chunchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | - Min Song
- Department of Transfusion Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China
| | - Hua Pei
- Department of Clinical Laboratory, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570311, China
| | | | | | - Jing Wang
- Zybio Inc, Chongqing, 400082, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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211
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Zheng Y, Vaissier Welborn V. Tuning the Catalytic Activity of Synthetic Enzyme KE15 with DNA. J Phys Chem B 2022; 126:3407-3413. [PMID: 35483007 DOI: 10.1021/acs.jpcb.2c00765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficiency improvement of synthetic enzymes through scaffold modifications suffers from limitations in terms of effectiveness, cost, and potential devastating consequences for protein structural stability. Here, we propose an alternative to scaffold modification, within electrostatic preorganization theory, where the enzyme's greater environment is designed to support the evolution of the reaction in the active site. We demonstrate the feasibility of such an approach by placing a (polar) DNA fragment in the surroundings of the Kemp eliminase enzyme KE15 (structure from Houk's group) and computing the resulting change in catalytic activity. We find that the introduction of a DNA fragment magnifies the contribution of protein residues to the stabilization of the transition state, estimated from electric field calculations with polarizable molecular dynamics. Our randomly generated test systems reveal a 2.0 kcal/mol reduction in activation energy, suggesting that even more significant catalytic improvements could be made by optimizing DNA size, sequence, and orientation with respect to the enzyme, validating our approach.
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Affiliation(s)
- Yi Zheng
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
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212
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Kuťák D, Melo L, Schroeder F, Jelic-Matošević Z, Mutter N, Bertoša B, Barišić I. CATANA: an online modelling environment for proteins and nucleic acid nanostructures. Nucleic Acids Res 2022; 50:W152-W158. [PMID: 35544315 PMCID: PMC9252799 DOI: 10.1093/nar/gkac350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.
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Affiliation(s)
- David Kuťák
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia.,Visitlab, Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Lucas Melo
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Fabian Schroeder
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Zoe Jelic-Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Natalie Mutter
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
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213
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Hao P, Niu L, Luo Y, Wu N, Zhao Y. Surface Engineering of Lipid Vesicles Based on DNA Nanotechnology. Chempluschem 2022; 87:e202200074. [PMID: 35604011 DOI: 10.1002/cplu.202200074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/01/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Pengyan Hao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Liqiong Niu
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Yuanyuan Luo
- Xi'an Jiaotong University School of Life Science and Technology CHINA
| | - Na Wu
- Xi'an Jiaotong University School of Life Science and Technology No.28, West Xianning Road 710049 Xi'an CHINA
| | - Yongxi Zhao
- Xi'an Jiaotong University School of Life Science and Technology CHINA
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214
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Udomprasert A, Wootthichairangsan C, Duangrat R, Chaithongyot S, Zhang Y, Nixon R, Liu W, Wang R, Ponglikitmongkol M, Kangsamaksin T. Enhanced Functional Properties of Three DNA Origami Nanostructures as Doxorubicin Carriers to Breast Cancer Cells. ACS APPLIED BIO MATERIALS 2022; 5:2262-2272. [PMID: 35500214 DOI: 10.1021/acsabm.2c00114] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous studies have shown that chemotherapeutic efficacy could be enhanced with targeted drug delivery. Various DNA origami nanostructures have been investigated as drug carriers. Here, we compared drug delivery functionalities of three similar DNA origami nanostructures, Disc, Donut, and Sphere, that differ in structural dimension. Our results demonstrated that Donut was the most stable and exhibited the highest Dox-loading capacity. MUC1 aptamer modification in our nanostructures increased cellular uptake in MUC1-high MCF-7. Among the three nanostructures, unmodified Donut exerted the highest Dox cytotoxicity in MCF-7, and MUC1 aptamer modification did not further improve its effect, implicating that Dox delivery by Donut was efficient. However, all Dox-loaded nanostructures showed comparable cytotoxicity in MDA-MB-231 due to the innate sensitivity of this cell line to Dox. Our results successfully demonstrated that functional properties of DNA origami nanocarriers could be tuned by structural design, and three-dimensional Donut appeared to be the most efficient nanocarrier.
