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Liu X, Shi Q, Qi P, Wang Z, Zhang T, Zhang S, Wu J, Guo Z, Chen J, Zhang Q. Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis. Asian J Pharm Sci 2024; 19:100910. [PMID: 38948397 PMCID: PMC11214190 DOI: 10.1016/j.ajps.2024.100910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024] Open
Abstract
The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.
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Affiliation(s)
- Xuyao Liu
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Qi Shi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Peng Qi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ziming Wang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Tongyue Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Sijia Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jiayan Wu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jie Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Qiang Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
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2
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Sun S, Yang H, Wu Z, Zhang S, Xu J, Shi P. CRISPR/Cas systems combined with DNA nanostructures for biomedical applications. Chem Commun (Camb) 2024; 60:3098-3117. [PMID: 38406926 DOI: 10.1039/d4cc00290c] [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: 02/27/2024]
Abstract
DNA nanostructures are easy to design and construct, have good biocompatibility, and show great potential in biosensing and drug delivery. Numerous distinctive and versatile DNA nanostructures have been developed and explored for biomedical applications. In addition to DNA nanostructures that are completely assembled from DNA, composite DNA nanostructures obtained by combining DNA with other organic or inorganic materials are also widely used in related research. The CRISPR/Cas system has attracted great attention as a powerful gene editing technology and is also widely used in biomedical diagnosis. Many researchers are committed to exploring new possibilities by combining DNA nanostructures with CRISPR/Cas systems. These explorations provide support for the development of new detection methods and cargo delivery pathways, provide inspiration for improving relevant gene editing platforms, and further expand the application scope of DNA nanostructures and CRISPR/Cas systems. This paper mainly reviews the design principles and biomedical applications of CRISPR/Cas combined with DNA nanostructures based on the types of DNA nanostructures. Finally, the application status, challenges and development prospects of CRISPR/Cas combined with DNA nanostructures in detection and delivery are summarized. It is expected that this review will enable researchers to better understand the current state of the field and provide insights into the application of CRISPR/Cas systems and the development of DNA nanostructures.
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Affiliation(s)
- Shujuan Sun
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Haoqi Yang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Ziyong Wu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
| | - Jingjuan Xu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, P. R. China.
| | - Pengfei Shi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276000, P. R. China.
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Wang Y, Wang H, Li Y, Yang C, Tang Y, Lu X, Fan J, Tang W, Shang Y, Yan H, Liu J, Ding B. Chemically Conjugated Branched Staples for Super-DNA Origami. J Am Chem Soc 2024; 146:4178-4186. [PMID: 38301245 DOI: 10.1021/jacs.3c13331] [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: 02/03/2024]
Abstract
DNA origami, comprising a long folded DNA scaffold and hundreds of linear DNA staple strands, has been developed to construct various sophisticated structures, smart devices, and drug delivery systems. However, the size and diversity of DNA origami are usually constrained by the length of DNA scaffolds themselves. Herein, we report a new paradigm of scaling up DNA origami assembly by introducing a novel branched staple concept. Owing to their covalent characteristics, the chemically conjugated branched DNA staples we describe here can be directly added to a typical DNA origami assembly system to obtain super-DNA origami with a predefined number of origami tiles in one pot. Compared with the traditional two-step coassembly system (yields <10%), a much greater yield (>80%) was achieved using this one-pot strategy. The diverse superhybrid DNA origami with the combination of different origami tiles can be also efficiently obtained by the hybrid branched staples. Furthermore, the branched staples can be successfully employed as the effective molecular glues to stabilize micrometer-scale, super-DNA origami arrays (e.g., 10 × 10 array of square origami) in high yields, paving the way to bridge the nanoscale precision of DNA origami with the micrometer-scale device engineering. This rationally developed assembly strategy for super-DNA origami based on chemically conjugated branched staples presents a new avenue for the development of multifunctional DNA origami-based materials.
