1
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Sun M, Song R, Fang Y, Xu J, Yang Z, Zhang H. DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39314016 DOI: 10.1021/acsami.4c13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.
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Affiliation(s)
- Mengqiu Sun
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Song
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
| | - Yangwu Fang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
| | - Jiuzhou Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhaoqi Yang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Physical Sciences, Great Bay University, Dongguan 523000, China
- Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen 518063, China
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2
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Lee H, Xie T, Kang B, Yu X, Schaffter SW, Schulman R. Plug-and-play protein biosensors using aptamer-regulated in vitro transcription. Nat Commun 2024; 15:7973. [PMID: 39266511 PMCID: PMC11393120 DOI: 10.1038/s41467-024-51907-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 08/19/2024] [Indexed: 09/14/2024] Open
Abstract
Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors and digital protein biosensors with detection ranges that can be tuned over two orders of magnitude and can exceed the binding affinity of the aptamer. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors that could have diverse applications in research and biotechnology.
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Affiliation(s)
- Heonjoon Lee
- Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tian Xie
- Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Byunghwa Kang
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Xinjie Yu
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Rebecca Schulman
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Chemistry, Johns Hopkins University, Baltimore, MD, USA.
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3
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Nag S, Bisker G. Driven Self-Assembly of Patchy Particles Overcoming Equilibrium Limitations. J Chem Theory Comput 2024. [PMID: 39255461 DOI: 10.1021/acs.jctc.4c01118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Bridging biological complexity and synthetic material design, we investigate dissipative self-assembly in patchy particle systems. Utilizing Monte Carlo and Molecular Dynamics simulations, we demonstrate how external driving forces mitigate equilibrium trade-offs between assembly time and structural stability, traditionally encountered in self-assembly processes. Our findings also extend to biological-mimicking environments, where we explore the dynamics of patchy particles under crowded conditions. This comprehensive analysis offers insights into advanced material design, opening avenues for innovations in nanotechnology applications.
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Affiliation(s)
- Shubhadeep Nag
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gili Bisker
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
- The Center for Computational Molecular and Materials Science, Tel Aviv University, Tel Aviv 6997801, Israel
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4
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Shi R, Chen KL, Fern J, Deng S, Liu Y, Scalise D, Huang Q, Cowan NJ, Gracias DH, Schulman R. Programming gel automata shapes using DNA instructions. Nat Commun 2024; 15:7773. [PMID: 39237499 PMCID: PMC11377784 DOI: 10.1038/s41467-024-51198-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/31/2024] [Indexed: 09/07/2024] Open
Abstract
The ability to transform matter between numerous physical states or shapes without wires or external devices is a major challenge for robotics and materials design. Organisms can transform their shapes using biomolecules carrying specific information and localize at sites where transitions occur. Here, we introduce gel automata, which likewise can transform between a large number of prescribed shapes in response to a combinatorial library of biomolecular instructions. Gel automata are centimeter-scale materials consisting of multiple micro-segments. A library of DNA activator sequences can each reversibly grow or shrink different micro-segments by polymerizing or depolymerizing within them. We develop DNA activator designs that maximize the extent of growth and shrinking, and a photolithography process for precisely fabricating gel automata with elaborate segmentation patterns. Guided by simulations of shape change and neural networks that evaluate gel automata designs, we create gel automata that reversibly transform between multiple, wholly distinct shapes: four different letters and every even or every odd numeral. The sequential and repeated metamorphosis of gel automata demonstrates how soft materials and robots can be digitally programmed and reprogrammed with information-bearing chemical signals.
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Affiliation(s)
- Ruohong Shi
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kuan-Lin Chen
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joshua Fern
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Siming Deng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA
| | - Yixin Liu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Qi Huang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Noah J Cowan
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA
| | - David H Gracias
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Center for MicroPhysiological Systems (MPS), Johns Hopkins University, Baltimore, MD, USA.
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Laboratory for Computational Sensing and Robotics (LCSR), Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
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5
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Lan Y, Li X, Liu B, Lu J, Zuo B, Wang Y, Cao S, Fu X, Yue Q, Luo X, Zhong X, Dong Y, Wang Z, Yang T, Xie X, Zeng T, Zhang M, Wang Y, Shen Y, Zuo H, Zhao Y, Zhang C, Guo H. Framework nucleic acid-based nanoparticles enhance temozolomide sensitivity in glioblastoma. Drug Resist Updat 2024; 76:101122. [PMID: 39079407 DOI: 10.1016/j.drup.2024.101122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 08/17/2024]
Abstract
O6-methylguanine DNA methyltransferase (MGMT) is a crucial determinant of temozolomide (TMZ) sensitivity in patients with glioblastoma (GBM). The therapeutic potential of small interfering RNA (siRNA) targeting MGMT to enhance TMZ sensitivity has been hampered by serum nuclease degradation, off-target effects, poor accumulation at tumor sites, and low circulation in blood stream. In this study, we developed a framework nucleic acid-based nanoparticles (FNN), which is constructed from a six-helix DNA bundle, to encapsulate and protect siMGMT for improving TMZ sensitivity in GBM treatment. For better blood-brain barrier (BBB) penetration and GBM targeting, we conjugated Angiopep-2 (ANG) targeting modules to each end of the FNN. Nucleolin (NCL)-responsive locks were engineered along the sides of the six-helix DNA bundle, which safeguard siMGMT before tumor entry. Upon interaction with tumor-overexpressed NCL, these locks unlock, exposing siMGMT, this allows for effective suppression of MGMT, resulting in a significant improvement of TMZ therapeutic efficacy in GBM. This innovative strategy has the potential to transform the current treatment landscape for GBM.
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Affiliation(s)
- Yufei Lan
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xiaodie Li
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Boyang Liu
- Department of Neurosurgery, Department of Neuro-oncological Surgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Jiankun Lu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Boming Zuo
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
| | | | - Xin Fu
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Qu Yue
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xin Luo
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xiangyang Zhong
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yaoyuan Dong
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Zhao Wang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Tao Yang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Xinyun Xie
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Tianci Zeng
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Manqing Zhang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yuankai Wang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yixiong Shen
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Huaqin Zuo
- Department of Hematology, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, Jiangsu 225001, China.
| | - Yan Zhao
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Chao Zhang
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China.
| | - Hongbo Guo
- Department of Neurosurgery, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China.
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6
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Nava G, Carzaniga T, Casiraghi L, Bot E, Zanchetta G, Damin F, Chiari M, Weber G, Bellini T, Mollica L, Buscaglia M. Weak-cooperative binding of a long single-stranded DNA chain on a surface. Nucleic Acids Res 2024; 52:8661-8674. [PMID: 38989620 PMCID: PMC11347152 DOI: 10.1093/nar/gkae576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/04/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Binding gene-wide single-stranded nucleic acids to surface-immobilized complementary probes is an important but challenging process for biophysical studies and diagnostic applications. The challenge comes from the conformational dynamics of the long chain that affects its accessibility and weakens its hybridization to the probes. We investigated the binding of bacteriophage genome M13mp18 on several different 20-mer probes immobilized on the surface of a multi-spot, label-free biosensor, and observed that only a few of them display strong binding capability with dissociation constant as low as 10 pM. Comparing experimental data and computational analysis of the M13mp18 chain structural features, we found that the capturing performance of a specific probe is directly related to the multiplicity of binding sites on the genomic strand, and poorly connected with the predicted secondary and tertiary structure. We show that a model of weak cooperativity of transient bonds is compatible with the measured binding kinetics and accounts for the enhancement of probe capturing observed when more than 20 partial pairings with binding free energy lower than -10 kcal mol-1 are present. This mechanism provides a specific pattern of response of a genomic strand on a panel of properly selected oligomer probe sequences.
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Affiliation(s)
- Giovanni Nava
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Thomas Carzaniga
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Luca Casiraghi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Erik Bot
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Giuliano Zanchetta
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Francesco Damin
- Istituto di Scienze e Tecnologie Chimiche ‘Giulio Natta’, National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, 20131 Milano, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche ‘Giulio Natta’, National Research Council of Italy (SCITEC-CNR), via Mario Bianco 11, 20131 Milano, Italy
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Tommaso Bellini
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Luca Mollica
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
| | - Marco Buscaglia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, via F.lli Cervi 93, 20054 Segrate (MI), Italy
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7
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Singh A, Parvin P, Saha B, Das D. Non-equilibrium self-assembly for living matter-like properties. Nat Rev Chem 2024:10.1038/s41570-024-00640-z. [PMID: 39179623 DOI: 10.1038/s41570-024-00640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
The soft and wet machines of life emerged as the spatially enclosed ensemble of biomolecules with replicating capabilities integrated with metabolic reaction cycles that operate at far-from-equilibrium. A thorough step-by-step synthetic integration of these elements, namely metabolic and replicative properties all confined and operating far-from-equilibrium, can set the stage from which we can ask questions related to the construction of chemical-based evolving systems with living matter-like properties - a monumental endeavour of systems chemistry. The overarching concept of this Review maps the discoveries on this possible integration of reaction networks, self-reproduction and compartmentalization under non-equilibrium conditions. We deconvolute the events of reaction networks and transient compartmentalization and extend the discussion towards self-reproducing systems that can be sustained under non-equilibrium conditions. Although enormous challenges lie ahead in terms of molecular diversity, information transfer, adaptation and selection that are required for open-ended evolution, emerging strategies to generate minimal metabolic cycles can extend our growing understanding of the chemical emergence of the biosphere of Earth.
