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Chen Q, Xia X, Liang Z, Zuo T, Xu G, Wei F, Yang J, Hu Q, Zhao Z, Tang BZ, Cen Y. Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310728. [PMID: 38229573 DOI: 10.1002/smll.202310728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/26/2023] [Indexed: 01/18/2024]
Abstract
DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+. Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.
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Affiliation(s)
- Qiutong Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Xinyi Xia
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zhigang Liang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Tongshan Zuo
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Guanhong Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Fangdi Wei
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Jing Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Qin Hu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zheng Zhao
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Ben Zhong Tang
- Clinical Translational Research Center of Aggregation-Induced Emission, The Second Affiliated Hospital, School of Medicine, School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, P. R. China
| | - Yao Cen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
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Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. NATURE REVIEWS. MATERIALS 2023; 8:123-138. [PMID: 37206669 PMCID: PMC10191391 DOI: 10.1038/s41578-022-00517-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 05/21/2023]
Abstract
DNA origami has emerged as a powerful method to generate DNA nanostructures with dynamic properties and nanoscale control. These nanostructures enable complex biophysical studies and the fabrication of next-generation therapeutic devices. For these applications, DNA origami typically needs to be functionalized with bioactive ligands and biomacromolecular cargos. Here, we review methods developed to functionalize, purify, and characterize DNA origami nanostructures. We identify remaining challenges, such as limitations in functionalization efficiency and characterization. We then discuss where researchers can contribute to further advance the fabrication of functionalized DNA origami.
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Affiliation(s)
- Grant A. Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
| | - Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
- Address correspondence to or
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Gür FN, Kempter S, Schueder F, Sikeler C, Urban MJ, Jungmann R, Nickels PC, Liedl T. Double- to Single-Strand Transition Induces Forces and Motion in DNA Origami Nanostructures. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2101986. [PMID: 34337805 PMCID: PMC7611957 DOI: 10.1002/adma.202101986] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/07/2021] [Indexed: 05/30/2023]
Abstract
The design of dynamic, reconfigurable devices is crucial for the bottom-up construction of artificial biological systems. DNA can be used as an engineering material for the de-novo design of such dynamic devices. A self-assembled DNA origami switch is presented that uses the transition from double- to single-stranded DNA and vice versa to create and annihilate an entropic force that drives a reversible conformational change inside the switch. It is distinctively demonstrated that a DNA single-strand that is extended with 0.34 nm per nucleotide - the extension this very strand has in the double-stranded configuration - exerts a contractive force on its ends leading to large-scale motion. The operation of this type of switch is demonstrated via transmission electron microscopy, DNA-PAINT super-resolution microscopy and darkfield microscopy. The work illustrates the intricate and sometimes counter-intuitive forces that act in nanoscale physical systems that operate in fluids.
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Affiliation(s)
- Fatih N Gür
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Susanne Kempter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Florian Schueder
- Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, 06510, United States
| | - Christoph Sikeler
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Maximilian J Urban
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Research Group Molecular Imaging and Bionanotechnology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp C Nickels
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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Li Y, Huang CZ, Li YF. Ultrasensitive Electrochemiluminescence Detection of MicroRNA via One-Step Introduction of a Target-Triggered Branched Hybridization Chain Reaction Circuit. Anal Chem 2019; 91:9308-9314. [DOI: 10.1021/acs.analchem.9b02580] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yang Li
- College of School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Cheng Zhi Huang
- College of Pharmaceutical Science, Southwest University, Chongqing 400716, People’s Republic of China
| | - Yuan Fang Li
- College of School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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