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Affiliation(s)
- Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yan Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Changping Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yue Tang
- Arizona State University, Tempe, Arizona 85281, United States
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jing Fan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Wantao Tang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Hao Yan
- Arizona State University, Tempe, Arizona 85281, United States
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Tang W, Tong T, Wang H, Lu X, Yang C, Wu Y, Wang Y, Liu J, Ding B. A DNA Origami-Based Gene Editing System for Efficient Gene Therapy in Vivo. Angew Chem Int Ed Engl 2023; 62:e202315093. [PMID: 37906116 DOI: 10.1002/anie.202315093] [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: 10/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
DNA nanostructures have played an important role in the development of novel drug delivery systems. Herein, we report a DNA origami-based CRISPR/Cas9 gene editing system for efficient gene therapy in vivo. In our design, a PAM-rich region precisely organized on the surface of DNA origami can easily recruit and load sgRNA/Cas9 complex by PAM-guided assembly and pre-designed DNA/RNA hybridization. After loading the sgRNA/Cas9 complex, the DNA origami can be further rolled up by the locking strands with a disulfide bond. With the incorporation of DNA aptamer and influenza hemagglutinin (HA) peptide, the cargo-loaded DNA origami can realize the targeted delivery and effective endosomal escape. After reduction by GSH, the opened DNA origami can release the sgRNA/Cas9 complex by RNase H cleavage to achieve a pronounced gene editing of a tumor-associated gene for gene therapy in vivo. This rationally developed DNA origami-based gene editing system presents a new avenue for the development of gene therapy.
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Affiliation(s)
- Wantao Tang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Ting Tong
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Hong Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Changping Yang
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yushuai Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Xu Z, Dong Y, Ma N, Zhu X, Zhang X, Yin H, Chen S, Zhu JJ, Tian Y, Min Q. Confinement in Dual-Chain-Locked DNA Origami Nanocages Programs Marker-Responsive Delivery of CRISPR/Cas9 Ribonucleoproteins. J Am Chem Soc 2023; 145:26557-26568. [PMID: 38039555 DOI: 10.1021/jacs.3c04074] [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: 12/03/2023]
Abstract
Delivery of CRISPR/Cas9 ribonucleoproteins (RNPs) offers a powerful tool for therapeutic genome editing. However, precise manipulation of CRISPR/Cas9 RNPs to switch the machinery on and off according to diverse disease microenvironments remains challenging. Here, we present dual-chain-locked DNA origami nanocages (DL-DONCs) that can confine Cas9 RNPs in the inner cavity for efficient cargo delivery and dual-marker-responsive genome editing in the specified pathological states. By engineering of ATP or miRNA-21-responsive dsDNAs as chain locks on the DONCs, the permeability of nanocages and accessibility of encapsulated Cas9 RNPs can be finely regulated. The resulting DL-DONCs enabled steric protection of bioactive Cas9 RNPs from premature release and deactivation during transportation while dismounting the dual chain locks in response to molecular triggers after internalization into tumor cells, facilitating the escape of Cas9 RNPs from the confinement for gene editing. Due to the dual-marker-dominated uncaging mechanism, the gene editing efficiency could be exclusively determined by the combined level of ATP and miRNA-21 in the target cellular environment. By targeting the tumor-associated PLK-1 gene, the DL-DONCs-enveloped Cas9 RNPs have demonstrated superior inhibitory effects on the proliferation of tumor cells in vitro and in vivo. The developed DL-DONCs provide a custom-made platform for the precise manipulation of Cas9 RNPs, which can be potentially applied to on-demand gene editing for classified therapy in response to arbitrary disease-associated biomolecules.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Yuxiang Dong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ningning Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Shiqing Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, People's Republic of China
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Torelli E, Shirt-Ediss B, Navarro SA, Manzano M, Vizzini P, Krasnogor N. Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing. Int J Mol Sci 2023; 24:ijms24108483. [PMID: 37239830 DOI: 10.3390/ijms24108483] [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: 02/14/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Binary light-up aptamers are intriguing and emerging tools with potential in different fields. Herein, we demonstrate the versatility of a split Broccoli aptamer system able to turn on the fluorescence signal only in the presence of a complementary sequence. First, an RNA three-way junction harbouring the split system is assembled in an E. coli-based cell-free TX-TL system where the folding of the functional aptamer is demonstrated. Then, the same strategy is introduced into a 'bio-orthogonal' hybrid RNA/DNA rectangle origami characterized by atomic force microscopy: the activation of the split system through the origami self-assembly is demonstrated. Finally, our system is successfully used to detect the femtomoles of a Campylobacter spp. DNA target sequence. Potential applications of our system include the real-time monitoring of the self-assembly of nucleic-acid-based devices in vivo and of the intracellular delivery of therapeutic nanostructures, as well as the in vitro and in vivo detection of different DNA/RNA targets.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Ben Shirt-Ediss
