51
|
Li J, Yan R, Shi S, Lin Y. Recent progress and application of the tetrahedral framework nucleic acid materials on drug delivery. Expert Opin Drug Deliv 2023; 20:1511-1530. [PMID: 37898874 DOI: 10.1080/17425247.2023.2276285] [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: 09/16/2023] [Accepted: 10/24/2023] [Indexed: 10/30/2023]
Abstract
INTRODUCTION The application of DNA framework nucleic acid materials in the biomedical field has witnessed continual expansion. Among them, tetrahedral framework nucleic acids (tFNAs) have gained significant traction as the foremost biological vectors due to their superior attributes of editability, low immunogenicity, biocompatibility, and biodegradability. tFNAs have demonstrated promising results in numerous in vitro and in vivo applications. AREAS COVERED This review summarizes the latest research on tFNAs in drug delivery, including a discussion of the advantages of tFNAs in regulating biological behaviors, and highlights the updated development and advantageous applications of tFNAs-based nanostructures from static design to dynamically responsive design. EXPERT OPINION tFNAs possess distinct biological regulatory attributes and can be taken up by cells without the requirement of transfection, differentiating them from other biological vectors. tFNAs can be easily physically/chemically modified and seamlessly incorporated with other functional systems. The static design of the tFNAs-based drug delivery system makes it versatile, reproducible, and predictable. Further use of the dynamic response mechanism of DNA to external stimuli makes tFNAs-based drug delivery more effective and specific, improving the uptake and utilization of the payload by the intended target. Dynamic targeting is poised to become the future primary approach for drug delivery.
Collapse
Affiliation(s)
- Jiajie Li
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, Department of Plastic Surgery and Cosmetic Dermatology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Ran Yan
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Sichuan Provincial Engineering Research Center of Oral Biomaterials, Chengdu, Sichuan, China
| |
Collapse
|
52
|
Li Z, Zhou J, Wang C, Liu R, Hu J, Lv Y. Isotope-encoded tetrahedral DNA for multiple SARS-CoV-2 variant diagnosis. Chem Sci 2023; 14:6654-6662. [PMID: 37350832 PMCID: PMC10283508 DOI: 10.1039/d3sc01960h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an unprecedented demand for accurate and cost-effective diagnostic assays to discriminate between different variants. Whilst many bioassays have been successfully demonstrated for SARS-CoV-2 detection, diagnosis of its variants remains challenging and mainly relies on time-consuming and costly sequencing techniques. Herein, we proposed a triplevalent tetrahedral DNA nanostructure (tTDN) with three overhang isotope probes capable of multiplex simultaneous analysis. HV69/70 del (alpha-specific), K417N (beta-specific) and T478K (delta-specific) and omicron with common mutations above of the SARS-CoV-2 S gene were detected selectively with the aid of the TDN scaffold and MNAzyme system, and a sensitive strategy enabling the screening of four kinds of variants of concern (VOC) was achieved.
Collapse
Affiliation(s)
- Ziyan Li
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Jing Zhou
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Chaoqun Wang
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University Chengdu 610064 Sichuan China
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta Edmonton T6G 2G3 Alberta Canada
| | - Yi Lv
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University Chengdu 610064 Sichuan China
| |
Collapse
|
53
|
Zhou Z, Lin N, Ouyang Y, Liu S, Zhang Y, Willner I. Cascaded, Feedback-Driven, and Spatially Localized Emergence of Constitutional Dynamic Networks Driven by Enzyme-Free Catalytic DNA Circuits. J Am Chem Soc 2023. [PMID: 37257165 DOI: 10.1021/jacs.3c02083] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The enzyme-free catalytic hairpin assembly (CHA) process is introduced as a functional reaction module for guided, high-throughput, emergence, and evolution of constitutional dynamic networks, CDNs, from a set of nucleic acids. The process is applied to assemble networks of variable complexities, functionalities, and spatial confinement, and the systems provide possible mechanistic pathways for the evolution of dynamic networks under prebiotic conditions. Subjecting a set of four or six structurally engineered hairpins to a promoter P1 leads to the CHA-guided emergence of a [2 × 2] CDN or the evolution of a [3 × 3] CDN, respectively. Reacting of a set of branched three-arm DNA-hairpin-functionalized junctions to the promoter strand activates the CHA-induced emergence of a three-dimensional (3D) CDN framework emulating native gene regulatory networks. In addition, activation of a two-layer CHA cascade circuit or a cross-catalytic CHA circuit and cascaded driving feedback-driven evolution of CDNs are demonstrated. Also, subjecting a four-hairpin-modified DNA tetrahedron nanostructure to an auxiliary promoter strand simulates the evolution of a dynamically equilibrated DNA tetrahedron-based CDN that undergoes secondary fueled dynamic reconfiguration. Finally, the effective permeation of DNA tetrahedron structures into cells is utilized to integrate the four-hairpin-functionalized tetrahedron reaction module into cells. The spatially localized miRNA-triggered CHA evolution and reconfiguration of CDNs allowed the logic-gated imaging of intracellular RNAs. Beyond the bioanalytical applications of the systems, the study introduces possible mechanistic pathways for the evolution of functional networks under prebiotic conditions.
Collapse
Affiliation(s)
- Zhixin Zhou
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - 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
| | - Songqin Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - 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
| |
Collapse
|
54
|
Freitag JS, Möser C, Belay R, Altattan B, Grasse N, Pothineni BK, Schnauß J, Smith DM. Integration of functional peptides into nucleic acid-based nanostructures. NANOSCALE 2023; 15:7608-7624. [PMID: 37042085 DOI: 10.1039/d2nr05429a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In many applications such as diagnostics and therapy development, small peptide fragments consisting of only a few amino acids are often attractive alternatives to bulky proteins. This is due to factors such as the ease of scalable chemical synthesis and numerous methods for their discovery. One drawback of using peptides is that their activity can often be negatively impacted by the lack of a rigid, 3D stabilizing structure provided by the rest of the protein. In many cases, this can be alleviated by different methods of rational templating onto nanomaterials, which provides additional possibilities to use concepts of multivalence or rational nano-engineering to enhance or even create new types of function or structure. In recent years, nanostructures made from the self-assembly of DNA strands have been used as scaffolds to create functional arrangements of peptides, often leading to greatly enhanced biological activity or new material properties. This review will give an overview of nano-templating approaches based on the combination of DNA nanotechnology and peptides. This will include both bioengineering strategies to control interactions with cells or other biological systems, as well as examples where the combination of DNA and peptides has been leveraged for the rational design of new functional materials.
Collapse
Affiliation(s)
- Jessica S Freitag
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Christin Möser
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Robel Belay
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Basma Altattan
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | - Nico Grasse
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
| | | | - Jörg Schnauß
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Unconventional Computing Lab, UWE, Bristol, BS16 1QY, UK
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
- Institute of Clinical Immunology, University of Leipzig Medical Faculty, 04103 Leipzig, Germany
| |
Collapse
|
55
|
Tian R, Shang Y, Wang Y, Jiang Q, Ding B. DNA Nanomaterials-Based Platforms for Cancer Immunotherapy. SMALL METHODS 2023; 7:e2201518. [PMID: 36651129 DOI: 10.1002/smtd.202201518] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Indexed: 05/17/2023]
Abstract
The past few decades have witnessed the evolving paradigm for cancer therapy from nonspecific cytotoxic agents to selective, mechanism-based therapeutics, especially immunotherapy. In particular, the integration of nanomaterials with immunotherapy is proven to improve the therapeutic outcome and minimize off-target toxicity in the treatment. As a novel nanomaterial, DNA-based self-assemblies featuring uniform geometries, feasible modifications, programmability, surface addressability, versatility, and intrinsic biocompatibility, are extensively exploited for innovative and effective cancer immunotherapy. In this review, the successful employment of DNA nanoplatforms for cancer immunotherapy, including the delivery of immunogenic cell death inducers, adjuvants and vaccines, immune checkpoint blockers as well as the application in immune cell engineering and adoptive cell therapy is summarized. The remaining challenges and future perspectives regarding the pharmacokinetics/pharmacodynamics, in vivo fate and immunogenicity of DNA materials, and the design of intelligent DNA nanomedicine for individualized cancer immunotherapy are also discussed.