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Affiliation(s)
- Anuttara Udomprasert
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand
| | | | - Ratchanee Duangrat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Supattra Chaithongyot
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Yuwei Zhang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Rachel Nixon
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | | | - Thaned Kangsamaksin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
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215
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Wang M, Li X, He F, Li J, Wang HH, Nie Z. The Advances in Designer DNA Nanorobots Enabling Programmable Functions. Chembiochem 2022; 23:e202200119. [DOI: 10.1002/cbic.202200119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Fang He
- Hunan University College of Chemistry and Chemical Engineering CHINA
| | - Juan Li
- Hunan University College of Biology CHINA
| | - Hong-Hui Wang
- Hunan University College of Biology 410082 Changsha CHINA
| | - Zhou Nie
- Hunan University College of Chemistry and Chemical Engineering Yuelushan, Changsha, Hunan, 410082, P.R.China 410082 Changsha CHINA
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216
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Piranej S, Bazrafshan A, Salaita K. Chemical-to-mechanical molecular computation using DNA-based motors with onboard logic. NATURE NANOTECHNOLOGY 2022; 17:514-523. [PMID: 35347272 PMCID: PMC9119907 DOI: 10.1038/s41565-022-01080-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 01/13/2022] [Indexed: 05/15/2023]
Abstract
DNA has become the biomolecule of choice for molecular computation that may one day complement conventional silicon-based processors. In general, DNA computation is conducted in individual tubes, is slow in generating chemical outputs in response to chemical inputs and requires fluorescence readout. Here, we introduce a new paradigm for DNA computation where the chemical input is processed and transduced into a mechanical output using dynamic DNA-based motors operating far from equilibrium. We show that DNA-based motors with onboard logic (DMOLs) can perform Boolean functions (NOT, YES, AND and OR) with 15 min readout times. Because DMOLs are micrometre-sized, massive arrays of DMOLs that are identical or uniquely encoded by size and refractive index can be multiplexed and perform motor-to-motor communication on the same chip. Finally, DMOL computational outputs can be detected using a conventional smartphone camera, thus transducing chemical information into the electronic domain in a facile manner, suggesting potential applications.
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Affiliation(s)
- Selma Piranej
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | | | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA, USA.
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
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217
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Benson E, Marzo RC, Bath J, Turberfield AJ. A DNA molecular printer capable of programmable positioning and patterning in two dimensions. Sci Robot 2022; 7:eabn5459. [PMID: 35442702 DOI: 10.1126/scirobotics.abn5459] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nanoscale manipulation and patterning usually require costly and sensitive top-down techniques such as those used in scanning probe microscopies or in semiconductor lithography. DNA nanotechnology enables exploration of bottom-up fabrication and has previously been used to design self-assembling components capable of linear and rotary motion. In this work, we combine three independently controllable DNA origami linear actuators to create a nanoscale robotic printer. The two-axis positioning mechanism comprises a moveable gantry, running on parallel rails, threading a mobile sleeve. We show that the device is capable of reversibly positioning a write head over a canvas through the addition of signaling oligonucleotides. We demonstrate "write" functionality by using the head to catalyze a local DNA strand-exchange reaction, selectively modifying pixels on a canvas. This work demonstrates the power of DNA nanotechnology for creating nanoscale robotic components and could find application in surface manufacturing, biophysical studies, and templated chemistry.
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Affiliation(s)
- Erik Benson
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
| | - Rafael Carrascosa Marzo
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
| | - Jonathan Bath
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
| | - Andrew J Turberfield
- Department of Physics, University of Oxford, Clarendon Laboratory, Oxford, UK.,The Kavli Institute for Nanoscience Discovery, University of Oxford, New Biochemistry Building, Oxford, UK
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218
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Chakraborty B, Das S, Gupta A, Xiong Y, Vyshnavi TV, Kizer ME, Duan J, Chandrasekaran AR, Wang X. Aptamers for Viral Detection and Inhibition. ACS Infect Dis 2022; 8:667-692. [PMID: 35220716 PMCID: PMC8905934 DOI: 10.1021/acsinfecdis.1c00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 02/07/2023]
Abstract
Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.
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Affiliation(s)
- Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sreyashi Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Arushi Gupta
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - T-V Vyshnavi
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jinwei Duan
- Department of Chemistry and Materials Science, Chang’an University, Xi’an, Shaanxi 710064, China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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219
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Muire PJ, Thompson MA, Christy RJ, Natesan S. Advances in Immunomodulation and Immune Engineering Approaches to Improve Healing of Extremity Wounds. Int J Mol Sci 2022; 23:4074. [PMID: 35456892 PMCID: PMC9032453 DOI: 10.3390/ijms23084074] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 12/04/2022] Open
Abstract
Delayed healing of traumatic wounds often stems from a dysregulated immune response initiated or exacerbated by existing comorbidities, multiple tissue injury or wound contamination. Over decades, approaches towards alleviating wound inflammation have been centered on interventions capable of a collective dampening of various inflammatory factors and/or cells. However, a progressive understanding of immune physiology has rendered deeper knowledge on the dynamic interplay of secreted factors and effector cells following an acute injury. There is a wide body of literature, both in vitro and in vivo, abstracted on the immunomodulatory approaches to control inflammation. Recently, targeted modulation of the immune response via biotechnological approaches and biomaterials has gained attention as a means to restore the pro-healing phenotype and promote tissue regeneration. In order to fully realize the potential of these approaches in traumatic wounds, a critical and nuanced understanding of the relationships between immune dysregulation and healing outcomes is needed. This review provides an insight on paradigm shift towards interventional approaches to control exacerbated immune response following a traumatic injury from an agonistic to a targeted path. We address such a need by (1) providing a targeted discussion of the wound healing processes to assist in the identification of novel therapeutic targets and (2) highlighting emerging technologies and interventions that utilize an immunoengineering-based approach. In addition, we have underscored the importance of immune engineering as an emerging tool to provide precision medicine as an option to modulate acute immune response following a traumatic injury. Finally, an overview is provided on how an intervention can follow through a successful clinical application and regulatory pathway following laboratory and animal model evaluation.