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Affiliation(s)
- Abhishek Singh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Payel Parvin
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Bapan Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India
| | - Dibyendu Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, India.
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8
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Zhan P, Yang J, Ding L, Jing X, Hipp K, Nussberger S, Yan H, Liu N. 3D DNA origami pincers that multitask on giant unilamellar vesicles. SCIENCE ADVANCES 2024; 10:eadn8903. [PMID: 39151012 PMCID: PMC11328896 DOI: 10.1126/sciadv.adn8903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 07/10/2024] [Indexed: 08/18/2024]
Abstract
Proteins self-assemble to function in living cells. They may execute essential tasks in the form of monomers, complexes, or supramolecular cages via oligomerization, achieving a sophisticated balance between structural topology and functional dynamics. The modularity and programmability make DNA origami unique in mimicking these key features. Here, we demonstrate three-dimensional reconfigurable DNA origami pincers (DOPs) that multitask on giant unilamellar vesicles (GUVs). By programmably adjusting their pinching angle, the DOPs can dynamically control the degree of GUV remodeling. When oligomerized on the GUV to form origami cages, the DOP units interact with one another and undergo reorganization, resulting in the capture, compartmentalization, and detachment of lipid fragments. This oligomerization process is accompanied with membrane disruptions, enabling the passage of cargo across the membrane. We envisage that interfacing synthetic cells with engineered, multifunctional DNA nanostructures may help to confer customized cellular properties, unleashing the potential of both fields.
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Affiliation(s)
- Pengfei Zhan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022 Hangzhou, Zhejiang, China
- 2nd Physics Institute, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Juanjuan Yang
- 2nd Physics Institute, University of Stuttgart, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Longjiang Ding
- 2nd Physics Institute, University of Stuttgart, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Xinxin Jing
- 2nd Physics Institute, University of Stuttgart, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
| | - Katharina Hipp
- Electron Microscopy, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Stephan Nussberger
- Department of Biophysics, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ 85287, USA
| | - Na Liu
- 2nd Physics Institute, University of Stuttgart, D-70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, D-70569 Stuttgart, Germany
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9
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Wang Q, Xu H, Qi Z, Mei J, Tian H, Qu DH. Dynamic Near-Infrared Circularly Polarized Luminescence Encoded by Transient Supramolecular Chiral Assemblies. Angew Chem Int Ed Engl 2024; 63:e202407385. [PMID: 38736176 DOI: 10.1002/anie.202407385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
Circularly polarized luminescence (CPL) is promising for applications in many fields. However, most systems involving CPL are within the visible range; near-infrared (NIR) CPL-active materials, especially those that exhibit high glum values and can be controlled spatially and temporally, are rare. Herein, dynamic NIR-CPL with a glum value of 2.5×10-2 was achieved through supramolecular coassembly and energy-transfer strategies. The chiral assemblies formed by the coassembly between adenosine triphosphate (ATP) and a pyrene derivative exhibited a red CPL signal (glum of 10-3). The further introduction of sulfo-cyanine5 resulted in a energy-transfer process, which not only led to the NIR CPL but also increased the glum value to 10-2. Temporal control of these chiral assemblies was realized by introducing alkaline phosphatase to fabricate a biomimetic enzyme-catalyzed network, allowing the dynamic NIR CPL signal to be turned on. Based on these enzyme-regulated temporally controllable dynamic CPL-active chiral assemblies, a multilevel information encryption system was further developed. This study provides a pioneering example for the construction of dynamic NIR CPL materials with the ability to perform temporal control via the supramolecular assembly strategy, which is expected to aid in the design of supramolecular complex systems that more closely resemble natural biological systems.
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Affiliation(s)
- Qian Wang
- 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Hanren Xu
- 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhen Qi
- 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ju Mei
- 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Da-Hui Qu
- 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, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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10
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Rong Q, Deng Y, Chen F, Yin Z, Hu L, Su X, Zhou D. Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2400142. [PMID: 38676334 DOI: 10.1002/smll.202400142] [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: 03/28/2024] [Indexed: 04/28/2024]
Abstract
Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 100 to 102 min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.
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Affiliation(s)
- Qinze Rong
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yingnan Deng
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
- Sinopec Key Laboratory of Research and Application of Medical and Hygienic Materials, Sinopec (Beijing) Research Institute of Chemical Industry Co., Ltd., Beijing, 100013, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xin Su
- State Key Laboratory of Organic-Inorganic Composites, Beijing Key Laboratory of Bioprocess, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing, 100071, China
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11
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Lin N, Ouyang Y, Qin Y, Karmi O, Sohn YS, Liu S, Nechushtai R, Zhang Y, Willner I, Zhou Z. Spatially Localized Entropy-Driven Evolution of Nucleic Acid-Based Constitutional Dynamic Networks for Intracellular Imaging and Spatiotemporal Programmable Gene Therapy. J Am Chem Soc 2024; 146:20685-20699. [PMID: 39012486 PMCID: PMC11295181 DOI: 10.1021/jacs.4c03651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]
Abstract
The primer-guided entropy-driven high-throughput evolution of the DNA-based constitutional dynamic network, CDN, is introduced. The entropy gain associated with the process provides a catalytic principle for the amplified emergence of the CDN. The concept is applied to develop a programmable, spatially localized DNA circuit for effective in vitro and in vivo theranostic, gene-regulated treatment of cancer cells. The localized circuit consists of a DNA tetrahedron core modified at its corners with four tethers that include encoded base sequences exhibiting the capacity to emerge and assemble into a [2 × 2] CDN. Two of the tethers are caged by a pair of siRNA subunits, blocking the circuit into a mute, dynamically inactive configuration. In the presence of miRNA-21 as primer, the siRNA subunits are displaced, resulting in amplified release of the siRNAs silencing the HIF-1α mRNA and fast dynamic reconfiguration of the tethers into a CDN. The resulting CDN is, however, engineered to be dynamically reconfigured by miRNA-155 into an equilibrated mixture enriched with a DNAzyme component, catalyzing the cleavage of EGR-1 mRNA. The DNA tetrahedron nanostructure stimulates enhanced permeation into cancer cells. The miRNA-triggered entropy-driven reconfiguration of the spatially localized circuit leads to the programmable, cooperative bis-gene-silencing of HIF-1α and EGR-1 mRNAs, resulting in the effective and selective apoptosis of breast cancer cells and effective inhibition of tumors in tumor bearing mice.
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Affiliation(s)
- Nina Lin
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Yu Ouyang
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yunlong Qin
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Songqin Liu
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Rachel Nechushtai
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Yuanjian Zhang
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
| | - Itamar Willner
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhixin Zhou
- School
of Chemistry and Chemical Engineering, Southeast
University, Nanjing 211189, China
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12
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Wu Y, Wang GA, Yang Q, Li F. Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry. J Am Chem Soc 2024; 146:18041-18049. [PMID: 38899479 DOI: 10.1021/jacs.4c04721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Folding thermodynamics, quantitatively described using parameters such as ΔGfold°, ΔHfold°, and ΔSfold°, is essential for characterizing the stability and functionality of noncanonical nucleic acid structures but remains difficult to measure at the molecular level. Leveraging the programmability of dynamic deoxyribonucleic acid (DNA) chemistry, we introduce a DNA-based molecular tool capable of performing a free energy shift assay (FESA) that directly characterizes the thermodynamics of noncanonical DNA structures in their native environments. FESA operates by the rational design of a reference DNA probe that is energetically equivalent to a target noncanonical nucleic acid structure in a series of toehold-exchange reactions, yet is structurally incapable of folding. As a result, a free energy shift (ΔΔGrxn°) is observed when plotting the reaction yield against the free energy of each toehold-exchange. We mathematically demonstrated that ΔGfold°, ΔHfold°, and ΔSfold° of the analyte can be calculated based on ΔΔGrxn°. After validating FESA using six DNA hairpins by comparing the measured ΔGfold°, ΔHfold°, and ΔSfold° values against predictions made by NUPACK software, we adapted FESA to characterize noncanonical nucleic acid structures, encompassing DNA triplexes, G-quadruplexes, and aptamers. This adaptation enabled the successful characterization of the folding thermodynamics for these complex structures under various experimental conditions. The successful development of FESA marks a paradigm shift and a technical advancement in characterizing the thermodynamics of noncanonical DNA structures through molecular tools. It also opens new avenues for probing fundamental chemical and biophysical questions through the lens of molecular engineering and dynamic DNA chemistry.