Collapse
Affiliation(s)
- Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, Beijing, 100190, China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| |
Collapse
|
56
|
Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
Collapse
Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| |
Collapse
|
57
|
Liu B, Wang F, Chao J. Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing. SENSORS (BASEL, SWITZERLAND) 2023; 23:3313. [PMID: 36992023 PMCID: PMC10051322 DOI: 10.3390/s23063313] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.
Collapse
Affiliation(s)
- Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| |
Collapse
|
58
|
Wang W, Chen Y, Yin H, Lv J, Lin M, Wu ZS. Center backbone-rigidified DNA polygonal nanostructures and bottom face-templated polyhedral pyramids with structural stability in a complex biological medium. Acta Biomater 2023; 161:100-111. [PMID: 36905953 DOI: 10.1016/j.actbio.2023.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/15/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Due to the sequence programmability, good biocompatibility, versatile functionalities and vast sequence space, DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures in one, two and three dimensions that are capable of engineering of multiple functional nucleic acids into a useful tool to implement intended tasks in biological and medical field. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging mainly because of the molecular flexibility-based uncontrollability of size and shape. In this contribution, utilizing gel electrophoretic analysis and atomic force microscopy, we demonstrate the modeling assembly technique for the construction of wireframe DNA nanostructures that can be divided into two categories: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the construction of DNA polygons and polyhedral pyramids, respectively. The highest assembly efficiency (AE) is about 100%, while the lowest AE is not less than 50%. Moreover, when adding one edge for polygons or one side face for pyramids, we only need to add one oligonucleotide strand. Especially, the advanced polygons (e.g., pentagon and hexagon) of definite shape are for the first time constructed. Along this line, introduction of cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours even if the vulnerable nicks are not sealed. The proposed modeling assembly technique represents important progress toward the development of DNA nanotechnology and is expected to promote the application of DNA nanostructures in biological and biomedical fields. STATEMENT OF SIGNIFICANCE: DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging. In this contribution, we demonstrate the modeling technique for the construction of different wireframe DNA nanostructures: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the assembly of DNA polygons and polyhedral pyramids, respectively. Moreover, cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours, promoting the application of DNA nanostructures in biological and biomedical fields.
Collapse
Affiliation(s)
- Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Jingrui Lv
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China.
| |
Collapse
|
59
|
Mogheiseh M, Etemadi E, Hasanzadeh Ghasemi R. Design, molecular dynamics simulation, and investigation of the mechanical behavior of DNA origami nanotubes with auxetic and honeycomb structures. J Biomol Struct Dyn 2023; 41:14822-14831. [PMID: 36889931 DOI: 10.1080/07391102.2023.2186719] [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: 01/04/2023] [Accepted: 02/22/2023] [Indexed: 03/10/2023]
Abstract
Numerous applications of DNA origami nanotubes for load-bearing purposes necessitate the improvement of properties and mechanical behavior of these types of structures, as well as the use of innovative structures such as metamaterials. To this end, the present study aims to investigate the design, molecular dynamics (MD) simulation, and mechanical behavior of DNA origami nanotube structures consisting of honeycomb and re-entrant auxetic cross-sections. The results revealed both structures kept their structural stability. In addition, DNA origami based-nanotube with auxetic cross-section exhibits negative Poisson's ratio (NPR) under tensile loading. Furthermore, MD simulation results demonstrated that the values of stiffness, specific stiffness, energy absorption, and specific energy absorption in the structure with an auxetic cross-section are higher than that of a honeycomb cross-section, similar to their behavior in macro-scale structures. The finding of this study is to propose re-entrant auxetic structure as the next generation of DNA origami nanotubes. In addition, it can be utilized to aid scientists with the design and fabrication of novel auxetic DNA origami structures.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Maryam Mogheiseh
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
| | - Ehsan Etemadi
- Department of Mechanical Engineering, Hakim Sabzevari University, Sabzevar, Iran
- School of Fashion & Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | | |
Collapse
|
60
|
Vilcapoma J, Patel A, Chandrasekaran AR, Halvorsen K. The role of size in biostability of DNA tetrahedra. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531312. [PMID: 36945546 PMCID: PMC10028801 DOI: 10.1101/2023.03.06.531312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The potential for using DNA nanostructures for drug delivery applications requires understanding and ideally tuning their biostability. Here we investigate how biological degradation varies with size of a DNA nanostructure. We designed DNA tetrahedra of three edge lengths ranging from 13 to 20 bp and analyzed nuclease resistance for two nucleases and biostability in fetal bovine serum. We found that DNase I had similar digestion rates across sizes but appeared to incompletely digest the smallest tetrahedron, while T5 exonuclease was notably slower to digest the largest tetrahedron. In fetal bovine serum, the 20 bp tetrahedron was degraded ~four times faster than the 13 bp. These results show that DNA nanostructure size can influence nuclease degradation, but suggest a complex relationship that is nuclease specific.
Collapse
|
61
|
Wu Y, Feng J, Hu G, Zhang E, Yu HH. Colorimetric Sensors for Chemical and Biological Sensing Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23052749. [PMID: 36904948 PMCID: PMC10007638 DOI: 10.3390/s23052749] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 06/12/2023]
Abstract
Colorimetric sensors have been widely used to detect numerous analytes due to their cost-effectiveness, high sensitivity and specificity, and clear visibility, even with the naked eye. In recent years, the emergence of advanced nanomaterials has greatly improved the development of colorimetric sensors. This review focuses on the recent (from the years 2015 to 2022) advances in the design, fabrication, and applications of colorimetric sensors. First, the classification and sensing mechanisms of colorimetric sensors are briefly described, and the design of colorimetric sensors based on several typical nanomaterials, including graphene and its derivatives, metal and metal oxide nanoparticles, DNA nanomaterials, quantum dots, and some other materials are discussed. Then the applications, especially for the detection of metallic and non-metallic ions, proteins, small molecules, gas, virus and bacteria, and DNA/RNA are summarized. Finally, the remaining challenges and future trends in the development of colorimetric sensors are also discussed.
Collapse
Affiliation(s)
- Yu Wu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Jing Feng
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - Guang Hu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, China
| | - En Zhang
- Chongqing Institute for Food and Drug Control, Chongqing 401121, China
| | - Huan-Huan Yu
- Chongqing Institute for Food and Drug Control, Chongqing 401121, China
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
62
|
Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
Collapse
Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
63
|
Huang J, Gambietz S, Saccà B. Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202253. [PMID: 35775957 DOI: 10.1002/smll.202202253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.
Collapse
Affiliation(s)
- Jing Huang
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Sabrina Gambietz
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| | - Barbara Saccà
- ZMB, Faculty of Biology, University Duisburg-Essen, 45141, Essen, Germany
| |
Collapse
|
64
|
Cheng L, Yang F, Zhao Y, Liu Z, Yao X, Zhang J. Tetrahedron supported CRISPR/Cas13a cleavage for electrochemical detection of circular RNA in bladder cancer. Biosens Bioelectron 2023; 222:114982. [PMID: 36493719 DOI: 10.1016/j.bios.2022.114982] [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: 10/10/2022] [Revised: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
As a diagnostic biomarker, the detection of circular RNA (circRNA) is vital for the early screening of bladder cancer. Usually, the low abundance of circRNA in clinic samples results in the necessarily complicated extraction before detection. In this work, a tetrahedron supported CRISPR/Cas13a cleavage has been explored for direct electrochemical detection of circRNA in urine from bladder cancer. CRISPR/Cas13a system has been reasonably designed to recognize the characteristic back-splice junction site of circRNA. The activated CRISPR/Cas13a by circRNA can cleave uracil bases composed of DNA tetrahedron immobilized on the surface of gold electrode, resulting in the breakage of DNA tetrahedron and the release of electrochemical active molecule methylene blue. By virtue of highly catalytic efficiency of CRISPR/Cas13a and rigid structure of tetrahedron, the developed electrochemical biosensor can directly detect circRNA in 25 μL urine sample with the lowest detection limit of 0.089 fM and linear detection range from 10 fM to 50 nM in less than 10 min, so as to avoid complicated extraction process and benefit for on-site detection.
Collapse
Affiliation(s)
- Liangfen Cheng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Fuhan Yang
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, PR China
| | - Yining Zhao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Ziye Liu
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200092, PR China.