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Affiliation(s)
- Preeti J. Muire
- Combat Wound Care Research Department, US Army Institute of Surgical Research, JBSA Ft Sam Houston, San Antonio, TX 78234, USA; (M.A.T.); (R.J.C.)
| | | | | | - Shanmugasundaram Natesan
- Combat Wound Care Research Department, US Army Institute of Surgical Research, JBSA Ft Sam Houston, San Antonio, TX 78234, USA; (M.A.T.); (R.J.C.)
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220
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Zhang C, Zheng T, Ma Q, Yang L, Zhang M, Wang J, Teng X, Miao Y, Lin HC, Yang Y, Han D. Logical Analysis of Multiple Single-Nucleotide-Polymorphisms with Programmable DNA Molecular Computation for Clinical Diagnostics. Angew Chem Int Ed Engl 2022; 61:e202117658. [PMID: 35137499 DOI: 10.1002/anie.202117658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 11/07/2022]
Abstract
Analyzing complex single-nucleotide-polymorphism (SNP) combinations in the genome is important for research and clinical applications, given that different SNP combinations can generate different phenotypic consequences. Recent works have shown that DNA-based molecular computing is powerful for simultaneously sensing and analyzing complex molecular information. Here, we designed a switching circuit-based DNA computational scheme that can integrate the sensing of multiple SNPs and simultaneously perform logical analysis of the detected SNP information to directly report clinical outcomes. As a demonstration, we successfully achieved automatic and accurate identification of 21 different blood group genotypes from 83 clinical blood samples with 100 % accuracy compared to sequencing data in a more rapid manner (3 hours). Our method enables a new mode of automatic and logical sensing and analyzing subtle molecular information for clinical diagnosis, as well as guiding personalized medication.
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Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tingting Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junyan Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaoyan Teng
- Department of Laboratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 201306, China
| | - Yanyan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hsiao-Chu Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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221
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Feola L, Trianni V. Adaptive Strategies for Team Formation in Minimalist Robot Swarms. IEEE Robot Autom Lett 2022. [DOI: 10.1109/lra.2022.3150479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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222
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DNA origami‐based nano‐hunter enriches low‐abundance point mutations by targeting wild-type gene segments. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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223
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Wu T, Cao Y, Liu Q, Wu X, Shang Y, Piao J, Li Y, Dong Y, Liu D, Wang H, Liu J, Ding B. Genetically Encoded Double-Stranded DNA-Based Nanostructure Folded by a Covalently Bivalent CRISPR/dCas System. J Am Chem Soc 2022; 144:6575-6582. [PMID: 35357193 DOI: 10.1021/jacs.2c01760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA nanotechnology has been widely employed in the construction of various functional nanostructures. However, most DNA nanostructures rely on hybridization between multiple single-stranded DNAs. Herein, we report a general strategy for the construction of a double-stranded DNA-ribonucleoprotein (RNP) hybrid nanostructure by folding double-stranded DNA with a covalently bivalent clustered regularly interspaced short palindromic repeats (CRISPR)/nuclease-dead CRISPR-associated protein (dCas) system. In our design, dCas9 and dCas12a can be efficiently fused together through a flexible and stimuli-responsive peptide linker. After activation by guide RNAs, the covalently bivalent dCas9-12a RNPs (staples) can precisely recognize their target sequences in the double-stranded DNA scaffold and pull them together to construct a series of double-stranded DNA-RNP hybrid nanostructures. The genetically encoded hybrid nanostructure can protect genetic information in the folded state, similar to the natural DNA-protein hybrids present in chromosomes, and elicit efficient stimuli-responsive gene transcription in the unfolded form. This rationally developed double-stranded DNA folding and unfolding strategy presents a new avenue for the development of DNA nanotechnology.
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Affiliation(s)
- Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yuanwei Cao
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Haoyi Wang
- University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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224
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MacCulloch T, Novacek A, Stephanopoulos N. Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules. Chem Commun (Camb) 2022; 58:4044-4047. [PMID: 35260875 DOI: 10.1039/d1cc04970d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a proximity-enhanced method to synthesize a peptide flanked by two different oligonucleotide handles. Our method relies on sequential bioorthogonal reactions, and partial hybridization of the second handle to the first. We demonstrate the synthesis of a protease-responsive DNA "latch" and a cyclic bioactive peptide using this method.
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Affiliation(s)
- Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA. .,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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225
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Chang X, Yang Q, Lee J, Zhang F. Self-Assembled Nucleic Acid Nanostructures for Biomedical Applications. Curr Top Med Chem 2022; 22:652-667. [PMID: 35319373 DOI: 10.2174/1568026622666220321140729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 11/22/2022]
Abstract
Structural DNA nanotechnology has been developed into a powerful method for creating self-assembled nanomaterials. Their compatibility with biosystems, nanoscale addressability, and programmable dynamic features make them appealing candidates for biomedical research. This review paper focuses on DNA self-assembly strategies and designer nanostructures with custom functions for biomedical applications. Specifically, we review the development of DNA self-assembly methods, from simple DNA motifs consisting of a few DNA strands to complex DNA architectures assembled by DNA origami. Three advantages are discussed using structural DNA nanotechnology for biomedical applications: (1) precise spatial control, (2) molding and guiding other biomolecules, and (3) using reconfigurable DNA nanodevices to overcome biomedical challenges. Finally, we discuss the challenges and opportunities of employing DNA nanotechnology for biomedical applications, emphasizing diverse assembly strategies to create a custom DNA nanostructure with desired functions.