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Affiliation(s)
- Yuqin Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Qianfan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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13
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Valentini M, Ercolani G, Di Stefano S. Kinetic Trapping of an Out-of-Equilibrium Dynamic Library of Imines by Changing Solvent. Chemistry 2024; 30:e202401104. [PMID: 38584126 DOI: 10.1002/chem.202401104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/09/2024]
Abstract
A well-behaved dynamic library composed of two imines and corresponding amines was subjected to the action of an activated carboxylic acid (ACA), whose decarboxylation is known to be base promoted, in different solvents, namely CD2Cl2, CD3CN, and mixtures of them. Two non-equilibrium systems are consequently obtained: i) a dissipative (CD2Cl2) and ii) an out-of-equilibrium (CD3CN) dynamic library whose composition goes back to equilibrium after a given time. In the former case, the library is fully coupled with the decarboxylation of the ACA, while in the latter, an energy ratchet operates. In the mixed solvents, the library exhibits a mediated behavior. Interestingly, in the presence of an excess of added ACA, the different behavior of the imine library in the two solvents is expected to manifest only when the excess acid is consumed.
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Affiliation(s)
- Matteo Valentini
- Department of Chemistry, Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma -, Meccanismi di Reazione, P.le A. Moro 5, I-00185, Roma, Italy
| | - Gianfranco Ercolani
- Department of Chemical Science and Technology, Università di Roma Tor Vergata, Via della Ricerca Scientifica, I-00133, Roma, Italy
| | - Stefano Di Stefano
- Department of Chemistry, Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma -, Meccanismi di Reazione, P.le A. Moro 5, I-00185, Roma, Italy
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14
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Alkhamis O, Canoura J, Wang L, Xiao Y. Nuclease-assisted selection of slow-off rate aptamers. SCIENCE ADVANCES 2024; 10:eadl3426. [PMID: 38865469 PMCID: PMC11168469 DOI: 10.1126/sciadv.adl3426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 05/09/2024] [Indexed: 06/14/2024]
Abstract
Conventional directed evolution methods offer the ability to select bioreceptors with high binding affinity for a specific target in terms of thermodynamic properties. However, there is a lack of analogous approaches for kinetic selection, which could yield affinity reagents that exhibit slow off-rates and thus remain tightly bound to targets for extended periods. Here, we describe an in vitro directed evolution methodology that uses the nuclease flap endonuclease 1 to achieve the efficient discovery of aptamers that have slow dissociation rates. Our nuclease-assisted selection strategy can yield specific aptamers for both small molecules and proteins with off-rates that are an order of magnitude slower relative to those obtained with conventional selection methods while still retaining excellent overall target affinity in terms of thermodynamics. This new methodology provides a generalizable approach for generating slow off-rate aptamers for diverse targets, which could, in turn, prove valuable for applications including molecular devices, bioimaging, and therapy.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
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15
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Song M, Tian J, Wang L, Dong S, Fu K, Chen S, Liu C. Efficient Delivery of Lomitapide using Hybrid Membrane-Coated Tetrahedral DNA Nanostructures for Glioblastoma Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311760. [PMID: 38569065 DOI: 10.1002/adma.202311760] [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: 11/07/2023] [Revised: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Glioblastoma (GBM) is the most aggressive and prevalent primary malignant tumor of the central nervous system. Traditional chemotherapy has poor therapeutic effects and significant side effects due to drug resistance, the natural blood-brain barrier (BBB), and nonspecific distribution, leading to a lack of clinically effective therapeutic drugs. Here, 1430 small molecule compounds are screened based on a high-throughput drug screening platform and a novel anti-GBM drug, lomitapide (LMP) is obtained. Furthermore, a bionic nanodrug delivery system (RFA NPs) actively targeting GBM is constructed, which mainly consists of tetrahedral DNA nanocages (tFNA NPs) loaded with LMP as the core and a folate-modified erythrocyte-cancer cell-macrophage hybrid membrane (FRUR) as the shell. FRUR camouflage conferred unique features on tFNA NPs, including excellent biocompatibility, improved pharmacokinetic profile, efficient BBB permeability, and tumor targeting ability. The results show that the LMP RFA NPs exhibited superior and specific anti-GBM activities, reduced off-target drug delivery, prolonged lifespan, and has negligible side effects in tumor-bearing mice. This study combines high-throughput drug screening with biomimetic nanodrug delivery system technology to provide a theoretical and practical basis for drug development and the optimization of clinical treatment strategies for GBM treatment.
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Affiliation(s)
- Mingming Song
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiameng Tian
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Li Wang
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Shuqi Dong
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Kun Fu
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Siyu Chen
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
| | - Chang Liu
- Department of Endocrinology, Nanjing Drum Tower Hospital, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 211198, China
- Jiangsu Provincial University Key Laboratory of Drug Discovery for Metabolic Inflammatory Diseases, China Pharmaceutical University, Nanjing, 211198, China
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16
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Samanta A, Baranda Pellejero L, Masukawa M, Walther A. DNA-empowered synthetic cells as minimalistic life forms. Nat Rev Chem 2024; 8:454-470. [PMID: 38750171 DOI: 10.1038/s41570-024-00606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2024] [Indexed: 06/13/2024]
Abstract
Cells, the fundamental units of life, orchestrate intricate functions - motility, adaptation, replication, communication, and self-organization within tissues. Originating from spatiotemporally organized structures and machinery, coupled with information processing in signalling networks, cells embody the 'sensor-processor-actuator' paradigm. Can we glean insights from these processes to construct primitive artificial systems with life-like properties? Using de novo design approaches, what can we uncover about the evolutionary path of life? This Review discusses the strides made in crafting synthetic cells, utilizing the powerful toolbox of structural and dynamic DNA nanoscience. We describe how DNA can serve as a versatile tool for engineering entire synthetic cells or subcellular entities, and how DNA enables complex behaviour, including motility and information processing for adaptive and interactive processes. We chart future directions for DNA-empowered synthetic cells, envisioning interactive systems wherein synthetic cells communicate within communities and with living cells.
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Affiliation(s)
- Avik Samanta
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India.
| | | | - Marcos Masukawa
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany
| | - Andreas Walther
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz, Germany.
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17
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Abraham GR, Chaderjian AS, N Nguyen AB, Wilken S, Saleh OA. Nucleic acid liquids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2024; 87:066601. [PMID: 38697088 DOI: 10.1088/1361-6633/ad4662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 05/02/2024] [Indexed: 05/04/2024]
Abstract
The confluence of recent discoveries of the roles of biomolecular liquids in living systems and modern abilities to precisely synthesize and modify nucleic acids (NAs) has led to a surge of interest in liquid phases of NAs. These phases can be formed primarily from NAs, as driven by base-pairing interactions, or from the electrostatic combination (coacervation) of negatively charged NAs and positively charged molecules. Generally, the use of sequence-engineered NAs provides the means to tune microsopic particle properties, and thus imbue specific, customizable behaviors into the resulting liquids. In this way, researchers have used NA liquids to tackle fundamental problems in the physics of finite valence soft materials, and to create liquids with novel structured and/or multi-functional properties. Here, we review this growing field, discussing the theoretical background of NA liquid phase separation, quantitative understanding of liquid material properties, and the broad and growing array of functional demonstrations in these materials. We close with a few comments discussing remaining open questions and challenges in the field.
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Affiliation(s)
- Gabrielle R Abraham
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Aria S Chaderjian
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
| | - Anna B N Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
| | - Sam Wilken
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
| | - Omar A Saleh
- Physics Department,University of California, Santa Barbara, CA 93106, United States of America
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States of America
- Materials Department, University of California, Santa Barbara, CA 93106, United States of America
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18
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Wang L, Luo W, Weng Z, Wang Z, Wu Y, Zhao R, Han X, Liu X, Zhang J, Yang Y, Xie G. Building a stable and robust anti-interference DNA dissipation system by eliminating the accumulation of systemic specified errors. Anal Chim Acta 2024; 1302:342493. [PMID: 38580407 DOI: 10.1016/j.aca.2024.342493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The emergence of DNA nanotechnology has enabled the systematic design of diverse bionic dissipative behaviors under the precise control of nucleic acid nanodevices. Nevertheless, when compared to the dissipation observed in robust living systems, it is highly desirable to enhance the anti-interference for artificial DNA dissipation to withstand perturbations and facilitate repairs within the complex biological environments. RESULTS In this study, we introduce strategically designed "trash cans" to facilitate kinetic control over interferences, transforming the stochastic binding of individual components within a homogeneous solution into a competitive binding process. This approach effectively eliminates incorrect binding and the accumulation of systemic interferences while ensuring a consistent pattern of energy fluctuation from response to silence. Remarkably, even in the presence of numerous interferences differing by only one base, we successfully achieve complete system reset through multiple cycles, effectively restoring the energy level to a minimum. SIGNIFICANCE The system was able to operate stably without any adverse effect under conditions of irregular interference, high-abundance interference, and even multiplex interferences including DNA and RNA crosstalk. This work not only provides an effective paradigm for constructing robust DNA dissipation systems but also greatly broadens the potential of DNA dissipation for applications in high-precision molecular recognition and complex biological reaction networks.