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai, 200444, PR China.
| |
Collapse
|
65
|
Tandon A, Kim B, Mariyappan K, Kokkiligadda S, Jeon S, Jeong JH, Park SH. Multidimensional Honeycomb-like DNA Nanostructures Made of C-Motifs. ACS Biomater Sci Eng 2023; 9:608-616. [PMID: 36595627 DOI: 10.1021/acsbiomaterials.2c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Thanks to its remarkable properties of self-assembly and molecular recognition, DNA can be used in the construction of various dimensional nanostructures to serve as templates for decorating nanomaterials with nanometer-scale precision. Accordingly, this study discusses a design strategy for fabricating such multidimensional DNA nanostructures made of simple C-motifs. One-dimensional (1D) honeycomb-like tubes (1HTs) and two-dimensional (2D) honeycomb-like lattices (2HLs) were constructed using a C-motif with an arm length of 14 nucleotides (nt) at an angle of 240° along the counterclockwise direction. We designed and fabricated four different types of 1HTs and three different 2HLs. The study used atomic force microscopy to characterize the distinct topologies of the 1D and 2D DNA nanostructures (i.e., 1HTs and 2HLs, respectively). The width deviation of the 1HTs and height suppression percentage of the 2HLs were calculated and discussed. Our study can be provided to construct various dimensional DNA nanostructures easily with high efficiency.
Collapse
Affiliation(s)
- Anshula Tandon
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Byeonghoon Kim
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea.,Scale Up Partners, LLC., Seoul 03100, Korea
| | - Karthikeyan Mariyappan
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Samanth Kokkiligadda
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| | - Sohee Jeon
- Nanomechanical Systems Research Division, Korea Institute of Machinery and Materials (KIMM), Daejeon 34103, Korea
| | - Jun-Ho Jeong
- Nanomechanical Systems Research Division, Korea Institute of Machinery and Materials (KIMM), Daejeon 34103, Korea.,Department of Nanomechatronics, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Sung Ha Park
- Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea
| |
Collapse
|
66
|
Zhang P, Zhuo Y, Chai YQ, Yuan R. Structural DNA tetrahedra and its electrochemical-related surface sensing. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
67
|
Hu X, Huang Y, Zheng H, Liu J, Liu M, Xie M, Fan C, Chen N. Dendrimer-like Hierarchical Framework Nucleic Acid for Real-Time Imaging of Intracellular Trafficking. ACS APPLIED MATERIALS & INTERFACES 2023; 15:3839-3850. [PMID: 36637993 DOI: 10.1021/acsami.2c20504] [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: 06/17/2023]
Abstract
Framework nucleic acids (FNAs) represent a new type of DNA-based nanomaterials and possess great potentials in biosensing, bioimaging, and molecular delivery. Hierarchical DNA nanostructures that consist of multiple FNA monomers increase the capacity for drug delivery and multifunctional modification. However, there are relatively few studies devoted to the behavior and regulation of hierarchical FNAs in living cells, impeding their further applications. Herein, we constructed a dendritic nanostructure with five tetrahedral DNA nanocages and characterized the real-time internalization, inter-organelle trafficking, and exocytosis in living mammalian cells. In comparison to FNA monomers, FNA dendrimers exhibit increased endocytosis and prolonged cellular retention. Single-particle tracking on hundreds of FNA dendrimers exhibits no interference on the mobility or kinetics of subcellular organelles, implying that FNAs as well as their higher-order derivatives are ideal intracellular imaging probes and nanocarriers. Our study validates the suitability and superiority of hierarchical DNA nanostructures as high-valency scaffolds for biomedical applications.
Collapse
Affiliation(s)
- Xingjie Hu
- College of Chemistry and Materials Science, The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai200234, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai200025, China
| | - Yan Huang
- College of Chemistry and Materials Science, The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai200234, China
| | - Hong Zheng
- College of Chemistry and Materials Science, The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai200234, China
| | - Jiahui Liu
- College of Chemistry and Materials Science, The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai200234, China
| | - Mengmeng Liu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai200241, China
| | - Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing210023, 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, Shanghai200240, China
| | - Nan Chen
- College of Chemistry and Materials Science, The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, and Shanghai Frontiers Science Center of Biomimetic Catalysis, Shanghai Normal University, Shanghai200234, China
| |
Collapse
|
68
|
Singh R, Yadav P, Naveena A H, Bhatia D. Cationic lipid modification of DNA tetrahedral nanocages enhances their cellular uptake. NANOSCALE 2023; 15:1099-1108. [PMID: 36562521 DOI: 10.1039/d2nr05749b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Self-assembled DNA nanocages are among the most promising candidates for bioimaging and payload delivery into cells. DNA nanocages have great potential to efficiently address drug resistance and nucleic acid delivery problems due to precise control of their shape and size, and excellent biocompatibility. Although DNA nanostructures demonstrate some cellular uptake, because they bear a highly negative charge, the uptake of tetrahedral nanostructures is hindered by electrostatic repulsion. In this study, we describe a method to enhance the cellular uptake of DNA nanostructures using a binary system containing DNA and a positively charged head group with a hydrophobic lipid chain containing lipids for cellular internalization. Here we represent the functionalization of a model cage, DNA tetrahedron (TD) with a cationic lipid, N-[1-(2,3-dioleyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA). Atomic force microscopy (AFM) and other standard characterization techniques were used to explore the co-assembly of the DNA tetrahedron and DOTMA. We revealed a simple confocal microscopy-based approach to show the enhancement in the cellular uptake of DNA nanocages. This new method will find multiple applications in delivery applications such as gene transfection, drug delivery and targeted bioimaging.
Collapse
Affiliation(s)
- Ramesh Singh
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Pankaj Yadav
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Hema Naveena A
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.
| |
Collapse
|
69
|
Zhang P, Ouyang Y, Zhuo Y, Chai Y, Yuan R. Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging. Anal Chem 2023; 95:407-419. [PMID: 36625113 DOI: 10.1021/acs.analchem.2c04540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu Ouyang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China.,Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| |
Collapse
|
70
|
Wang W, Xiao D, Lin L, Gao X, Peng L, Chen J, Xiao K, Zhu S, Chen J, Zhang F, Xiong Y, Chen H, Liao B, Zhou L, Lin Y. Antifibrotic Effects of Tetrahedral Framework Nucleic Acids by Inhibiting Macrophage Polarization and Macrophage-Myofibroblast Transition in Bladder Remodeling. Adv Healthc Mater 2023; 12:e2203076. [PMID: 36603196 DOI: 10.1002/adhm.202203076] [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: 11/27/2022] [Revised: 12/20/2022] [Indexed: 01/07/2023]
Abstract
Bladder outlet obstruction (BOO) is a prevalent condition arising from urethral stricture, posterior urethral valves, and benign prostatic hyperplasia. Long-term obstruction can lead to bladder remodeling, which is characterized by inflammatory cell infiltration, detrusor hypertrophy, and fibrosis. Until now, there are no efficacious therapeutic options for BOO-induced remodeling. Tetrahedral framework nucleic acids (tFNAs) are a type of novel 3D DNA nanomaterials that possess excellent antifibrotic effects. Here, to determine the treatment effects of tFNAs on BOO-induced remodeling is aimed. Four single-strand DNAs are self-assembled to form tetrahedral framework DNA nanostructures, and the antifibrotic effects of tFNAs are investigated in an in vivo BOO animal model and an in vitro transforming growth factor beta1 (TGF-β1)-induced fibrosis model. The results demonstrated that tFNAs could ameliorate BOO-induced bladder fibrosis and dysfunction by inhibiting M2 macrophage polarization and the macrophage-myofibroblast transition (MMT) process. Furthermore, tFNAs regulate M2 polarization and the MMT process by deactivating the signal transducer and activator of transcription (Stat) and TGF-β1/small mothers against decapentaplegic (Smad) pathways, respectively. This is the first study to reveal that tFNAs might be a promising nanomaterial for the treatment of BOO-induced remodeling.