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Affiliation(s)
- Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ 07102, USA
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226
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Li Y, Bao Q, Yang S, Yang M, Mao C. Bionanoparticles in cancer imaging, diagnosis, and treatment. VIEW 2022. [DOI: 10.1002/viw.20200027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yan Li
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Qing Bao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
| | - Shuxu Yang
- Department of Neurosurgery Sir Run Run Shaw Hospital School of Medicine Zhejiang University Hangzhou Zhejiang China
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Chuanbin Mao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
- Department of Chemistry and Biochemistry Stephenson Life Science Research Center University of Oklahoma Norman Oklahoma USA
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227
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Acoustic power management by swarms of microscopic robots. JOURNAL OF MICRO-BIO ROBOTICS 2022. [DOI: 10.1007/s12213-022-00148-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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228
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Pal N. Single-Molecule FRET: A Tool to Characterize DNA Nanostructures. Front Mol Biosci 2022; 9:835617. [PMID: 35330798 PMCID: PMC8940195 DOI: 10.3389/fmolb.2022.835617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
DNA nanostructures often involve temporally evolving spatial features. Tracking these temporal behaviors in real time requires sophisticated experimental methods with sufficiently high spatial and temporal resolution. Among the several strategies developed for this purpose, single-molecule FRET (smFRET) offers avenues to observe the structural rearrangement or locomotion of DNA nanostructures in real time and quantitatively measure the kinetics as well at the single nanostructure level. In this mini review, we discuss a few applications of smFRET-based techniques to study DNA nanostructures. These examples exemplify how smFRET signals not only have played an important role in the characterization of the nanostructures but also often have helped to improve the design and overall performance of the nanostructures and the devices designed from those structures. Overall, this review consolidates the potential of smFRET in providing crucial quantitative information on structure–function relations in DNA nanostructures.
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229
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Aydin O, Passaro AP, Raman R, Spellicy SE, Weinberg RP, Kamm RD, Sample M, Truskey GA, Zartman J, Dar RD, Palacios S, Wang J, Tordoff J, Montserrat N, Bashir R, Saif MTA, Weiss R. Principles for the design of multicellular engineered living systems. APL Bioeng 2022; 6:010903. [PMID: 35274072 PMCID: PMC8893975 DOI: 10.1063/5.0076635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.
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Affiliation(s)
| | - Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ritu Raman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Robert P. Weinberg
- School of Pharmacy, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts 02115, USA
| | | | - Matthew Sample
- Center for Ethics and Law in the Life Sciences, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sebastian Palacios
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jesse Tordoff
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nuria Montserrat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - M. Taher A. Saif
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ron Weiss
- Author to whom correspondence should be addressed:
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230
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Lin-Shiao E, Pfeifer WG, Shy BR, Saffari Doost M, Chen E, Vykunta VS, Hamilton JR, Stahl EC, Lopez DM, Sandoval Espinoza CR, Deyanov AE, Lew RJ, Poirer MG, Marson A, Castro CE, Doudna JA. CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells. Nucleic Acids Res 2022; 50:1256-1268. [PMID: 35104875 PMCID: PMC8860605 DOI: 10.1093/nar/gkac049] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/22/2022] Open
Abstract
DNA nanostructures are a promising tool to deliver molecular payloads to cells. DNA origami structures, where long single-stranded DNA is folded into a compact nanostructure, present an attractive approach to package genes; however, effective delivery of genetic material into cell nuclei has remained a critical challenge. Here, we describe the use of DNA nanostructures encoding an intact human gene and a fluorescent protein encoding gene as compact templates for gene integration by CRISPR-mediated homology-directed repair (HDR). Our design includes CRISPR–Cas9 ribonucleoprotein binding sites on DNA nanostructures to increase shuttling into the nucleus. We demonstrate efficient shuttling and genomic integration of DNA nanostructures using transfection and electroporation. These nanostructured templates display lower toxicity and higher insertion efficiency compared to unstructured double-stranded DNA templates in human primary cells. Furthermore, our study validates virus-like particles as an efficient method of DNA nanostructure delivery, opening the possibility of delivering nanostructures in vivo to specific cell types. Together, these results provide new approaches to gene delivery with DNA nanostructures and establish their use as HDR templates, exploiting both their design features and their ability to encode genetic information. This work also opens a door to translate other DNA nanodevice functions, such as biosensing, into cell nuclei.