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Affiliation(s)
- Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Xin Liu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Jianhong Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yujun Yang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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19
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Kang H, Yang Y, Wei B. Synthetic molecular switches driven by DNA-modifying enzymes. Nat Commun 2024; 15:3781. [PMID: 38710688 DOI: 10.1038/s41467-024-47742-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/10/2024] [Indexed: 05/08/2024] Open
Abstract
Taking inspiration from natural systems, in which molecular switches are ubiquitous in the biochemistry regulatory network, we aim to design and construct synthetic molecular switches driven by DNA-modifying enzymes, such as DNA polymerase and nicking endonuclease. The enzymatic treatments on our synthetic DNA constructs controllably switch ON or OFF the sticky end cohesion and in turn cascade to the structural association or disassociation. Here we showcase the concept in multiple DNA nanostructure systems with robust assembly/disassembly performance. The switch mechanisms are first illustrated in minimalist systems with a few DNA strands. Then the ON/OFF switches are realized in complex DNA lattice and origami systems with designated morphological changes responsive to the specific enzymatic treatments.
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Affiliation(s)
- Hong Kang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yuexuan Yang
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China
| | - Bryan Wei
- School of Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
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20
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Bai D, Zhang J, Zhang Y, Yu H, Zhang L, Han X, Lv K, Wang L, Luo W, Wu Y, Zhou X, Wang W, Feng T, Xie G. A Spatially Controlled Proximity Split Tweezer Switch for Enhanced DNA Circuit Construction and Multifunctional Transduction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307421. [PMID: 38072808 DOI: 10.1002/smll.202307421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/15/2023] [Indexed: 05/03/2024]
Abstract
DNA strand displacement reactions are vital for constructing intricate nucleic acid circuits, owing to their programmability and predictability. However, the scarcity of effective methods for eliminating circuit leakages has hampered the construction of circuits with increased complexity. Herein, a versatile strategy is developed that relies on a spatially controlled proximity split tweezer (PST) switch to transduce the biomolecular signals into the independent oligonucleotides. Leveraging the double-stranded rigidity of the tweezer works synergistically with the hindering effect of the hairpin lock, effectively minimizing circuit leakage compared with sequence-level methods. In addition, the freely designed output strand is independent of the target binding sequence, allowing the PST switch conformation to be modulated by nucleic acids, small molecules, and proteins, exhibiting remarkable adaptability to a wide range of targets. Using this platform, established logical operations between different types of targets for multifunctional transduction are successfully established. Most importantly, the platform can be directly coupled with DNA catalytic circuits to further enhance transduction performance. The uniqueness of this platform lies in its design straightforwardness, flexibility, scalable intricacy, and system compatibility. These attributes pave a broad path toward nucleic acid-based development of sophisticated transduction networks, making them widely applied in basic science research and biomedical applications.
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Affiliation(s)
- Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Yaoyi Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Li Zhang
- Department of Forensic, Chongqing Medical University, Chongqing, 400016, P. R. China
| | - Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 40016, P. R. China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P.R. China
| | - Wang Luo
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - You Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Xi Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Tong Feng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, No. 1 Yi Xue Yuan Road, Chongqing, 400016, P. R. China
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21
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Hu M, Yang M, Cheng X, Wu T. Time-Controlled Authentication Strategies for Molecular Information Transfer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400261. [PMID: 38676342 DOI: 10.1002/smll.202400261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Modern cryptography based on computational complexity theory is mainly constructed with silicon-based circuits. As DNA nanotechnology penetrates the molecular domain, utilizing molecular cryptography for data access protection in the biomolecular domain becomes a unique approach to information security. However, building security devices and strategies with robust security and compatibility is still challenging. Here, this study reports a time-controlled molecular authentication strategy using DNAzyme and DNA strand displacement as the basic framework. A time limit exists for authorization and access, and this spontaneous shutdown design further protects secure access. Multiple hierarchical authentications, temporal Boolean logic authentication, and enzyme authentication strategies are constructed based on DNA networks'good compatibility and programmability. This study gives proof of concept for the detection and protection of bioinformation about single nucleotide variants and miRNA, highlighting their potential in biosensing and security protection.
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Affiliation(s)
- Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mengyao Yang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xianzhi Cheng
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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22
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Solra M, Kapila R, Das S, Bhatt P, Rana S. Transient Metallo-Lipidoid Assemblies Amplify Covalent Catalysis of Aqueous and Non-Aqueous Reactions. Angew Chem Int Ed Engl 2024; 63:e202400348. [PMID: 38315883 DOI: 10.1002/anie.202400348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Dissipative supramolecular assemblies are hallmarks of living systems, contributing to their complex, dynamic structures and emerging functions. Living cells can spatiotemporally control diverse biochemical reactions in membrane compartments and condensates, regulating metabolite levels, signal transduction or remodeling of the cytoskeleton. Herein, we constructed membranous compartments using self-assembly of lipid-like amphiphiles (lipidoid) in aqueous medium. The new double-tailed lipidoid features Cu(II) coordinated with a tetravalent chelator that dictates the binding of two amphiphilic ligands in cis-orientation. Hydrophobic interactions between the lipidoids coupled with intermolecular hydrogen bonding led to a well-defined bilayer vesicle structure. Oil-soluble SNAr reaction is efficiently upregulated in the hydrophobic cavity, acting as a catalytic crucible. The modular system allows easy incorporation of exposed primary amine groups, which augments the catalysis of retro aldol and C-N bond formation reactions. Moreover, a higher-affinity chelator enables consumption of the Cu(II) template leveraging the differential thermodynamic stability, which allows a controllable lifetime of the vesicular assemblies. Concomitant temporal upregulation of the catalytic reactions could be tuned by the metal ion concentration. This work offers new possibilities for metal ion-mediated dynamic supramolecular systems, opening up a massive repertoire of functionally active dynamic "life-like" materials.
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Affiliation(s)
- Manju Solra
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Rohit Kapila
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Sourav Das
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Preeti Bhatt
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
| | - Subinoy Rana
- Materials Research Centre, Division of Chemical Sciences, Indian Institute of Science, C. V. Raman Road, Bangalore, 560012, India
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23
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Ranganath VA, Maity I. Artificial Homeostasis Systems Based on Feedback Reaction Networks: Design Principles and Future Promises. Angew Chem Int Ed Engl 2024; 63:e202318134. [PMID: 38226567 DOI: 10.1002/anie.202318134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/17/2024]
Abstract
Feedback-controlled chemical reaction networks (FCRNs) are indispensable for various biological processes, such as cellular mechanisms, patterns, and signaling pathways. Through the intricate interplay of many feedback loops (FLs), FCRNs maintain a stable internal cellular environment. Currently, creating minimalistic synthetic cells is the long-term objective of systems chemistry, which is motivated by such natural integrity. The design, kinetic optimization, and analysis of FCRNs to exhibit functions akin to those of a cell still pose significant challenges. Indeed, reaching synthetic homeostasis is essential for engineering synthetic cell components. However, maintaining homeostasis in artificial systems against various agitations is a difficult task. Several biological events can provide us with guidelines for a conceptual understanding of homeostasis, which can be further applicable in designing artificial synthetic systems. In this regard, we organize our review with artificial homeostasis systems driven by FCRNs at different length scales, including homogeneous, compartmentalized, and soft material systems. First, we stretch a quick overview of FCRNs in different molecular and supramolecular systems, which are the essential toolbox for engineering different nonlinear functions and homeostatic systems. Moreover, the existing history of synthetic homeostasis in chemical and material systems and their advanced functions with self-correcting, and regulating properties are also emphasized.