Collapse
Affiliation(s)
- Wei Wang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Dexuan Xiao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Lede Lin
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaoshuai Gao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Liao Peng
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Jiawei Chen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Kaiwen Xiao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Shiyu Zhu
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Jixiang Chen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Fuxun Zhang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Yang Xiong
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Huiling Chen
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Banghua Liao
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Liang Zhou
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, No. 37 Guo Xue Xiang, Chengdu, Sichuan, 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| |
Collapse
|
71
|
Zhu L, Luo J, Ren K. Nucleic acid-based artificial nanocarriers for gene therapy. J Mater Chem B 2023; 11:261-279. [PMID: 36524395 DOI: 10.1039/d2tb01179d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.
Collapse
Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| |
Collapse
|
72
|
Haydell M, Ma Y. DNA Origami: Recent Progress and Applications. Methods Mol Biol 2023; 2639:3-19. [PMID: 37166708 DOI: 10.1007/978-1-0716-3028-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This chapter explores the basic concept of DNA origami and its various types. By showing the progress made in structural DNA nanotechnology during the last 15 years, the chapter draws attention to the capability of DNA origami to construct complex structures in both 2D and 3D level. As well as looking at a few examples of dynamic DNA nanostructures, the chapter also explores the possible applications of DNA origami in different fields, such as biological computing, nanorobotics, and DNA walkers.
Collapse
Affiliation(s)
- Michael Haydell
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yinzhou Ma
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing, China.
- Beijing Innovation Center for Engineering Science and Advanced Technology, Peking University, Beijing, China.
| |
Collapse
|
73
|
Yang C, Wu X, Liu J, Ding B. Stimuli-responsive nucleic acid nanostructures for efficient drug delivery. NANOSCALE 2022; 14:17862-17870. [PMID: 36458678 DOI: 10.1039/d2nr05316k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Based on complementary base pairing, nucleic acid molecules have acted as engineerable building blocks to prepare versatile nanostructures with unique shapes and sizes. Benefiting from excellent programmability and biocompatibility, rationally designed nucleic acid nanostructures have been widely employed in biomedical applications. With the development of the chemical biology of nucleic acids, various stimuli-responsive nucleic acid nanostructures have been constructed by tailored chemical modification with multifunctional components. In this minireview, we summarize the representative and latest research about the employment of stimuli-responsive nucleic acid nanostructures for drug delivery in response to endogenous and exogenous stimuli (redox gradient, pH, nuclease, biomacromolecule, and light). We also discuss the broad prospects and remaining challenges of nucleic acid nanotechnology in biomedical applications.
Collapse
Affiliation(s)
- Changping Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, 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, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Materials Science and Engineering, Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
74
|
Mao X, Liu M, Li Q, Fan C, Zuo X. DNA-Based Molecular Machines. JACS AU 2022; 2:2381-2399. [PMID: 36465542 PMCID: PMC9709946 DOI: 10.1021/jacsau.2c00292] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 05/17/2023]
Abstract
Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.
Collapse
Affiliation(s)
- Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mengmeng Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, 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
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- 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
| |
Collapse
|
75
|
Zhang Y, Xu H, Jiang L, Liu Z, Lian C, Ding X, Wan C, Liu N, Wang Y, Yu Z, Zhu L, Yin F, Li Z. Sulfonium-Driven Neoantigen-Released DNA Nanodevice as a Precise Vaccine for Tumor Immunotherapy and Prevention. ACS NANO 2022; 16:19509-19522. [PMID: 36318615 DOI: 10.1021/acsnano.2c09708] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Peptide-based neoantigen vaccines hold tremendous potential for personalized tumor immunotherapy. However, effective delivery and controllable release of antigen peptides remain major challenges in stimulating robust and sustained immune responses. Programmable DNA nanodevices provide accurate fixed positions for antigens, which are convenient for the calculation of clinical dosage, and hold great potential as precise carriers. Here, a peptide-nucleic acid conjugate was prepared, which was driven by a propargyl sulfonium-based efficient and reversible bio-orthogonal reaction under weakly alkaline conditions, and folded into regular DNA nanodevice vaccines. The well-defined nanoplatform not only exhibits outstanding stability in serum, satisfactory safety, and effective internalization by antigen-presenting cells (RAW264.7 and BMDCs) but also obviously enhances cytokine (TNF-α, IL-6, and IL-12) secretion for further immune response. In vivo, the nanovaccine cooperating with OVA model antigens and CpG adjuvants stimulated an antigen-specific CD8+T cell response, significantly preventing the lung metastases of melanoma. In the B16-OVA tumor-bearing model, the growth inhibition rate of melanoma reached up to 50%. Similarly, the DNA nanodevice with neoantigen induced up to a maximum degree of complete MC-38 tumor regression in 80% of mice, possibly owing to antigen peptide reversible release driven by sulfonium and further cross-presentation. In brief, this study demonstrates that DNA nanodevices with sulfonium centers can provide a precise, biocompatible, and effective co-delivery vaccine platform for tumor immunotherapy and prevention.
Collapse
Affiliation(s)
- Yaping Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Hongkun Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Leying Jiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Zhaodi Liu
- Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei 230022, P.R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
| | - Xiaofeng Ding
- Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei 230022, P.R. China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Na Liu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Yuena Wang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| | - Zhiqiang Yu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, P.R. China
| | - Lizhi Zhu
- Department of Pharmacy, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), The First Affiliated Hospital of Shenzhen University, Shenzhen 518055, P.R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518055, P.R. China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, P.R. China
| |
Collapse
|
76
|
Majikes JM, Liddle JA. Synthesizing the biochemical and semiconductor worlds: the future of nucleic acid nanotechnology. NANOSCALE 2022; 14:15586-15595. [PMID: 36268635 PMCID: PMC10949957 DOI: 10.1039/d2nr04040a] [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] [Indexed: 06/16/2023]
Abstract
Since its inception nearly 40 years ago [Kallenbach, et al., Nature, 1983, 305, 829; N. C. Seeman, J. Theoretical Biology, 1982, 99, 237], Nucleic Acid Nanotechnology (NAN) has matured and is beginning to find commercial applications. For the last 20 years, it has been suggested that NAN might be an effective replacement for parts of the semiconductor lithography or protein engineering workflows. However, in that time, these incumbent technologies have made significant advances, and our understanding of NAN's strengths and weaknesses has progressed, suggesting that the greatest opportunities in fact lie elsewhere. Given the commitment of resources necessary to bring new technologies to the market and the desire to use those resources as wisely as possible, we conduct a critical examination of where NAN may benefit from, and provide benefit to, adjacent technologies and compete least with market incumbents. While the accuracy of our conclusions may be limited by our ability to extrapolate from the current state of NAN to its future commercial success, we conclude that the next promising direction is to create a bridge between biology and semiconductor technology. We also hope to stimulate a robust conversation around this technology's capabilities with the goal of building consensus on those research and development efforts that would advance NAN to the greatest effect in real-world applications.
Collapse
Affiliation(s)
- Jacob M Majikes
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| | - J Alexander Liddle
- Physical Measurement Laboratory, National Institute Standards and Technology, 100 Bureau drive, Gaithersburg, MD, 20878, USA.
| |
Collapse
|
77
|
Li R, Zheng M, Madhvacharyula AS, Du Y, Mao C, Choi JH. Mechanical deformation behaviors and structural properties of ligated DNA crystals. Biophys J 2022; 121:4078-4090. [PMID: 36181269 PMCID: PMC9675025 DOI: 10.1016/j.bpj.2022.09.036] [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: 07/28/2022] [Revised: 09/21/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022] Open
Abstract
DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.
Collapse
Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | | | - Yancheng Du
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana.
| |
Collapse
|
78
|
Rhouati A, Rhouati A, Marty JL. A Review on Aptamers Selection and Application in Heart Diseases Diagnosis. Curr Top Med Chem 2022; 22:2463-2473. [PMID: 36045527 DOI: 10.2174/1568026622666220831114322] [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: 10/14/2021] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 01/20/2023]
Abstract
Biomarkers detection and quantification in biological fluids play a key role in the screening, diagnosing and treating several diseases. Recently, a large number of aptamers have been selected and applied for the sensing of different biomarkers. Combined with different transducers, aptamers provide simple and rapid tools that allow highly sensitive and selective detection. Cardiology requires an accurate assessment of cardiac biomarkers for a complete diagnosis of cardiovascular diseases. The analysis is generally performed by immunoassays using antibodies as biorecognition elements. This review paper focuses on using aptamers as a promising alternative for antibodies in cardiac biomarkers biosensing. First, the different aptamers specific to the most important cardiac biomarkers are Troponin I, the peptide of B-type natriuretic peptide and myoglobin. Then, in the second part, we overview the electrochemical aptasensors principle and characteristics reported in the literature in the last five years.