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Affiliation(s)
- Enrique Lin-Shiao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wolfgang G Pfeifer
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Brian R Shy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mohammad Saffari Doost
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evelyn Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vivasvan S Vykunta
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Jennifer R Hamilton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elizabeth C Stahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Diana M Lopez
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Cindy R Sandoval Espinoza
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexander E Deyanov
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Michael G Poirer
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Alexander Marson
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Carlos E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.,Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley 94720, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA 94720, USA.,Gladstone Institutes, University of California, San Francisco, San Francisco, CA, 94158, USA
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231
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Aye SL, Sato Y. Therapeutic Applications of Programmable DNA Nanostructures. MICROMACHINES 2022; 13:315. [PMID: 35208439 PMCID: PMC8876680 DOI: 10.3390/mi13020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022]
Abstract
Deoxyribonucleic acid (DNA) nanotechnology, a frontier in biomedical engineering, is an emerging field that has enabled the engineering of molecular-scale DNA materials with applications in biomedicine such as bioimaging, biodetection, and drug delivery over the past decades. The programmability of DNA nanostructures allows the precise engineering of DNA nanocarriers with controllable shapes, sizes, surface chemistries, and functions to deliver therapeutic and functional payloads to target cells with higher efficiency and enhanced specificity. Programmability and control over design also allow the creation of dynamic devices, such as DNA nanorobots, that can react to external stimuli and execute programmed tasks. This review focuses on the current findings and progress in the field, mainly on the employment of DNA nanostructures such as DNA origami nanorobots, DNA nanotubes, DNA tetrahedra, DNA boxes, and DNA nanoflowers in the biomedical field for therapeutic purposes. We will also discuss the fate of DNA nanostructures in living cells, the major obstacles to overcome, that is, the stability of DNA nanostructures in biomedical applications, and the opportunities for DNA nanostructure-based drug delivery in the future.
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Affiliation(s)
| | - Yusuke Sato
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan;
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232
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Zhang C, Zheng T, Ma Q, Yang L, Zhang M, Wang J, Teng X, Miao Y, Lin H, Yang Y, Han D. Logical Analysis of Multiple Single‐Nucleotide‐Polymorphisms with Programmable DNA Molecular Computation for Clinical Diagnostics. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Tingting Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Junyan Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Xiaoyan Teng
- Department of Laboratory Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai 201306 China
| | - Yanyan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Hsiao‐chu Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yang Yang
- Department of Thoracic Surgery Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai 200433 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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233
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Sakai Y, Wilkens GD, Wolski K, Zapotoczny S, Heddle JG. Topogami: Topologically Linked DNA Origami. ACS NANOSCIENCE AU 2022; 2:57-63. [PMID: 35211697 PMCID: PMC8861903 DOI: 10.1021/acsnanoscienceau.1c00027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
DNA origami is a widely used DNA nanotechnology that allows construction of two-dimensional and three-dimensional nanometric shapes. The designability and rigidity of DNA origami make it an ideal material for construction of topologically linked molecules such as catenanes, which are attractive for their potential as motors and molecular machines. However, a general method for production of topologically linked DNA origami has been lacking. Here, we show that catenated single-stranded DNA circles can be produced and used as a universal scaffold for the production of topologically linked (catenated) DNA origami structures where the individual linked structures can be of any arbitrary design. Assembly of these topologically linked DNA origami structures is achieved via a simple one-pot annealing protocol.
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Affiliation(s)
- Yusuke Sakai
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
| | - Gerrit D Wilkens
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland.,Postgraduate School of Molecular Medicine, Żwirki I Wigury 61, 02-091 Warsaw, Poland
| | - Karol Wolski
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Szczepan Zapotoczny
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387 Krakow, Poland
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234
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Liu F, Liu X, Huang Q, Arai T. Recent Progress of Magnetically Actuated DNA Micro/Nanorobots. CYBORG AND BIONIC SYSTEMS 2022; 2022:9758460. [PMID: 36285315 PMCID: PMC9494703 DOI: 10.34133/2022/9758460] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/22/2021] [Indexed: 01/12/2023] Open
Abstract
In the past few decades, the field of DNA origami-based micro/nanotechnology has developed dramatically and spawned attention increasingly, as its high integrality, rigid structure, and excellent resistance ability to enzyme digestion. Many two-dimensional and three-dimensional DNA nanostructures coordinated with optical, chemical, or magnetic triggers have been designed and assembled, extensively used as versatile templates for molecular robots, nanosensors, and intracellular drug delivery. The magnetic field has been widely regarded as an ideal driving and operating system for micro/nanomaterials, as it does not require high-intensity lasers like light control, nor does it need to change the chemical composition similar to chemical activation. Herein, we review the recent achievements in the induction and actuation of DNA origami-based nanodevices that respond to magnetic fields. These magnetic actuation-based DNA nanodevices were regularly combined with magnetic beads or gold nanoparticles and applied to generate single-stranded scaffolds, assemble various DNA nanostructures, and purify specific DNA nanostructures. Moreover, they also produced artificial magnetism or moved regularly driven by external magnetic fields to explain deeper scientific issues.