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Silvia A Navarro
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Marisa Manzano
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Priya Vizzini
- Dipartimento di Scienze AgroAlimentari, Ambientali e Animali, Università degli Studi di Udine, 33100 Udine, Italy
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), Centre for Synthetic Biology and Bioeconomy (CSBB), Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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Hao Y, Li M, Zhang Q, Shi J, Li J, Li Q, Fan C, Wang F. DNA Origami‐Based Single‐Molecule CRISPR Machines for Spatially Resolved Searching. Angew Chem Int Ed Engl 2022; 61:e202205460. [DOI: 10.1002/anie.202205460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Yaya Hao
- 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
| | - Mingqiang Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - Qian Zhang
- 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
| | - Jiye Shi
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
| | - Jiang Li
- Division of Physical Biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China
- The Interdisciplinary Research Center Shanghai Synchrotron Radiation Facility Zhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201210 China
| | - Qian Li
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
| | - 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
| | - Fei Wang
- School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine Shanghai Jiao Tong University Shanghai 200240 China
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8
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Hao Y, Li M, Zhang Q, Shi J, Li J, Li Q, Fan C, Wang F. DNA origami‐based single‐molecule CRISPR machines for spatially resolved searching. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yaya Hao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHRISTMAS ISLAND
| | - Mingqiang Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Qian Zhang
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Jiye Shi
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Division of Physical Biology CHINA
| | - Jiang Li
- Shanghai Institute of Applied Physics Chinese Academy of Sciences Division of Physical Biology CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Chunhai Fan
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Rd 800 200240 Shanghai CHINA
| | - Fei Wang
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
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Piskunen P, Latham R, West CE, Castronovo M, Linko V. Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience 2022; 25:104389. [PMID: 35633938 PMCID: PMC9130510 DOI: 10.1016/j.isci.2022.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective.
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10
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Liu L, Hong F, Liu H, Zhou X, Jiang S, Šulc P, Jiang JH, Yan H. A localized DNA finite-state machine with temporal resolution. SCIENCE ADVANCES 2022; 8:eabm9530. [PMID: 35333578 PMCID: PMC8956261 DOI: 10.1126/sciadv.abm9530] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/02/2022] [Indexed: 05/21/2023]
Abstract
The identity and timing of environmental stimulus play a pivotal role in living organisms in programming their signaling networks and developing specific phenotypes. The ability to unveil history-dependent signals will advance our understanding of temporally regulated biological processes. Here, we have developed a two-input, five-state DNA finite-state machine (FSM) to sense and record the temporally ordered inputs. The spatial organization of the processing units on DNA origami enables facile modulation of the energy landscape of DNA strand displacement reactions, allowing precise control of the reactions along predefined paths for different input orders. The use of spatial constraints brings about a simple, modular design for the FSM with a minimum set of orthogonal components and confers minimized leaky reactions and fast kinetics. The FSM demonstrates the capability of sensing the temporal orders of two microRNAs, highlighting its potential for temporally resolved biosensing and smart therapeutics.
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Affiliation(s)
- Lan Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Fan Hong
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Hao Liu
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xu Zhou
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
- Corresponding author. (H.Y.); (J.-H.J.)
| | - Hao Yan
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
- Corresponding author. (H.Y.); (J.-H.J.)