Collapse
Affiliation(s)
- Amina Rhouati
- Bioengineering Laboratory, Higher National School of Biotechnology, Constantine 25100-Algeria
| | - Adel Rhouati
- Cardiology Department, Ibn Badis University Hospital, University of Constantine 3, Constantine, Algeria
| | | |
Collapse
|
79
|
Muhammad Sajeer P, Simran, Nukala P, Manoj M. Varma. TEM based applications in solid state nanopores: From fabrication to liquid in-situ bio-imaging. Micron 2022; 162:103347. [DOI: 10.1016/j.micron.2022.103347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 10/31/2022]
|
80
|
Lin Y, Li Q, Wang L, Guo Q, Liu S, Zhu S, Sun Y, Fan Y, Sun Y, Li H, Tian X, Luo D, Shi S. Advances in regenerative medicine applications of tetrahedral framework nucleic acid-based nanomaterials: an expert consensus recommendation. Int J Oral Sci 2022; 14:51. [PMID: 36316311 PMCID: PMC9622686 DOI: 10.1038/s41368-022-00199-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/09/2022] [Accepted: 08/19/2022] [Indexed: 01/18/2023] Open
Abstract
With the emergence of DNA nanotechnology in the 1980s, self-assembled DNA nanostructures have attracted considerable attention worldwide due to their inherent biocompatibility, unsurpassed programmability, and versatile functions. Especially promising nanostructures are tetrahedral framework nucleic acids (tFNAs), first proposed by Turberfield with the use of a one-step annealing approach. Benefiting from their various merits, such as simple synthesis, high reproducibility, structural stability, cellular internalization, tissue permeability, and editable functionality, tFNAs have been widely applied in the biomedical field as three-dimensional DNA nanomaterials. Surprisingly, tFNAs exhibit positive effects on cellular biological behaviors and tissue regeneration, which may be used to treat inflammatory and degenerative diseases. According to their intended application and carrying capacity, tFNAs could carry functional nucleic acids or therapeutic molecules through extended sequences, sticky-end hybridization, intercalation, and encapsulation based on the Watson and Crick principle. Additionally, dynamic tFNAs also have potential applications in controlled and targeted therapies. This review summarized the latest progress in pure/modified/dynamic tFNAs and demonstrated their regenerative medicine applications. These applications include promoting the regeneration of the bone, cartilage, nerve, skin, vasculature, or muscle and treating diseases such as bone defects, neurological disorders, joint-related inflammatory diseases, periodontitis, and immune diseases.
Collapse
Affiliation(s)
- Yunfeng Lin
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qian Li
- grid.16821.3c0000 0004 0368 8293School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lihua Wang
- grid.458506.a0000 0004 0497 0637The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Zhangjiang Laboratory, Shanghai, China
| | - Quanyi Guo
- grid.488137.10000 0001 2267 2324Institute of Orthopedics, Chinese PLA General Hospital, Beijing Key Laboratory of Regenerative Medicine in Orthopedics, Key Laboratory of Musculoskeletal Trauma & War Injuries PLA, Beijing, China
| | - Shuyun Liu
- grid.488137.10000 0001 2267 2324Institute of Orthopedics, Chinese PLA General Hospital, Beijing Key Laboratory of Regenerative Medicine in Orthopedics, Key Laboratory of Musculoskeletal Trauma & War Injuries PLA, Beijing, China
| | - Shihui Zhu
- grid.73113.370000 0004 0369 1660Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yu Sun
- grid.73113.370000 0004 0369 1660Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
| | - Yujiang Fan
- grid.13291.380000 0001 0807 1581National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, China
| | - Yong Sun
- grid.13291.380000 0001 0807 1581College of Biomedical Engineering, Sichuan University, Chengdu, China
| | - Haihang Li
- Jiangsu Trautec Medical Technology Company Limited, Changzhou, China
| | - Xudong Tian
- Jiangsu Trautec Medical Technology Company Limited, Changzhou, China
| | - Delun Luo
- Chengdu Jingrunze Gene Technology Company Limited, Chengdu, China
| | - Sirong Shi
- grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
81
|
Kloes G, Bennett TJD, Chapet-Batlle A, Behjatian A, Turberfield AJ, Krishnan M. Far-Field Electrostatic Signatures of Macromolecular 3D Conformation. NANO LETTERS 2022; 22:7834-7840. [PMID: 36125326 PMCID: PMC9562458 DOI: 10.1021/acs.nanolett.2c02485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In solution as in vacuum, the electrostatic field distribution in the vicinity of a charged object carries information on its three-dimensional geometry. We report on an experimental study exploring the effect of molecular shape on long-range electrostatic interactions in solution. Working with DNA nanostructures carrying approximately equal amounts of total charge but each in a different three-dimensional conformation, we demonstrate that the geometry of the distribution of charge in a molecule has substantial impact on its electrical interactions. For instance, a tetrahedral structure, which is the most compact distribution of charge we tested, can create a far-field effect that is effectively identical to that of a rod-shaped molecule carrying half the amount of total structural charge. Our experiments demonstrate that escape-time electrometry (ETe) furnishes a rapid and facile method to screen and identify 3D conformations of charged biomolecules or molecular complexes in solution.
Collapse
Affiliation(s)
- Gunnar Kloes
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Timothy J. D. Bennett
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Alma Chapet-Batlle
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Ali Behjatian
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
| | - Madhavi Krishnan
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
- The Kavli
Institute for Nanoscience Discovery, Sherrington Road, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
82
|
Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2022; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
Collapse
Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
- Corresponding authors.
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Corresponding authors.
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Corresponding authors.
| |
Collapse
|
83
|
Kumar A, Ahmad A, Ansari MM, Gowd V, Rashid S, Chaudhary AA, Rudayni HA, Alsalamah SA, Khan R. Functionalized-DNA nanostructures as potential targeted drug delivery systems for cancer therapy. Semin Cancer Biol 2022; 86:54-68. [PMID: 36087856 DOI: 10.1016/j.semcancer.2022.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 01/14/2023]
Abstract
Seeman's pioneer idea has led to the foundation of DNA nanostructures, resulting in a remarkable advancement in DNA nanotechnology. Over the last few decades, remarkable advances in drug delivery techniques have resulted in the self-assembly of DNA for encapsulating candidate drug molecules. The nuclear targeting capability of DNA nanostructures is lies within their high spatial addressability and tremendous potential for active targeting. However, effective programming and assembling those DNA molecules remains a challenge, making the path to DNA nanostructures for real-world applications difficult. Because of their small size, most nanostructures are self-capable of infiltrating into the tumor cellular environment. Furthermore, to enable controlled and site-specific delivery of encapsulated drug molecules, DNA nanostructures are functionalized with special moieties that allow them to bind specific targets and release cargo only at targeted sites rather than non-specific sites, resulting in the prevention/limitation of cellular toxicity. In light of this, the current review seeks to shed light on the versatility of the DNA molecule as a targeting and encapsulating moiety for active drugs in order to achieve controlled and specific drug release with spatial and temporal precision. Furthermore, this review focused on the challenges associated with the construction of DNA nanostructures as well as the most recent advances in the functionalization of DNA nanostructures using various materials for controlled and targeted delivery of medications for cancer therapy.