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Affiliation(s)
- Fengyu Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaoming Liu
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiang Huang
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Tatsuo Arai
- Key Laboratory of Biomimetic Robots and Systems, Ministry of Education, State Key Laboratory of Intelligent Control and Decision of Complex System, Beijing Advanced Innovation Center for Intelligent Robots and Systems and School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Center for Neuroscience and Biomedical Engineering, The University of Electro-Communications, Tokyo 182-8585, Japan
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235
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Kumari G, Abhishek K, Singh S, Hussain A, Altamimi MA, Madhyastha H, Webster TJ, Dev A. A voyage from 3D to 4D printing in nanomedicine and healthcare: part I. Nanomedicine (Lond) 2022; 17:237-253. [PMID: 35109704 DOI: 10.2217/nnm-2021-0285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The transition from 3D to 4D printing has revolutionized various domains of healthcare, pharmaceuticals, design and architecture, and coating processes. The evolution from 3D printing to 4D printing (4DP) has added a fourth dimension as a time-dependent response. This review discusses the significance, demands, various types of smart materials/biomaterials, as well as bioinks and printers used in 4DP technology. This review also provides insights into the limitations of the bioprinting process and bioinks used in various bioprinting technologies and the challenges that come with these limitations. A brief discussion on the future potential of the fundamentals and capabilities of 4D printing is also discussed.
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Affiliation(s)
- Gourvi Kumari
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kumar Abhishek
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Sneha Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Afzal Hussain
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Mohammad A Altamimi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Harishkumar Madhyastha
- Department of Cardiovascular Physiology, School of Medicine, University of Miyazaki, Miyazaki, 889 1692, Japan
| | - Thomas J Webster
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Abhimanyu Dev
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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236
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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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237
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Wang Y, Lu X, Wu X, Li Y, Tang W, Yang C, Liu J, Ding B. Chemically Modified DNA Nanostructures for Drug Delivery. Innovation (N Y) 2022; 3:100217. [PMID: 35243471 PMCID: PMC8881720 DOI: 10.1016/j.xinn.2022.100217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Based on predictable, complementary base pairing, DNA can be artificially pre-designed into versatile DNA nanostructures of well-defined shapes and sizes. With excellent addressability and biocompatibility, DNA nanostructures have been widely employed in biomedical research, such as bio-sensing, bio-imaging, and drug delivery. With the development of the chemical biology of nucleic acid, chemically modified nucleic acids are also gradually developed to construct multifunctional DNA nanostructures. In this review, we summarize the recent progress in the construction and functionalization of chemically modified DNA nanostructures. Their applications in the delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted. Furthermore, the remaining challenges and future prospects in drug delivery by chemically modified DNA nanostructures are discussed. With excellent addressability and biocompatibility, DNA nanostructures are promising candidates for bio-sensing, bio-imaging, and drug delivery The recent progress in chemical modifications of DNA nanostructures is summarized Chemically modified DNA nanostructures for efficient delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted Challenges and prospects of future development toward chemically modified DNA nanostructures for drug delivery are discussed
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238
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Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Adv Drug Deliv Rev 2022; 181:114081. [PMID: 34915069 PMCID: PMC8886801 DOI: 10.1016/j.addr.2021.114081] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 01/01/2023]
Abstract
With numerous recent advances, the field of therapeutic nucleic acid nanotechnology is now poised for clinical translation supported by several examples of FDA-approved nucleic acid nanoformulations including two recent mRNA-based COVID-19 vaccines. Within this rapidly growing field, a new subclass of nucleic acid therapeutics called nucleic acid nanoparticles (NANPs) has emerged in recent years, which offers several unique properties distinguishing it from traditional therapeutic nucleic acids. Key unique aspects of NANPs include their well-defined 3D structure, their tunable multivalent architectures, and their ability to incorporate conditional activations of therapeutic targeting and release functions that enable diagnosis and therapy of cancer, regulation of blood coagulation disorders, as well as the development of novel vaccines, immunotherapies, and gene therapies. However, non-consolidated research developments of this highly interdisciplinary field create crucial barriers that must be overcome in order to impact a broader range of clinical indications. Forming a consortium framework for nucleic acid nanotechnology would prioritize and consolidate translational efforts, offer several unifying solutions to expedite their transition from bench-to-bedside, and potentially decrease the socio-economic burden on patients for a range of conditions. Herein, we review the unique properties of NANPs in the context of therapeutic applications and discuss their associated translational challenges.