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11
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Zhang C, Yuan Y, Wu K, Wang Y, Zhu S, Shi J, Wang L, Li Q, Zuo X, Fan C, Chang C, Li J. Driving DNA Origami Assembly with a Terahertz Wave. NANO LETTERS 2022; 22:468-475. [PMID: 34968055 DOI: 10.1021/acs.nanolett.1c04369] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Terahertz (THz) waves show nontrivial interactions with living systems, but the underlying molecular mechanisms have yet to be explored. Here, we employ DNA origami as a model system to study the interactions between THz waves and DNA structures. We find that a 3-min THz illumination (35.2 THz) can drive the unwinding of DNA duplexes at ∼10 °C below their melting point. Computational study reveals that the THz wave can resonate with the vibration of DNA bases, provoking the hydrogen bond breaking. The cooperation of thermal and nonthermal effects allows the unfolding of undesired secondary structures and the THz illumination can generate diverse DNA origami assemblies with the yield (>80%) ∼ 4-fold higher than that by the contact heating at similar temperatures. We also demonstrate the in situ assembly of DNA origami in cell lysate. This method enables remotely controllable assembly of intact biomacromolecules, providing new insight into the bioeffects of THz waves.
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Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yifang Yuan
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics and Optoelectronic Engineering, Xidian University, Xi'an 700071, China
| | - Kaijie Wu
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yue Wang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shitai Zhu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China
- School of Physics, Peking University, Beijing 100084, China
- Key Laboratory of Physical Electronics and Devices of the Ministry of Education, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Jiang Li
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, 200240, Shanghai, China
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12
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Xu Z, Huang Y, Yin H, Zhu X, Tian Y, Min Q. DNA origami-based protein manipulation systems: From function regulation to biological application. Chembiochem 2021; 23:e202100597. [PMID: 34958167 DOI: 10.1002/cbic.202100597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Indexed: 11/07/2022]
Abstract
Proteins directly participate in tremendous physiological processes and mediate a variety of cellular functions. However, precise manipulation of proteins with predefined relative position and stoichiometry for understanding protein-protein interactions and guiding cellular behaviors are still challenging. With superior programmability of DNA molecules, DNA origami technology is able to construct arbitrary nanostructures that can accurately control the arrangement of proteins with various functionalities to solve these problems. Herein, starting from the classification of DNA origami nanostructures and the category of assembled proteins, we summarize the existing DNA origami-based protein manipulation systems (PMSs), review the advances on the regulation of their functions, and discuss their applications in cellular behavior modulation and disease therapy. Moreover, the limitations and potential directions of DNA origami-based PMSs are also presented, which may offer guidance for rational construction and ingenious application.
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Affiliation(s)
- Ziqi Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Yide Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Xurong Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering College of Engineering and Applied Sciences, Nanjing University, Nanjing, 210023, China
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13
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Wang DX, Wang J, Wang YX, Du YC, Huang Y, Tang AN, Cui YX, Kong DM. DNA nanostructure-based nucleic acid probes: construction and biological applications. Chem Sci 2021; 12:7602-7622. [PMID: 34168817 PMCID: PMC8188511 DOI: 10.1039/d1sc00587a] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022] Open
Abstract
In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.
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Affiliation(s)
- Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Ya-Xin Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yan Huang
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- College of Life Sciences, Nankai University Tianjin 300071 P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University Tianjin 300071 P. R. China
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University Tianjin 300071 P. R. China
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14
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Li F, Li J, Dong B, Wang F, Fan C, Zuo X. DNA nanotechnology-empowered nanoscopic imaging of biomolecules. Chem Soc Rev 2021; 50:5650-5667. [DOI: 10.1039/d0cs01281e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.
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Affiliation(s)
- Fan Li
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Jiang Li
- Bioimaging Center
- Shanghai Synchrotron Radiation Facility
- Zhangjiang Laboratory
- Shanghai Advanced Research Institute
- Chinese Academy of Sciences
| | - Baijun Dong
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules
- School of Chemistry and Chemical Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- China
| | - Chunhai Fan
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
| | - Xiaolei Zuo
- Institute of Molecular Medicine
- Department of Urology
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine
- Renji Hospital
- School of Medicine
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