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Affiliation(s)
- Vinay Ambekar Ranganath
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
| | - Indrajit Maity
- Centre for Nano and Material Sciences, Jain (Deemed-to-be University), Jain Global Campus, Bangalore, 562112, Karnataka, India
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24
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Ouyang Y, Willner I. Phototriggered Equilibrated and Transient Orthogonally Operating Constitutional Dynamic Networks Guiding Biocatalytic Cascades. J Am Chem Soc 2024; 146:6806-6816. [PMID: 38422481 PMCID: PMC10941189 DOI: 10.1021/jacs.3c13562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
The photochemical deprotection of structurally engineered o-nitrobenzylphosphate-caged hairpin nucleic acids is introduced as a versatile method to evolve constitutional dynamic networks, CDNs. The photogenerated CDNs, in the presence of fuel strands, interact with auxiliary CDNs, resulting in their dynamically equilibrated reconfiguration. By modification of the constituents associated with the auxiliary CDNs with glucose oxidase (GOx)/horseradish peroxidase (HRP) or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) cofactor, the photogenerated CDN drives the orthogonal operation upregulated/downregulated operation of the GOx/HRP and LDH/NAD+ biocatalytic cascade in the conjugate mixture of auxiliary CDNs. Also, the photogenerated CDN was applied to control the reconfiguration of coupled CDNs, leading to upregulated/downregulated formation of the antithrombin aptamer units, resulting in the dictated inhibition of thrombin activity (fibrinogen coagulation). Moreover, a reaction module consisting of GOx/HRP-modified o-nitrobenzyl phosphate-caged DNA hairpins, photoresponsive caged auxiliary duplexes, and nickase leads upon irradiation to the emergence of a transient, dissipative CDN activating in the presence of two alternate auxiliary triggers, achieving transient operation of up- and downregulated GOx/HRP biocatalytic cascades.
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Affiliation(s)
- Yu Ouyang
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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25
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Wu L, Wang GA, Li F. Plug-and-Play Module for Reversible and Continuous Control of DNA Strand Displacement Kinetics. J Am Chem Soc 2024; 146:6516-6521. [PMID: 38411013 DOI: 10.1021/jacs.3c09242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Regulatory modules for controlling the kinetics of toehold-mediated strand displacement (TMSD) play critical roles in designing dynamic and dissipative DNA chemical reaction networks (CRNs) but are hardwired into sequence designs. Herein, we introduce antitoehold (At), a plug-and-play module for reversible and continuous tuning of TMSD kinetics by temporarily occupying the toehold domain via a metastable duplex and base stacking. We demonstrate that kinetic control can be readily activated or deactivated in real time for any TMSD by simply adding At or anti-At. Continuous tuning of TMSD kinetics can also be achieved by altering the concentration of At. Moreover, the simple addition of At could readily reprogram existing TMSDs into a pulse-generation DNA CRN with continuous tunability. Our At approach also offers a new way for engineering continuously tunable DNA hybridization probes, which may find practical uses for discriminating clinically important mutations. Because of the simplicity, we anticipate that At will find wide applications for engineering DNA CRNs with diverse dynamic and dissipative behaviors, and DNA hybridization probes with tunable affinity and selectivity.
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Affiliation(s)
- Lang Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Guan A Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
- Department of Chemistry, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
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26
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Yang S, Wang M, Tian D, Zhang X, Cui K, Lü S, Wang HH, Long M, Nie Z. DNA-functionalized artificial mechanoreceptor for de novo force-responsive signaling. Nat Chem Biol 2024:10.1038/s41589-024-01572-x. [PMID: 38448735 DOI: 10.1038/s41589-024-01572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Synthetic signaling receptors enable programmable cellular responses coupling with customized inputs. However, engineering a designer force-sensing receptor to rewire mechanotransduction remains largely unexplored. Herein, we introduce nongenetically engineered artificial mechanoreceptors (AMRs) capable of reprogramming non-mechanoresponsive receptor tyrosine kinases (RTKs) to sense user-defined force cues, enabling de novo-designed mechanotransduction. AMR is a modular DNA-protein chimera comprising a mechanosensing-and-transmitting DNA nanodevice grafted on natural RTKs via aptameric anchors. AMR senses intercellular tensile force via an allosteric DNA mechano-switch with tunable piconewton-sensitive force tolerance, actuating a force-triggered dynamic DNA assembly to manipulate RTK dimerization and activate intracellular signaling. By swapping the force-reception ligands, we demonstrate the AMR-mediated activation of c-Met, a representative RTK, in response to the cellular tensile forces mediated by cell-adhesion proteins (integrin, E-cadherin) or membrane protein endocytosis (CI-M6PR). Moreover, AMR also allows the reprogramming of FGFR1, another RTK, to customize mechanobiological function, for example, adhesion-mediated neural stem cell maintenance.
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Affiliation(s)
- Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Dawei Tian
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Zhang
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Kaiqing Cui
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Shouqin Lü
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Mian Long
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China.
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27
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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28
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Zhang L, Fu Y, Tong Y, Xie G, Deng S. Dynamic DNA Assembly by Programmable Hybridization Chain Reaction Mimicking Tubulin. NANO LETTERS 2024; 24:2603-2610. [PMID: 38349971 DOI: 10.1021/acs.nanolett.3c04852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Dynamic biological structures involve the continual turnover of molecules within supramolecular assemblies such as tubulin. Inspired by dynamic biology self-organizing systems, we build an artificial dynamic structure based on DNA nanotechnology through a nonequilibrium chemical system. Herein, a metastable domain (MD), essentially a stem-loop structure, was introduced into DNA hairpins within hybridization chain reaction (HCR), thereby imparting dynamic activity to the DNA polymers. Hairpins with MD thermodynamically assemble to a high-energy polymer in the presence of trigger strands. The polymer can relax back to the stable unassembled state once the invader is added and finally relax to the activated hairpin by an anti-invader. Reversible assembly/disassembly of the HCR is achieved through invader/anti-invader cycles. We accomplished kinetic modulation, reversible conformational switching, cascading regulation, and enzyme activity control through the MD-HCR. We believe that the design of the MD-HCR could inspire the development of autonomous biological functions within artificial systems.
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Affiliation(s)
- Li Zhang
- Department of Forensic Medicine, Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yao Fu
- Department of Forensic Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Yanqiu Tong
- School of Tourism and Media, Chongqing Jiaotong University, Chongqing 400016, China
| | - Guoming Xie
- Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
| | - Shixiong Deng
- Department of Forensic Medicine, Chongqing Medical University, Chongqing 400016, China
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29
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Kemper U, Weizenmann N, Kielar C, Erbe A, Seidel R. Heavy Metal Stabilization of DNA Origami Nanostructures. NANO LETTERS 2024; 24:2429-2436. [PMID: 38363878 PMCID: PMC10905993 DOI: 10.1021/acs.nanolett.3c03751] [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: 09/29/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
DNA origami is a powerful tool to fold 3-dimensional DNA structures with nanometer precision. Its usage, however, is limited as high ionic strength, temperatures below ∼60 °C, and pH values between 5 and 10 are required to ensure the structural integrity of DNA origami nanostructures. Here, we demonstrate a simple and effective method to stabilize DNA origami nanostructures against harsh buffer conditions using [PdCl4]2-. It provided the stabilization of different DNA origami nanostructures against mechanical compression, temperatures up to 100 °C, double-distilled water, and pH values between 4 and 12. Additionally, DNA origami superstructures and bound cargos are stabilized with yields of up to 98%. To demonstrate the general applicability of our approach, we employed our protocol with a Pd metallization procedure at elevated temperatures. In the future, we think that our method opens up new possibilities for applications of DNA origami nanostructures beyond their usual reaction conditions.
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Affiliation(s)
- Ulrich Kemper
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Nicole Weizenmann
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Charlotte Kielar
- Institute
of Ion Beam Physics and Materials Research and Department of Nanoelectronics, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
- Insitute
of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Artur Erbe
- Institute
of Ion Beam Physics and Materials Research and Department of Nanoelectronics, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany
| | - Ralf Seidel
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
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30
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Huang C, Liu Q, Xu J, Chen C, You Q, Wang D, Qian H, Hu M. Intratracheal administration of programmable DNA nanostructures combats acute lung injury by targeting microRNA-155. Int J Pharm 2024; 651:123750. [PMID: 38159585 DOI: 10.1016/j.ijpharm.2023.123750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/12/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Acute lung injury (ALI) is an acute inflammatory process that can result in life-threatening consequences. Programmable DNA nanostructures have emerged as excellent nanoplatforms for microRNA-based therapeutics, offering potential nanomedicines for ALI treatment. Nonetheless, the traditional systematic administration of nanomedicines is constrained by low delivery efficiency, poor pharmacokinetics, and nonspecific side effects. Here, we identify macrophage microRNA-155 as a novel therapeutic target using the magnetic bead sorting technique. We further construct a DNA nanotubular nucleic acid drug antagonizing microRNA-155 (NT-155) for ALI treatment through intratracheal administration. Flow cytometry results demonstrate that NT-155, when inhaled, is taken up much more effectively by macrophages and dendritic cells in the bronchoalveolar lavage fluid of ALI mice. Furthermore, NT-155 effectively silences the overexpressed microRNA-155 in macrophages and exerts excellent inflammation inhibition effects in vitro and ALI mouse models. Mechanistically, NT-155 suppresses microRNA-155 expression and activates its target gene SOCS1, inhibiting the p-P65 signaling pathway and suppressing proinflammatory cytokine secretion. The current study suggests that deliberately designed nucleic acid drugs are promising nanomedicines for ALI treatment and the local administration may open up new practical applications of DNA in the future.