Collapse
Affiliation(s)
- Ajay Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Anas Ahmad
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Md Meraj Ansari
- Centre for Pharmaceutical Nanotechnology, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, S.A.S Nagar, Sector 67, Mohali, Punjab 160062, India
| | - Vemana Gowd
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Hassan Ahmed Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Sulaiman A Alsalamah
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh, 11623, Saudi Arabia
| | - Rehan Khan
- Chemical Biology Unit, Institute of Nano Science and Technology, Knowledge City, Sector-81, Mohali 140306, Punjab, India.
| |
Collapse
|
84
|
Xu Y, Wang C, Liu G, Zhao X, Qian Q, Li S, Mi X. Tetrahedral DNA framework based CRISPR electrochemical biosensor for amplification-free miRNA detection. Biosens Bioelectron 2022; 217:114671. [PMID: 36122469 DOI: 10.1016/j.bios.2022.114671] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/18/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
microRNA (miRNA) is a kind of small non-coding RNA that has been regarded as potential biomarkers for cancers. Sensitive and specific detection of miRNA at low expression levels is highly desirable but remains challenging, especially for amplification-free and portable point of care (POC) diagnostics. The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a has been recently discovered and used in the field of RNA detection. Nonetheless, most CRISPR/Cas13a-based methods were burdened with expensive equipment, time-consuming procedures, and complicated operations which were not suitable for POC analysis. In this work, we constructed a three-dimensional tetrahedral DNA framework based CRISPR-electrochemical biosensor (CRISPR-E). By combining tetrahedral DNA framework, CRISPR, and electrochemical biosensor, the process of activation, cleavage of Cas13a, and signal readout were all finished on the chip, and a simple, amplification-free and sensitive detection of miRNA-19b was realized. Under the optimal experimental conditions, a linear range from 10 pM to 104 pM with detection limit of 10 pM for miRNA-19b in buffer solution was achieved. Selectivity analysis indicated that our CRISPR-E had good distinguishing ability between miRNA-19b and miRNA-197. The results of miRNA-19b detection in mimic serum samples were consistent with that of the buffer solution. This all-on-chip strategy of our CRISPR-E is very suitable for POC testing.
Collapse
Affiliation(s)
- Yi Xu
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Chenguang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for State Market Regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai, 201203, China
| | - Xiaoshuang Zhao
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Qiuling Qian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuainai Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianqiang Mi
- State Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; CAS Center for Excellence in Superconducting Electronics (CENSE), Shanghai, 200050, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| |
Collapse
|
85
|
Patel A, Valsangkar V, Halvorsen K, Chandrasekaran AR. Purification of Self-Assembled DNA Tetrahedra Using Gel Electrophoresis. Curr Protoc 2022; 2:e560. [PMID: 36111849 PMCID: PMC9494925 DOI: 10.1002/cpz1.560] [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] [Indexed: 06/15/2023]
Abstract
DNA nanostructures have found applications in a variety of fields such as biosensing, drug delivery, cellular imaging, and computation. Several of these applications require purification of the DNA nanostructures once they are assembled. Gel electrophoresis-based purification of DNA nanostructures is one of the methods used for this purpose. Here, we describe a step-by-step protocol for a gel-based method to purify self-assembled DNA tetrahedra. With further optimization, this method could also be adapted for other DNA nanostructures. © 2022 Wiley Periodicals LLC. Basic Protocol: Purification of self-assembled DNA tetrahedra.
Collapse
Affiliation(s)
- Akul Patel
- The RNA Institute, University at Albany, State University of New York, New York
| | - Vibhav Valsangkar
- The RNA Institute, University at Albany, State University of New York, New York
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, New York
| | | |
Collapse
|
86
|
Ouyang Y, Zhang P, Willner I. Dynamic Catalysis Guided by Nucleic Acid Networks and DNA Nanostructures. Bioconjug Chem 2022; 34:51-69. [PMID: 35973134 PMCID: PMC9853509 DOI: 10.1021/acs.bioconjchem.2c00233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nucleic acid networks conjugated to native enzymes and supramolecular DNA nanostructures modified with enzymes or DNAzymes act as functional reaction modules for guiding dynamic catalytic transformations. These systems are exemplified with the assembly of constitutional dynamic networks (CDNs) composed of nucleic acid-functionalized enzymes, as constituents, undergoing triggered structural reconfiguration, leading to dynamically switched biocatalytic cascades. By coupling two nucleic acid/enzyme networks, the intercommunicated feedback-driven dynamic biocatalytic operation of the system is demonstrated. In addition, the tailoring of a nucleic acid/enzyme reaction network driving a dissipative, transient, biocatalytic cascade is introduced as a model system for out-of-equilibrium dynamically modulated biocatalytic transformation in nature. Also, supramolecular nucleic acid machines or DNA nanostructures, modified with DNAzyme or enzyme constituents, act as functional reaction modules driving temporal dynamic catalysis. The design of dynamic supramolecular machines is exemplified with the introduction of an interlocked two-ring catenane device that is dynamically reversibly switched between two states operating two different DNAzymes, and with the tailoring of a DNA-tweezers device functionalized with enzyme/DNAzyme constituents that guides the dynamic ON/OFF operation of a biocatalytic cascade by opening and closing the molecular device. In addition, DNA origami nanostructures provide functional scaffolds for the programmed positioning of enzymes or DNAzyme for the switchable operation of catalytic transformations. This is introduced by the tailored functionalization of the edges of origami tiles with nucleic acids guiding the switchable formation of DNAzyme catalysts through the dimerization/separation of the tiles. In addition, the programmed deposition of two-enzyme/cofactor constituents on the origami raft allowed the dynamic photochemical activation of the cofactor-mediated biocatalytic cascade on the spatially biocatalytic assembly on the scaffold. Furthermore, photoinduced "mechanical" switchable and reversible unlocking and closing of nanoholes in the origami frameworks allow the "ON" and "OFF" operation of DNAzyme units in the nanoholes, confined environments. The future challenges and potential applications of dynamic nucleic acid/enzyme and DNAzyme conjugates are discussed in the conclusion paragraph.
Collapse
|
87
|
Karthick V, Kumar Shrestha L, Kumar VG, Pranjali P, Kumar D, Pal A, Ariga K. Nanoarchitectonics horizons: materials for life sciences. NANOSCALE 2022; 14:10630-10647. [PMID: 35842941 DOI: 10.1039/d2nr02293a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nanoarchitectonics relies on the fabrication of materials at the atomic/molecular level to achieve the desired shape and function. Significant advances have been made in understanding the characteristics and spatial assemblies that contribute to material performance. Biomaterials undergo several changes when presented with various environmental cues. The ability to overcome such challenges, maintaining the integrity and effective functioning of native properties, can be regarded as a characteristic of a successful biomaterial. Control over the shape and efficacy of target materials can be tailored via various processes, like self-assembly, supramolecular chemistry, atomic/molecular manipulation, etc. Interplay between the physicochemical properties of materials and biomolecule recognition sites defines the structural rigidity in hierarchical structures. Materials including polymers, metal nanoparticles, nucleic acid systems, metal-organic frameworks, and carbon-based nanostructures can be viewed as promising prospects for developing biocompatible systems. This review discusses recent advances relating to such biomaterials for life science applications, where nanoarchitectonics plays a decisive role either directly or indirectly.
Collapse
Affiliation(s)
- V Karthick
- Centre for Ocean Research, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai 600119, India.
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
| | - Lok Kumar Shrestha
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
- Department of Materials Science, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - V Ganesh Kumar
- Centre for Ocean Research, Sathyabama Institute of Science and Technology, Jeppiaar Nagar, Rajiv Gandhi Salai, Chennai 600119, India.
| | - Pranjali Pranjali
- Department of Physics, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Aniruddha Pal
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Katsuhiko Ariga
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| |
Collapse
|
88
|
Han LT, Sun GG, Ruan LS, Li X. Structured Aptamers: A Flourishing Nanomaterial for Tumor Targeting. J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structured aptamers are nucleic acid systems produced using DNA nano self-assembly technology and can be constructed in a programmable manner. These aptamers are widely used in biomedical fields because of their low biological toxicity, weak immunogenicity, good cytocompatibility and
biocompatibility, stability, and facile modification ability. Additionally, structured aptamers achieve nano precision in spatial configuration and can be directly internalized into targets without the assistance of transfection reagents. They exhibit higher stability, rigidity, and binding
efficiency than aptamers alone. Therefore, structured aptamers have been universally applied in the tumor-targeting field and have emerged as a current research hotspot. Here, we introduce the assembly principle, assembly methods, and characterization methods of structured aptamers. Moreover,
the application status of structured aptamers for tumor detection and targeted therapy is summarized to provide new research directions for early diagnosis and drug research in the field of oncology.