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Affiliation(s)
- Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Weina Ke
- Biomedical Informatics and Data Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Piotr Grodzinski
- Nanodelivery Systems and Devices Branch, Cancer Imaging Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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239
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Xiang Z, Zhao J, Qu J, Song J, Li L. A Multivariate‐Gated DNA Nanodevice for Spatioselective Imaging of Pro‐metastatic Targets in Extracellular Microenvironment. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Zhichu Xiang
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Junle Qu
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
| | - Jun Song
- Center for Biomedical Optics and Photonics (CBOP) & College of Physics and Optoelectronic Engineering China Key Laboratory of Optoelectronic Devices and Systems Shenzhen University Shenzhen 518060 China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
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240
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Chen YR, Sun S, Yin H, Wang W, Liu R, Xu H, Yang Y, Wu ZS. Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array for in vivo theranostic application. J Mater Chem B 2022; 10:1969-1979. [PMID: 35014661 DOI: 10.1039/d1tb01978c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology is often used to build various nano-structures for signaling and/or drug delivery, but it essentially suffers from several major limitations, such as a large number of DNA strands and limited targeting ligands. Moreover, there is no report on in vivo two-dimensional DNA arrays because of various technical challenges. By cross-catenating two palindromic DNA rings, herein, we demonstrate a catenane-based grid-patterned periodic DNA monolayer array ([2]GDA) capable of preferentially accumulating in tumor tissues without any targeting ligands, with a thickness equal to the double-helical DNA monolayer (nearly 2 nm). The structural flexibility of [2]GDA enabled it to fold into a spherical object in solution, favoring cellular uptake. Thus, its cellular internalization activity was comparable with that of the commercial lipofectamine 3000. Moreover, [2]GDA retained the structural integrity over 24 h incubation in biological solutions, achieving a 360-fold improvement in in vivo stability. Significantly, anticancer drug-loaded [2]GDA exhibits desirable therapeutic efficacy in tumor-bearing animals without detectable side effects.
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Affiliation(s)
- Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ran Liu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ya Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
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241
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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: 7] [Impact Index Per Article: 3.5] [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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242
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Fan S, Ji B, Liu Y, Zou K, Tian Z, Dai B, Cui D, Zhang P, Ke Y, Song J. Spatiotemporal Control of Molecular Cascade Reactions by a Reconfigurable DNA Origami Domino Array. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Bin Ji
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
| | - Kexuan Zou
- 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
| | - Zhijin Tian
- Department of Chemistry University of Science & Technology of China 230026, Anhui Hefei China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences 310022, Zhejiang Hangzhou China
| | - Bin Dai
- 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
| | - Pengfei Zhang
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences 310022, Zhejiang Hangzhou China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA
| | - Jie Song
- Institute of Nano Biomedicine and Engineering Department of Instrument Science and Engineering School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai 200240 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences 310022, Zhejiang Hangzhou China
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243
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Poppleton E, Mallya A, Dey S, Joseph J, Šulc P. Nanobase.org: a repository for DNA and RNA nanostructures. Nucleic Acids Res 2022; 50:D246-D252. [PMID: 34747480 PMCID: PMC8728195 DOI: 10.1093/nar/gkab1000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/07/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
We introduce a new online database of nucleic acid nanostructures for the field of DNA and RNA nanotechnology. The database implements an upload interface, searching and database browsing. Each deposited nanostructures includes an image of the nanostructure, design file, an optional 3D view, and additional metadata such as experimental data, protocol or literature reference. The database accepts nanostructures in any preferred format used by the uploader for the nanostructure design. We further provide a set of conversion tools that encourage design file conversion into common formats (oxDNA and PDB) that can be used for setting up simulations, interactive editing or 3D visualization. The aim of the repository is to provide to the DNA/RNA nanotechnology community a resource for sharing their designs for further reuse in other systems and also to function as an archive of the designs that have been achieved in the field so far. Nanobase.org is available at https://nanobase.org/.
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Affiliation(s)
- Erik Poppleton
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Aatmik Mallya
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Swarup Dey
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
- Wyss Institute, Harvard University, Boston, MA 02115, USA
| | - Joel Joseph
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85281, USA
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244
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Peng Y, Lu B, Deng Y, Yang N, Li G. A dual-recognition-controlled electrochemical biosensor for accurate and sensitive detection of specific circulating tumor cells. Biosens Bioelectron 2022; 201:113973. [PMID: 35021133 DOI: 10.1016/j.bios.2022.113973] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/22/2022]
Abstract
Accurate and sensitive assay of specific circulating tumor cells (CTCs) is of importance for the diagnosis, treatment, and metastasis monitoring of cancer. Herein, we have proposed a dual-recognition-controlled electrochemical biosensor in this work for the detection of specific CTCs. To this sensor, two aptamer hairpin probes are designed to be able to separately bind to two adjacent proteins on the cell membrane to activate the associative toehold for strand displacement reaction, which will then trigger a dimer-like rolling cycle amplification reaction, and finally produce significantly amplified electrochemical signals for sensitive quantification of target CTCs. In our design, only the case that the two proteins are simultaneously expressed on the cell membrane can result in obvious signal responses, which may greatly improve the accuracy of CTCs analysis. The proposed biosensor can possess excellent selectivity to distinguish target cells from different cancer cells. Moreover, the combination of rolling cycle amplification and DNA nanostructure capture probes can effectively lower the detection limit to 3 cells mL-1. Notably, our biosensor can be applied to the assay of the target CTCs in the complex whole blood matrixes, verifying its strong stability and anti-interference. Thus, the as-proposed dual-recognition-controlled electrochemical biosensor may exhibit great promise in clinical cancer diagnosis and personalized medicine.
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Affiliation(s)
- Ying Peng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Bing Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Ying Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China
| | - Nana Yang
- Department of Obstetrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, PR China.