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Affiliation(s)
- Chaowang Huang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Qian Liu
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Laboratory of Pharmacy and Chemistry, and Laboratory of Tissue and Cell Biology, Lab Teaching & Management Center, Chongqing Medical University, Chongqing 400016, China
| | - Jing Xu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Chunfa Chen
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Qianyi You
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Dan Wang
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hang Qian
- Institute of Respiratory Diseases, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Chongqing Key Laboratory of Precision Medicine and Prevention of Major Respiratory Diseases, Chongqing 400037, China.
| | - Mingdong Hu
- Department of Geriatrics and Special Services Medicine, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China; Department of Health Management, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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31
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Takezawa Y, Zhang H, Mori K, Hu L, Shionoya M. Ligase-mediated synthesis of Cu II-responsive allosteric DNAzyme with bifacial 5-carboxyuracil nucleobases. Chem Sci 2024; 15:2365-2370. [PMID: 38362437 PMCID: PMC10866359 DOI: 10.1039/d3sc05042d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/17/2024] [Indexed: 02/17/2024] Open
Abstract
A CuII-responsive allosteric DNAzyme has been developed by introducing bifacial 5-carboxyuracil (caU) nucleobases, which form both hydrogen-bonded caU-A and metal-mediated caU-CuII-caU base pairs. The base sequence was logically designed based on a known RNA-cleaving DNAzyme so that the caU-modified DNAzyme (caU-DNAzyme) can form a catalytically inactive structure containing three caU-A base pairs and an active form with three caU-CuII-caU pairs. The caU-DNAzyme was synthesized by joining short caU-containing fragments with a standard DNA ligase. The activity of caU-DNAzyme was suppressed without CuII, but enhanced 21-fold with the addition of CuII. Furthermore, the DNAzyme activity was turned on and off during the reaction by the addition and removal of CuII ions. Both ligase-mediated synthesis and CuII-dependent allosteric regulation were achieved by the bifacial base pairing properties of caU. This study provides a new strategy for designing stimuli-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Hanci Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Lingyun Hu
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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32
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Han X, Yu H, Zhang L, Weng Z, Dai L, Wang L, Song L, Wang Z, Zhao R, Wang L, Wang W, Bai D, Guo Y, Lv K, Xie G. Movable toehold for leakless self-assembly circuits. Biosens Bioelectron 2024; 245:115823. [PMID: 37979548 DOI: 10.1016/j.bios.2023.115823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/30/2023] [Accepted: 11/05/2023] [Indexed: 11/20/2023]
Abstract
Nonenzymatic self-assembly circuit utilizing hairpin substrates has been developed to be a powerful tool for information transduction, amplification and computation. However, the sensitivity, stability and application of this circuit are impeded by the presence of leakage which refers to undesired triggering in the absence of input. Herein, we proposed a movable toehold principle to suppress leakage and accelerate the catalytic reaction through removing partial hairpin toehold responsible for the leakage and transferring it to the catalyst. With movable toehold, catalytic hairpin assembly (called mtCHA) exhibited an excellent signal-to-background ratio of over 100, high robustness and improved specificity. In more complex circuit, including proximity recognition, signal amplification of small molecules (such as ATP), logic network, autocatalysis circuit and two-layer cascade circuit, mtCHA also demonstrated satisfactory performance. Our findings suggest that mtCHA holds great potential for broader applications, and the approach of repurposing harmful fragments into beneficial candidates can provide valuable insights for other chemical systems.
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Affiliation(s)
- Xiaole Han
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hongyan Yu
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhi Weng
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ling Dai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Li Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Lin Song
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Weitao Wang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yongcan Guo
- Clinical Laboratory of Traditional Chinese Medicine Hospital Affiliated to Southwest Medical University, LuZhou Key Laboratory of Nanobiosensing and Microfluidic Point-of-Care Testing, Luzhou 646000, PR China.
| | - Ke Lv
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing, 400016, PR China.
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33
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Li XQ, Jia YL, Zhang YW, Shi PF, Chen HY, Xu JJ. Simulation-Assisted DNA Nanodevice Serve as a General Optical Platform for Multiplexed Analysis of Micrornas. Adv Healthc Mater 2024; 13:e2302652. [PMID: 37794560 DOI: 10.1002/adhm.202302652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/29/2023] [Indexed: 10/06/2023]
Abstract
Small frame nucleic acids (FNAs) serve as excellent carrier materials for various functional nucleic acid molecules, showcasing extensive potential applications in biomedicine development. The carrier module and function module combination is crucial for probe design, where an improper combination can significantly impede the functionality of sensing platforms. This study explores the effect of various combinations on the sensing performance of nanodevices through simulations and experimental approaches. Variances in response velocities, sensitivities, and cell uptake efficiencies across different structures are observed. Factors such as the number of functional molecules loaded, loading positions, and intermodular distances affect the rigidity and stability of the nanostructure. The findings reveal that the structures with full loads and moderate distances between modules have the lowest potential energy. Based on these insights, a multisignal detection platform that offers optimal sensitivity and response speed is developed. This research offers valuable insights for designing FNAs-based probes and presents a streamlined method for the conceptualization and optimization of DNA nanodevices.
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Affiliation(s)
- Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Lei Jia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Peng-Fei Shi
- College of Medicine, Linyi University, Linyi, 276005, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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34
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Greiss F, Lardon N, Schütz L, Barak Y, Daube SS, Weinhold E, Noireaux V, Bar-Ziv R. A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice. Nat Commun 2024; 15:883. [PMID: 38287055 PMCID: PMC10825189 DOI: 10.1038/s41467-024-45186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.
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Affiliation(s)
- Ferdinand Greiss
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Yoav Barak
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shirley S Daube
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Roy Bar-Ziv
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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35
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Hu M, Li X, Wu JN, Yang M, Wu T. DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates. ACS NANO 2024; 18:2184-2194. [PMID: 38193385 DOI: 10.1021/acsnano.3c09506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Toehold-mediated DNA strand displacement is the foundation of dynamic DNA nanotechnology, encompassing a wide range of tools with diverse functions, dynamics, and thermodynamic properties. However, a majority of these tools are limited to unidirectional reactions driven by thermodynamics. In response to the growing field of dissipative DNA nanotechnology, we present an approach: DNAzyme-based dissipative DNA strand displacement (D-DSD), which combines the principles of dynamic DNA nanotechnology and dissipative DNA nanotechnology. D-DSD introduces circular and dissipative characteristics, distinguishing it from the unidirectional reactions observed in conventional strand displacement. We investigated the reaction mechanism of D-DSD and devised temporal control elements. By substituting temporal components, we designed two distinct temporal AND gates using fewer than 10 strands, eliminating the need for complex network designs. In contrast to previous temporal logic gates, our temporal storage is not through dynamics control or cross-inhibition but through autoregressive storage, a more modular and scalable approach to memory storage. D-DSD preserves the fundamental structure of toehold-mediated strand displacement, while offering enhanced simplicity and versatility.
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Affiliation(s)
- Minghao Hu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Xiaolong Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jia-Ni Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Mengyao Yang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Tongbo Wu
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
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36
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Li S, Zhao D, Yang F, Liu S. Dynamic monitoring of an enzymatically driven dissipative toehold-mediated strand displacement reaction. Chem Commun (Camb) 2024; 60:570-573. [PMID: 38093688 DOI: 10.1039/d3cc05061k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A general strategy to program self-resettable and dissipative toehold-mediated strand displacement reactions was proposed, using DNA strands as the fuel and lambda exonuclease as the fuel-consuming unit. This non-equilibrium system is reversible and temporally controllable. Furthermore, it can be well integrated into a DNA network to temporally control its cascade reaction or dynamic behaviour.
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Affiliation(s)
- Shuang Li
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Disong Zhao
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Fangfang Yang
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Shufeng Liu
- College of Chemistry and Chemical Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China.