Collapse
Affiliation(s)
- Li-Ting Han
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Ge-Ge Sun
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Luo-Shan Ruan
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Xin Li
- Department of Gynaecology 2, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| |
Collapse
|
89
|
Li S, Liu Y, Zhang T, Lin S, Shi S, He J, Xie Y, Cai X, Tian T, Lin Y. A Tetrahedral Framework DNA-Based Bioswitchable miRNA Inhibitor Delivery System: Application to Skin Anti-Aging. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2204287. [PMID: 35901292 DOI: 10.1002/adma.202204287] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/21/2022] [Indexed: 02/05/2023]
Abstract
MicroRNA (miR)-based therapy shows strong potential; however, structural limitations pose a challenge in fully exploiting its biomedical functionality. Tetrahedral framework DNA (tFNA) has proven to be an ideal vehicle for miR therapy. Inspired by the ancient Chinese myth "Sun and Immortal Birds," a novel bioswitchable miR inhibitor delivery system (BiRDS) is designed with three miR inhibitors (the three immortal birds) and a nucleic acid core (the central sun). The BiRDS fuses miR inhibitors within the framework, maximizing their loading capacity, while allowing the system to retain the characteristics of small-sized tFNA and avoiding uncertainty associated with RNA exposure in traditional loading protocols. The RNase H-responsive sequence at the tail of each "immortal bird" enables the BiRDS to transform from a 3D to a 2D structure upon entering cells, promoting the delivery of miR inhibitors. To confirm the application potential, the BiRDS is used to deliver the miR-31 inhibitor, with antiaging effects on hair follicle stem cells, into a skin aging model. Superior skin penetration ability and RNA delivery are observed with significant anti-aging effects. These findings demonstrate the capability and editability of the BiRDS to improve the stability and delivery efficacy of miRs for future innovations.
Collapse
Affiliation(s)
- Songhang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yuhao Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Shiyu Lin
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, The Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jiajun He
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| |
Collapse
|
90
|
Hertel S, Spinney RE, Xu SY, Ouldridge TE, Morris RG, Lee LK. The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure. Nucleic Acids Res 2022; 50:7829-7841. [PMID: 35880577 PMCID: PMC9371923 DOI: 10.1093/nar/gkac590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/23/2022] [Accepted: 07/25/2022] [Indexed: 11/12/2022] Open
Abstract
The kinetics of DNA hybridization are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridize at different rates are not well understood. Secondary structure is one predictable factor that influences hybridization rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. In this context, we measured hybridization rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify our observations. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters. Our results indicate that greater repetition of Watson-Crick pairs increases the number of initial states able to proceed to full hybridization, with the stability of those pairings dictating the likelihood of such progression, thus providing new insight into the physical factors underpinning DNA hybridization rates.
Collapse
Affiliation(s)
- Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Thomas E Ouldridge
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
| |
Collapse
|
91
|
Rajwar A, Shetty SR, Vaswani P, Morya V, Barai A, Sen S, Sonawane M, Bhatia D. Geometry of a DNA Nanostructure Influences Its Endocytosis: Cellular Study on 2D, 3D, and in Vivo Systems. ACS NANO 2022; 16:10496-10508. [PMID: 35715010 DOI: 10.1021/acsnano.2c01382] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fabrication of nanoscale DNA devices to generate 3D nano-objects with precise control of shape, size, and presentation of ligands has shown tremendous potential for therapeutic applications. The interactions between the cell membrane and different topologies of 3D DNA nanostructures are crucial for designing efficient tools for interfacing DNA devices with biological systems. The practical applications of these DNA nanocages are still limited in cellular and biological systems owing to the limited understanding of their interaction with the cell membrane and endocytic pathway. The correlation between the geometry of DNA nanostructures and their internalization efficiency remains elusive. We investigated the influence of the shape and size of 3D DNA nanostructures on their cellular internalization efficiency. We found that one particular geometry, i.e., the tetrahedral shape, is more favored over other designed geometries for their cellular uptake in 2D and 3D cell models. This is also replicable for cellular processes like cell invasion assays in a 3D spheroid model, and passing the epithelial barriers in in vivo zebrafish model systems. Our work provides detailed information for the rational design of DNA nanodevices for their upcoming biological and biomedical applications.
Collapse
Affiliation(s)
- Anjali Rajwar
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Shravani Reddy Shetty
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Payal Vaswani
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Vinod Morya
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| | - Amlan Barai
- Bioscience and Bioengineering Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shamik Sen
- Bioscience and Bioengineering Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mahendra Sonawane
- Department of Biological Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai 400005, India
| | - Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat 382355, India
| |
Collapse
|
92
|
Li R, Wu X, Li J, Lu X, Zhao RC, Liu J, Ding B. A covalently conjugated branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. NANOSCALE 2022; 14:9369-9378. [PMID: 35726974 DOI: 10.1039/d2nr01252a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Targeted delivery of therapeutic drugs is essential for precise treatment of various diseases to reduce possible serious side-effects. A screened DNA aptamer has been widely developed for active targeting delivery. Herein, we report a facile strategy for the construction of a branched DNA aptamer cluster-based nanoplatform for efficiently targeted drug delivery. In our design, the terminal-modified DNA aptamer can be covalently conjugated to form a branched aptamer cluster by click reaction easily. The branched aptamer cluster-modified DNA tetrahedron (TET) demonstrates highly targeted cellular uptake with the modification of only one site. After loading the chemotherapeutic drug (doxorubicin, DOX), the DNA aptamer cluster-based nanoplatform elicits a remarkable and selective inhibition of tumor cell proliferation by much-enhanced targeted delivery. This covalently conjugated branched DNA aptamer cluster-based nanoplatform provides a new strategy for the development of targeted drug delivery.
Collapse
Affiliation(s)
- Runze Li
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
| | - Xiaohui Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
| | - Xuehe Lu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
| | - Robert Chunhua Zhao
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Dongdan Santiao No. 5, Beijing 100005, China.
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for NanoScience and Technology, 11 BeiYiTiao, ZhongGuanCun, 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, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
93
|
He W, Zhao Y, Xing S, Zhang Y, Wang L, Liu H. DNA Tetrahedron Framework Guided Conjugation and Assembly of Gold Nanoparticles. Chempluschem 2022; 87:e202200159. [PMID: 35822636 DOI: 10.1002/cplu.202200159] [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: 05/04/2022] [Revised: 06/13/2022] [Indexed: 11/11/2022]
Abstract
Au nanoparticles (AuNPs) have been extensively used to assemble programmable structures that feature various functions. One central challenge of precisely directed assembly is to make valence-programmable building blocks. Herein, we use the DNA tetrahedron framework to stoichiometrically conjugate to Au nanoparticles, which results in monovalent building blocks at nanometer scale. We further fabricated high-order Au-tetrahedron structures to verify the ability of the blocks for building assemblies. These structures represent an exploration of an avenue to monovalent AuNPs, and provide the feasibility of precisely manipulating nanoparticles into prescribed assemblies.
Collapse
Affiliation(s)
- Wei He
- Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yan Zhao
- Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, P. R. China
| | - Shu Xing
- Division of Physical Biology and Bioimaging Center, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, P. R. China
| | - Yinan Zhang
- Key Laboratory of Advanced Civil Engineering Materials of, Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201200, P. R. China
| | - Huajie Liu
- Key Laboratory of Advanced Civil Engineering Materials of, Ministry of Education, Shanghai Research Institute for Intelligent Autonomous Systems, School of Chemical Science and Engineering, Tongji University, Shanghai, 200092, P. R. China
| |
Collapse
|
94
|
Wang C, Xu Y, Li S, Zhou Y, Qian Q, Liu Y, Mi X. Designer tetrahedral DNA framework-based microfluidic technology for multivalent capture and release of circulating tumor cells. Mater Today Bio 2022; 16:100346. [PMID: 35833198 PMCID: PMC9272028 DOI: 10.1016/j.mtbio.2022.100346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/14/2022] Open
Abstract
Circulating tumor cells (CTCs) have been recognized as a general biomarker for the early detection, diagnosis and therapy monitoring of cancer. Due to their extreme rarity in peripheral blood, the isolation and analysis of CTCs with high efficiency, high purity and high viability remains a tremendous technological challenge. Herein, we combined tetrahedral DNA framework (TDFs), herringbone channel (HB) chip, together with aptamer-triggered hybridization chain reaction (apt-HCR) to develop an efficient microfluidic system (T-μFS) for capture and release of simulated CTCs. The capture efficiency of MCF-7 cells was from 83.3% to 94.2% when the cell numbers ranged from 10 to 103 using our T-μFS in the whole blood. The release efficiency of the MCF-7 cells was 96.2% and the MCF-7 cell viability after release was 94.6% using our T-μFS in PBS buffer. Reculture and RT-qPCR studies showed that there was almost no damage by the capture and release treatment for the MCF-7 cells viability. These results revealed that our T-μFS could be developed as an integrated and automatic technical platform with great performance for multivalent capture and release of CTCs and have a wide application prospect for tumor liquid biopsy. Three-dimensional amine modified tetrahedral DNA frameworks (TDFs) as rigid scaffolds were anchored on the aldehyde modified substrate of HB-chip, which provided the better spatial orientation compared with single-stranded DNA. Aptamer partially hybridized to an initiator was employed to trigger HCR reaction, and HCR produced modified long products with multi-branched arms for multivalent binding on TDFs to improve the capture efficiency of CTCs. This is the first time that only employed DNA nanostructures in a microfluidic device system to capture CTCs, and all DNA nanostructures could be efficiently removed by enzymes without harming cells.