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, PR China; Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
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245
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Wang C, O'Hagan MP, Li Z, Zhang J, Ma X, Tian H, Willner I. Photoresponsive DNA materials and their applications. Chem Soc Rev 2022; 51:720-760. [PMID: 34985085 DOI: 10.1039/d1cs00688f] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoresponsive nucleic acids attract growing interest as functional constituents in materials science. Integration of photoisomerizable units into DNA strands provides an ideal handle for the reversible reconfiguration of nucleic acid architectures by light irradiation, triggering changes in the chemical and structural properties of the nanostructures that can be exploited in the development of photoresponsive functional devices such as machines, origami structures and ion channels, as well as environmentally adaptable 'smart' materials including nanoparticle aggregates and hydrogels. Moreover, photoresponsive DNA components allow control over the composition of dynamic supramolecular ensembles that mimic native networks. Beyond this, the modification of nucleic acids with photosensitizer functionality enables these biopolymers to act as scaffolds for spatial organization of electron transfer reactions mimicking natural photosynthesis. This review provides a comprehensive overview of these exciting developments in the design of photoresponsive DNA materials, and showcases a range of applications in catalysis, sensing and drug delivery/release. The key challenges facing the development of the field in the coming years are addressed, and exciting emergent research directions are identified.
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Affiliation(s)
- Chen Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Michael P O'Hagan
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
| | - Ziyuan Li
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Junji Zhang
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials, Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, Frontiers Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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246
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Liu M, Wang L, Lo Y, Shiu SCC, Kinghorn AB, Tanner JA. Aptamer-Enabled Nanomaterials for Therapeutics, Drug Targeting and Imaging. Cells 2022; 11:159. [PMID: 35011722 PMCID: PMC8750369 DOI: 10.3390/cells11010159] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/06/2023] Open
Abstract
A wide variety of nanomaterials have emerged in recent years with advantageous properties for a plethora of therapeutic and diagnostic applications. Such applications include drug delivery, imaging, anti-cancer therapy and radiotherapy. There is a critical need for further components which can facilitate therapeutic targeting, augment their physicochemical properties, or broaden their theranostic applications. Aptamers are single-stranded nucleic acids which have been selected or evolved to bind specifically to molecules, surfaces, or cells. Aptamers can also act as direct biologic therapeutics, or in imaging and diagnostics. There is a rich field of discovery at the interdisciplinary interface between nanomaterials and aptamer science that has significant potential across biomedicine. Herein, we review recent progress in aptamer-enabled materials and discuss pending challenges for their future biomedical application.
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Affiliation(s)
- Mengping Liu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Lin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Young Lo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Andrew B. Kinghorn
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
| | - Julian A. Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China; (M.L.); (L.W.); (Y.L.); (S.C.-C.S.); (A.B.K.)
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR 999077, China
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247
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Keya JJ, Akter M, Kabir AMR, Ishii S, Kakugo A. Fabrication of Artificial Muscle from Microtubules, Kinesins, and DNA Origami Nanostructures. Methods Mol Biol 2022; 2430:231-240. [PMID: 35476336 DOI: 10.1007/978-1-0716-1983-4_15] [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: 06/14/2023]
Abstract
Fabrication of molecular devices using biomolecules through biomimetic approaches has witnessed a surge in interest in recent years. DNA a versatile programmable material offers an opportunity to realize complicated operations through the designing of various nanostructures such as DNA origami. Here we describe the methods to use DNA origami for the self-assembly of the biomolecular motor system, microtubule (MT)-kinesin. A rodlike DNA origami motif facilitates the self-assembly of MTs into asters. A smooth muscle like molecular contraction system could be realized following the method where DNA mediated self-assembly of MTs permits dynamic contraction in the presence of kinesins through an energy dissipative process.
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Affiliation(s)
| | - Mousumi Akter
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Satsuki Ishii
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo, Japan.
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan.
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248
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Perumal D, Kalathil J, Krishna J, Raj G, Harikrishnan KS, Uthpala ML, Gupta R, Varghese R. Supramolecular grafting of stimuli-responsive, carrier-free, self-deliverable nanoparticles of camptothecin and antisense DNA for combination cancer therapy. NEW J CHEM 2022. [DOI: 10.1039/d2nj01952c] [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
A supramolecular approach for the crafting of self-deliverable nanoparticles of antisense DNA and camptothecin for combination cancer therapy is reported.
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Affiliation(s)
- Devanathan Perumal
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Jemshiya Kalathil
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Jithu Krishna
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Gowtham Raj
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Kaloor S. Harikrishnan
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - M. L. Uthpala
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Ria Gupta
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
| | - Reji Varghese
- School of Chemistry, Indian Institute of Science Education and Research (IISER) Thiruvananthapuram, Trivandrum, 695551, Kerala, India
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249
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Zhai T, Sun C, Ye D, Xia K, Liu X, Fan C, Li Q, Shen J. Electrochemically driven assembly of framework nucleic acids. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2021.115901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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250
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The Future of Nanomedicine. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_24-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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