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37
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Yang Q, Chang X, Lee JY, Saji M, Zhang F. DNA T-shaped crossover tiles for 2D tessellation and nanoring reconfiguration. Nat Commun 2023; 14:7675. [PMID: 37996416 PMCID: PMC10667507 DOI: 10.1038/s41467-023-43558-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
DNA tiles serve as the fundamental building blocks for DNA self-assembled nanostructures such as DNA arrays, origami, and designer crystals. Introducing additional binding arms to DNA crossover tiles holds the promise of unlocking diverse nano-assemblies and potential applications. Here, we present one-, two-, and three-layer T-shaped crossover tiles, by integrating T junction with antiparallel crossover tiles. These tiles carry over the orthogonal binding directions from T junction and retain the rigidity from antiparallel crossover tiles, enabling the assembly of various 2D tessellations. To demonstrate the versatility of the design rules, we create 2-state reconfigurable nanorings from both single-stranded tiles and single-unit assemblies. Moreover, four sets of 4-state reconfiguration systems are constructed, showing effective transformations between ladders and/or rings with pore sizes spanning ~20 nm to ~168 nm. These DNA tiles enrich the design tools in nucleic acid nanotechnology, offering exciting opportunities for the creation of artificial dynamic DNA nanopores.
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Affiliation(s)
- Qi Yang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Xu Chang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Jung Yeon Lee
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Minu Saji
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, NJ, 07102, USA.
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38
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Hall-Thomsen H, Small S, Gavrilov M, Ha T, Schulman R, Moerman PG. Directing Uphill Strand Displacement with an Engineered Superhelicase. ACS Synth Biol 2023; 12:3424-3432. [PMID: 37844274 PMCID: PMC10661026 DOI: 10.1021/acssynbio.3c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 10/18/2023]
Abstract
The ability to finely tune reaction rates and binding energies between components has made DNA strand displacement circuits promising candidates to replicate the complex regulatory functions of biological reaction networks. However, these circuits often lack crucial properties, such as signal turnover and the ability to transiently respond to successive input signals that require the continuous input of chemical energy. Here, we introduce a method for providing such energy to strand displacement networks in a controlled fashion: an engineered DNA helicase, Rep-X, that transiently dehybridizes specific DNA complexes, enabling the strands in the complex to participate in downstream hybridization or strand displacement reactions. We demonstrate how this process can direct the formation of specific metastable structures by design and that this dehybridization process can be controlled by DNA strand displacement reactions that effectively protect and deprotect a double-stranded complex from unwinding by Rep-X. These findings can guide the design of active DNA strand displacement regulatory networks, in which sustained dynamical behavior is fueled by helicase-regulated unwinding.
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Affiliation(s)
- Helena Hall-Thomsen
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Shavier Small
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Momcilo Gavrilov
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
| | - Taekjip Ha
- Biophysics
and Biophysical Chemistry, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Biomedical
Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Rebecca Schulman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Computer
Science, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Pepijn Gerben Moerman
- Chemical
& Biomolecular Engineering, Johns Hopkins
University, Baltimore, Maryland 21218, United States
- Chemical
Engineering and Chemistry, Eindhoven University
of Technology, Eindhoven 5612 AP, Netherlands
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39
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Tang D, Shi J, Wu Y, Luo H, Yan J, Huang KJ, Tan X. Flexible Self-Powered Sensing System Based on Novel DNA Circuit Strategy and Graphdiyne for Thalassemia Gene by Rapid Naked-Eye Tracking and Open-Circuit Voltage. Anal Chem 2023; 95:16374-16382. [PMID: 37871958 DOI: 10.1021/acs.analchem.3c03841] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Based on the controllable instantaneous self-assembly ability of long-chain branched DNA nanostructures and the synergistic effect between nucleic acid amplification without enzymes, a highly sensitive and highly specific self-powered biosensing platform is developed. Two-dimensional graphdiyne is prepared, modified on flexible carbon cloth, and then functionalized with gold nanoparticles. When DNA mi-tubes are applied on it, target thalassemia gene CD122 triggers a dual-catalytic hairpin assembly reaction. The generated nanoscale DNA is precisely captured by the DNA mi-tube, exposing binding sites and activating the hybridization chain reaction to form long-chain branched DNA. Double-stranded DNA, along with dendritic DNA carrying a large number of guanine bases, precisely captures the signal molecule methylene blue (MB), generating a significant electrochemical signal. The redox reaction of MB also causes a proportional change in the system's color, achieving a colorimetric detection functionality. An efficient dual-mode self-powered sensing platform, therefore, is established for detecting the thalassemia gene CD122. The linear response range of target concentration to open-circuit voltage and RGB Blue value is 0.0001-10,000 pM. The detection limit under electrochemical mode is 36.3 aM (S/N = 3), and under colorimetric mode, it is as low as 12.1 aM (S/N = 3). The new method exhibits high sensitivity, excellent selectivity, and high accuracy, providing a universal strategy for designing novel biosensing platforms that can be extended to the detection of other biomolecules.
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Affiliation(s)
- Danyao Tang
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jinyue Shi
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Yeyu Wu
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Hu Luo
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Jun Yan
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Ke-Jing Huang
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
| | - Xuecai Tan
- Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Applied Analytical Chemistry, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, China
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40
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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41
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Fischer A, Ehrlich A, Plotkin Y, Ouyang Y, Asulin K, Konstantinos I, Fan C, Nahmias Y, Willner I. Stimuli-Responsive Hydrogel Microcapsules Harnessing the COVID-19 Immune Response for Cancer Therapeutics. Angew Chem Int Ed Engl 2023; 62:e202311590. [PMID: 37675854 DOI: 10.1002/anie.202311590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
The combination of gene therapy and immunotherapy concepts, along recent advances in DNA nanotechnology, have the potential to provide important tools for cancer therapies. We present the development of stimuli-responsive microcapsules, loaded with a viral immunogenetic agent, harnessing the immune response against the Coronavirus Disease 2019, COVID-19, to selectively attack liver cancer cells (hepatoma) or recognize breast cancer or hepatoma, by expression of green fluorescence protein, GFP. The pH-responsive microcapsules, modified with DNA-tetrahedra nanostructures, increased hepatoma permeation by 50 %. Incorporation of a GFP-encoding lentivirus vector inside the tumor-targeting pH-stimulated miRNA-triggered and Alpha-fetoprotein-dictated microcapsules enables the demonstration of neoplasm selectivity, with approximately 5,000-, 8,000- and 50,000-fold more expression in the cancerous cells, respectively. The incorporation of the SARS-CoV-2 spike protein in the gene vector promotes specific recognition of the immune-evading hepatoma by the COVID-19-analogous immune response, which leads to cytotoxic and inflammatory activity, mediated by serum components taken from vaccinated or recovered COVID-19 patients, resulting in effective elimination of the hepatoma (>85 % yield).
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Affiliation(s)
- Amit Fischer
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avner Ehrlich
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yevgeni Plotkin
- The Department of Anesthesiology, Critical Care and Pain Medicine, Hadassah University Hospital, Jerusalem, 9112001, Israel
- Faculty of Medicine, Hebrew University of Jerusalem Jerusalem, 9112001, (Israel)
| | - Yu Ouyang
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Klil Asulin
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ioannidis Konstantinos
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - 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
| | - Yaakov Nahmias
- Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Bio-hybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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42
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Ouyang Y, Dong J, Willner I. Dynamic DNA Networks-Guided Directional and Orthogonal Transient Biocatalytic Cascades. J Am Chem Soc 2023; 145:22135-22149. [PMID: 37773962 PMCID: PMC10571085 DOI: 10.1021/jacs.3c08020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Indexed: 10/01/2023]
Abstract
DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD+ biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD+-biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD+ cascade or vice versa. The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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43
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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44
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Wei H, Li F, Xue T, Wang H, Ju E, Li M, Tao Y. MicroRNA-122-functionalized DNA tetrahedron stimulate hepatic differentiation of human mesenchymal stem cells for acute liver failure therapy. Bioact Mater 2023; 28:50-60. [PMID: 37214257 PMCID: PMC10199164 DOI: 10.1016/j.bioactmat.2023.04.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023] Open
Abstract
As the most abundant liver-specific microRNA, microRNA-122 (miR122) played a crucial role in the differentiation of stem cells into hepatocytes. However, highly efficient miR122 delivery still confronts challenges including poor cellular uptake and easy biodegradation. Herein, we for the first time demonstrated that the tetrahedral DNA (TDN) nanoplatform had great potential in inducing the differentiation of human mesenchymal stem cells (hMSCs) into functional hepatocyte-like cells (HLCs) by transferring the liver-specific miR122 to hMSCs efficiently without any extrinsic factors. As compared with miR122, miR122-functionalized TDN (TDN-miR122) could significantly up-regulate the protein expression levels of mature hepatocyte markers and hepatocyte-specific marker genes in hMSCs, indicating that TDN-miR122 could particularly activate the hepatocyte-specific properties of hMSCs for developing cell-based therapies in vitro. The transcriptomic analysis further indicated the potential mechanism that TDN-miR122 assisted hMSCs differentiated into functional HLCs. The TDN-miR122-hMSCs exhibited hepatic cell morphology phenotype, significantly up-regulated specific hepatocyte genes and hepatic biofunctions in comparison with the undifferentiated MSCs. Preclinical in vivo transplantation appeared that TDN-miR122-hMSCs in combination with or without TDN could efficiently rescue acute liver failure injury through hepatocyte function supplement, anti-apoptosis, cellular proliferation promotion, and anti-inflammatory. Collectively, our findings may provide a new and facile approach for hepatic differentiation of hMSCs for acute liver failure therapy. Further large animal model explorations are needed to study their potential in clinical translation in the future.