Collapse
|
95
|
Design and simulation of DNA, RNA and hybrid protein-nucleic acid nanostructures with oxView. Nat Protoc 2022; 17:1762-1788. [PMID: 35668321 DOI: 10.1038/s41596-022-00688-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/18/2022] [Indexed: 11/08/2022]
Abstract
Molecular simulation has become an integral part of the DNA/RNA nanotechnology research pipeline. In particular, understanding the dynamics of structures and single-molecule events has improved the precision of nanoscaffolds and diagnostic tools. Here we present oxView, a design tool for visualization, design, editing and analysis of simulations of DNA, RNA and nucleic acid-protein nanostructures. oxView provides an accessible software platform for designing novel structures, tweaking existing designs, preparing them for simulation in the oxDNA/RNA molecular simulation engine and creating visualizations of simulation results. In several examples, we present procedures for using the tool, including its advanced features that couple the design capabilities with a coarse-grained simulation engine and scripting interface that can programmatically edit structures and facilitate design of complex structures from multiple substructures. These procedures provide a practical basis from which researchers, including experimentalists with limited computational experience, can integrate simulation and 3D visualization into their existing research programs.
Collapse
|
96
|
Shiu SCC, Whitehouse WL, Tanner JA. Designing aptamer-enabled DNA polyhedra using paper origami. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
97
|
Li F, Li Y, Tang T, Liao Y, Lu Y, Liu X, Wen Q. Dual-band terahertz all-silicon metasurface with giant chirality for frequency-undifferentiated near-field imaging. OPTICS EXPRESS 2022; 30:14232-14242. [PMID: 35473171 DOI: 10.1364/oe.455956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/26/2022] [Indexed: 06/14/2023]
Abstract
Chiral metasurfaces are widely used in imaging and biosensing due to their powerful light field control capabilities. Most of the work is devoted to achieving the goals of chirality enhancement and tunability, but lacks consideration of design complexity, loss, cost, and multi-band operation. In order to alleviate this situation, we propose a pair of dual-frequency giant chiral structures based on all-silicon, which can achieve excellent and opposite spin-selective transmission around 1.09 THz and 1.65 THz. The giant chirality derives from the in-plane electric and magnetic dipole moments excited in different degrees. Theoretically, the maximum circular dichroism at the two frequencies are both as high as 0.34, and the coverage bandwidths of the two giant chirality are 85.5 GHz and 41.4 GHz, respectively. The experimental results are in good agreement with the simulation results. Based on the dual-band giant chiral patterns, the terahertz near-field imaging of different Chinese character images is demonstrated at two frequencies. The frequency-undifferentiated characteristics, good intensity contrast and three-dimensional imaging information are shown by the results. This work provides new ideas for the design of terahertz devices with simple structure and multi-functions, which are expected to be applied in the field of terahertz imaging or multi-channel communication.
Collapse
|
98
|
[Application of tetrahedral framework nucleic acids in the treatment of osteoarthritis]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2022; 36:505-510. [PMID: 35426293 PMCID: PMC9011070 DOI: 10.7507/1002-1892.202112054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To introduce the characteristics of tetrahedral framework nucleic acids (tFNA), focusing on its application in the treatment of osteoarthritis (OA) and relationship with microRNA (miRNA), and prospect the application of tFNA in the treatment of OA and the new idea of constructing miR-tFNA functional complex to treat OA. METHODS Recent studies were extensively reviewed to analyze the mechanism of tFNA and its relationship with OA and miRNA. RESULTS tFNA, a new type of new carrier, can not only play an indirect role in the treatment of OA as a small molecular carrier with therapeutic effect, but also play a direct role through the regulation of chondrocytes. It can bind with the miRNA that can regulate OA. The therapeutic effect of constructing tFNA functional complex loaded with miRNA has been verified in various diseases, and tFNA has advantages compared with other vectors. CONCLUSION tFNA, a novel framework nucleic acid structure, plays an important role in the treatment of OA. Constructing miR-tFNA functional complex may be an innovative idea in the treatment of OA.
Collapse
|
99
|
Zhu CY, Li FL, Zhang YW, Gupta RK, Patel SKS, Lee JK. Recent Strategies for the Immobilization of Therapeutic Enzymes. Polymers (Basel) 2022; 14:polym14071409. [PMID: 35406282 PMCID: PMC9003532 DOI: 10.3390/polym14071409] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
Therapeutic enzymes play important roles in modern medicine due to their high affinity and specificity. However, it is very expensive to use them in clinical medicine because of their low stability and bioavailability. To improve the stability and effectiveness of therapeutic enzymes, immobilization techniques have been employed to enhance the applications of therapeutic enzymes in the past few years. Reported immobilization techniques include entrapment, adsorption, and covalent attachment. In addition, protein engineering is often used to improve enzyme properties; however, all methods present certain advantages and limitations. For carrier-bound immobilization, the delivery and release of the immobilized enzyme depend on the properties of the carrier and enzyme. In this review, we summarize the advantages and challenges of the current strategies developed to deliver therapeutic enzymes and provide a future perspective on the immobilization technologies used for therapeutic enzyme delivery.
Collapse
Affiliation(s)
- Chen-Yuan Zhu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
| | - Fei-Long Li
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, China; (C.-Y.Z.); (F.-L.L.)
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
| | - Rahul K. Gupta
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
| | - Sanjay K. S. Patel
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul 05029, Korea;
- Correspondence: (Y.-W.Z.); (S.K.S.P.); (J.-K.L.); Tel.: +82-2-450-3505 (J.-K.L.)
| |
Collapse
|
100
|
Liu X, Wang T, Wu Y, Tan Y, Jiang T, Li K, Lou B, Chen L, Liu Y, Liu Z. Aptamer based probes for living cell intracellular molecules detection. Biosens Bioelectron 2022; 208:114231. [PMID: 35390719 DOI: 10.1016/j.bios.2022.114231] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 12/21/2022]
Abstract
Biosensors have been employed for monitoring and imaging biological events and molecules. Sensitive detection of different biomolecules in vivo can reflect the changes of physiological conditions in real-time, which is of great significance for the diagnosis and treatment of diseases. The detection of intracellular molecules concentration change can indicate the occurrence and development of disease. But the analysis process of the existing detection methods, such as Western blot detection of intracellular protein, polymerase chain reaction (PCR) technique quantitative analysis of intracellular RNA and DNA, usually need to extract the cell lysis which is complex and time-consuming. Fluorescence bioimaging enables in situ monitoring of intracellular molecules in living cells. By combining the specificity of aptamer for intracellular molecules binding, and biocompatibility of fluorescent materials and nanomaterials, biosensors with different nanostructures have been developed to enter into living cells for analysis. This review summarizes the fluorescence detection methods based on aptamer for intracellular molecules detection. The principles, limit of detection, advantages, and disadvantages of different platforms for intracellular molecular fluorescent response are summarized and reviewed. Finally, the current challenges and future developments were discussed and proposed.
Collapse
Affiliation(s)
- Xiaoqin Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Ting Wang
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yuwei Wu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Ting Jiang
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, Hunan Province, PR China.
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, PR China.
| |
Collapse
|