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Affiliation(s)
- Hongyan Wei
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, 510630, China
| | - Fenfang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, 510630, China
| | - Tiantian Xue
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Haixia Wang
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Enguo Ju
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, 510630, China
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou, 510630, China
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45
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Bucci J, Irmisch P, Del Grosso E, Seidel R, Ricci F. Timed Pulses in DNA Strand Displacement Reactions. J Am Chem Soc 2023; 145:20968-20974. [PMID: 37710955 PMCID: PMC10540199 DOI: 10.1021/jacs.3c06664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Indexed: 09/16/2023]
Abstract
Inspired by naturally occurring regulatory mechanisms that allow complex temporal pulse features with programmable delays, we demonstrate here a strategy to achieve temporally programmed pulse output signals in DNA-based strand displacement reactions (SDRs). To achieve this, we rationally designed input strands that, once bound to their target duplex, can be gradually degraded, resulting in a pulse output signal. We also designed blocker strands that suppress strand displacement and determine the time at which the pulse reaction is generated. We show that by controlling the degradation rate of blocker and input strands, we can finely control the delayed pulse output over a range of 10 h. We also prove that it is possible to orthogonally delay two different pulse reactions in the same solution by taking advantage of the specificity of the degradation reactions for the input and blocker strands. Finally, we show here two possible applications of such delayed pulse SDRs: the time-programmed pulse decoration of DNA nanostructures and the sequentially appearing and self-erasing formation of DNA-based patterns.
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Affiliation(s)
- Juliette Bucci
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Patrick Irmisch
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Erica Del Grosso
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Ralf Seidel
- Molecular
Biophysics Group, Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103 Leipzig, Germany
| | - Francesco Ricci
- Department
of Chemical Sciences and Technologies, University
of Rome, Tor Vergata,
Via della Ricerca Scientifica, 00133 Rome, Italy
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46
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Li Z, Wang J, Willner I. Alternate Strategies to Induce Dynamically Modulated Transient Transcription Machineries. ACS NANO 2023; 17:18266-18279. [PMID: 37669432 PMCID: PMC10540262 DOI: 10.1021/acsnano.3c05336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
Emulating native transient transcription machineries modulating temporal gene expression by synthetic circuits is a major challenge in the area of systems chemistry. Three different methods to operate transient transcription machineries and to modulate the gated transcription processes of target RNAs are introduced. One method involves the design of a reaction module consisting of transcription templates being triggered by promoter fuel strands transcribing target RNAs and in parallel generating functional DNAzymes in the transcription templates, modulating the dissipative depletion of the active templates and the transient operation of transcription circuits. The second approach involves the application of a reaction module consisting of two transcription templates being activated by a common fuel promoter strand. While one transcription template triggers the transcription of the target RNA, the second transcription template transcribes the anti-fuel strand, displacing the promoter strand associated with the transcription templates, leading to the depletion of the transcription templates and to the dynamic transient modulation of the transcription process. The third strategy involves the assembly of a reaction module consisting of a reaction template triggered by a fuel promoter strand transcribing the target RNA. The concomitant nickase-stimulated depletion of the promoter strand guides the transient modulation of the transcription process. Via integration of two parallel fuel-triggered transcription templates in the three transcription reaction modules and application of template-specific blocker units, the parallel and gated transiently modulated transcription of two different RNA aptamers is demonstrated. The nickase-stimulated transiently modulated transcription reaction module is applied as a functional circuit guiding the dynamic expression of gated, transiently operating, catalytic DNAzymes.
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Affiliation(s)
| | | | - Itamar Willner
- The Institute of Chemistry, The Center
for Nanoscience and Nanotechnology, The
Hebrew University of Jerusalem, Jerusalem 91904, Israel
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47
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Zhang X, Liu Y, Wang B, Zhou S, Shi P, Cao B, Zheng Y, Zhang Q, Kirilov Kasabov N. Biomolecule-Driven Two-Factor Authentication Strategy for Access Control of Molecular Devices. ACS NANO 2023; 17:18178-18189. [PMID: 37703447 DOI: 10.1021/acsnano.3c05070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
The rise of DNA nanotechnology is promoting the development of molecular security devices and marking an essential change in information security technology, to one that can resist the threats resulting from the increase in computing power, brute force attempts, and quantum computing. However, developing a secure and reliable access control strategy to guarantee the confidentiality of molecular security devices is still a challenge. Here, a biomolecule-driven two-factor authentication strategy for access control of molecular devices is developed. Importantly, the two-factor is realized by applying the specificity and nicking properties of the nicking enzyme and the programmable design of the DNA sequence, endowing it with the characteristic of a one-time password. To demonstrate the feasibility of this strategy, an access control module is designed and integrated to further construct a role-based molecular access control device. By constructing a command library composed of three commands (Ca, Cb, Ca and Cb), the authorized access of three roles in the molecular device is realized, in which the command Ca corresponds to the authorization of role A, Cb corresponds to the authorization of role B, and Ca and Cb corresponds to the authorization of role C. In this way, when users access the device, they not only need the correct factor but also need to apply for role authorization in advance to obtain secret information. This strategy provides a highly robust method for the research on access control of molecular devices and lays the foundation for research on the next generation of information security.
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Affiliation(s)
- Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Dalian 116622, China
| | - Peijun Shi
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Nikola Kirilov Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand
- Intelligent Systems Research Center, Ulster University, Londonderry BT48, United Kingdom
- IICT, Bulgarian Academy of Sciences, Sofia 1040, Bulgaria
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48
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Mastracco P, Copp SM. Beyond nature's base pairs: machine learning-enabled design of DNA-stabilized silver nanoclusters. Chem Commun (Camb) 2023; 59:10360-10375. [PMID: 37575075 DOI: 10.1039/d3cc02890a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Sequence-encoded biomolecules such as DNA and peptides are powerful programmable building blocks for nanomaterials. This paradigm is enabled by decades of prior research into how nucleic acid and amino acid sequences dictate biomolecular interactions. The properties of biomolecular materials can be significantly expanded with non-natural interactions, including metal ion coordination of nucleic acids and amino acids. However, these approaches present design challenges because it is often not well-understood how biomolecular sequence dictates such non-natural interactions. This Feature Article presents a case study in overcoming challenges in biomolecular materials with emerging approaches in data mining and machine learning for chemical design. We review progress in this area for a specific class of DNA-templated metal nanomaterials with complex sequence-to-property relationships: DNA-stabilized silver nanoclusters (AgN-DNAs) with bright, sequence-tuned fluorescence colors and promise for biophotonics applications. A brief overview of machine learning concepts is presented, and high-throughput experimental synthesis and characterization of AgN-DNAs are discussed. Then, recent progress in machine learning-guided design of DNA sequences that select for specific AgN-DNA fluorescence properties is reviewed. We conclude with emerging opportunities in machine learning-guided design and discovery of AgN-DNAs and other sequence-encoded biomolecular nanomaterials.
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Affiliation(s)
- Peter Mastracco
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, USA.
| | - Stacy M Copp
- Department of Materials Science and Engineering, University of California, Irvine, California 92697, USA.
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, USA
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49
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Takezawa Y, Kanemaru D, Kudo N, Shionoya M. Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation. Dalton Trans 2023; 52:11025-11029. [PMID: 37309206 DOI: 10.1039/d3dt01508d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Incorporation of interstrand metal complexes into DNA is a versatile strategy for metal-dependent stabilization and structural induction of DNA supramolecular structures. In this study, we have synthesized DNA three-way junction (3WJ) structures modified with phenanthroline (phen) ligands. The phen-modified 3WJ was found to be thermally stabilized (ΔTm = +16.9 °C) by the formation of an interstrand NiII(phen)3 complex. Furthermore, NiII-mediated structure induction of 3WJs was demonstrated with the phen-modified strands and their unmodified counterparts. This study suggests that ligand-modified 3WJs would be useful structural motifs for the construction of metal-responsive DNA molecular systems.
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Affiliation(s)
- Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Daisuke Kanemaru
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Naofumi Kudo
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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50
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Dong J, Willner I. Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription. Angew Chem Int Ed Engl 2023; 62:e202307898. [PMID: 37380611 DOI: 10.1002/anie.202307898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.
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Affiliation(s)
- Jiantong Dong
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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