1
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Baral B, Panigrahi B, Kar A, Tulsiyan KD, Suryakant U, Mandal D, Subudhi U. Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:493-510. [PMID: 37583574 PMCID: PMC10424151 DOI: 10.1016/j.omtn.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/14/2023] [Indexed: 08/17/2023]
Abstract
Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.
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Affiliation(s)
- Bineeth Baral
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bijayananda Panigrahi
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
- Biopioneer Private Limited, Bhubaneswar 751024, Odisha, India
| | - Avishek Kar
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kiran D. Tulsiyan
- School of Chemical Sciences, National Institute of Science Education & Research, Bhubaneswar 752050, India
- Homi Bhaba National Institute, Mumbai 400094, India
| | - Uday Suryakant
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Dindyal Mandal
- School of Biotechnology, Kalinga Institute of Industrial Technology Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Umakanta Subudhi
- DNA Nanotechnology & Application Laboratory, Environment & Sustainability Department, CSIR-Institute of Minerals & Materials Technology, Bhubaneswar 751013, Odisha, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad 201002, India
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2
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Wang J, Li P, Wang C, Liu N, Xing D. Molecularly or atomically precise nanostructures for bio-applications: how far have we come? MATERIALS HORIZONS 2023; 10:3304-3324. [PMID: 37365977 DOI: 10.1039/d3mh00574g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
A huge variety of nanostructures are promising for biomedical applications, but only a few have been practically applied. Among the various reasons, the limited structural preciseness is a critical one, as it increases the difficulty in product quality control, accurate dosing, and ensuring the repeatability of material performance. Constructing nanoparticles with molecule-like preciseness is becoming a new research field. In this review, we focus on the artificial nanomaterials that can currently be molecularly or atomically precise, including DNA nanostructures, some metallic nanoclusters, dendrimer nanoparticles and carbon nanostructures, describing their syntheses, bio-applications and limitations, in view of up-to-date studies. A perspective on their potential for clinical translation is also given. This review is expected to provide a particular rationale for the future design of nanomedicines.
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Affiliation(s)
- Jie Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ping Li
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao 266071, China
| | - Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ning Liu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
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3
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Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
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Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
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4
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Li R, Madhvacharyula AS, Du Y, Adepu HK, Choi JH. Mechanics of dynamic and deformable DNA nanostructures. Chem Sci 2023; 14:8018-8046. [PMID: 37538812 PMCID: PMC10395309 DOI: 10.1039/d3sc01793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.
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Affiliation(s)
- Ruixin Li
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Anirudh S Madhvacharyula
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Yancheng Du
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Harshith K Adepu
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University 585 Purdue Mall West Lafayette Indiana 47907 USA
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5
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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.
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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
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6
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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.
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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
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7
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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.
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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
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8
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Lyu J, Yang M, Zhang C, Luo Y, Qin T, Su Z, Huang Z. DNA nanostructures directed by RNA clamps. NANOSCALE 2021; 13:19870-19874. [PMID: 34825903 DOI: 10.1039/d1nr03919a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA chains can be folded rationally by using DNA staples, and the programmed structures are of great potential in nanomaterial studies. However, due to the short DNA staples forming duplexes and displaying limitations in structural diversity and stability, the folded DNA nanostructures are usually generated with structural mis-formations, low yields and poor efficiencies, which can restrict their folding patterns and applications. To overcome these problems, we set out to use RNA as a clamp to form polygons, and herein demonstrated the ability to use a structural RNA-but not its corresponding DNA-to fold DNA chains into nanostructures with high efficiency (up to a 95.1% yield). Furthermore, we discovered that the 2'-methylated version of the RNA can, compared to the unmodified RNA, even more efficiently fold DNA chains (up to a 98.5% yield). Interestingly, the RNA clamp can fold DNA scaffolds with one, two or four folding units into the same square shape. Furthermore, the RNA can direct the DNA chains with three, four and five folding units into triangular, square and pentagonal nano-shapes, respectively. In addition, we confirmed their enlarged nano-shapes by performing electron microscopy (EM) imaging. These formed nanostructures revealed the potential cooperation between the DNA scaffold and RNA clamp. Moreover, our research demonstrated a novel strategy, involving using RNA clamps displaying structural diversity and duplex stability, for folding DNA into diverse nanostructures.
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Affiliation(s)
- Jiazhen Lyu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Mei Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Tong Qin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041 Chengdu, China
| | - Zhen Huang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, China.,SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu 610000, Sichuan, P. R. China.
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9
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Li M, Yin F, Song L, Mao X, Li F, Fan C, Zuo X, Xia Q. Nucleic Acid Tests for Clinical Translation. Chem Rev 2021; 121:10469-10558. [PMID: 34254782 DOI: 10.1021/acs.chemrev.1c00241] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Overexpressed or underexpressed as well as mutated nucleic acids have been implicated in many diseases. Therefore, nucleic acid tests (NATs) are extremely important. Inspired by intracellular DNA replication and RNA transcription, in vitro NATs have been extensively developed to improve the detection specificity, sensitivity, and simplicity. The principles of NATs can be in general classified into three categories: nucleic acid hybridization, thermal-cycle or isothermal amplification, and signal amplification. Driven by pressing needs in clinical diagnosis and prevention of infectious diseases, NATs have evolved to be a rapidly advancing field. During the past ten years, an explosive increase of research interest in both basic research and clinical translation has been witnessed. In this review, we aim to provide comprehensive coverage of the progress to analyze nucleic acids, use nucleic acids as recognition probes, construct detection devices based on nucleic acids, and utilize nucleic acids in clinical diagnosis and other important fields. We also discuss the new frontiers in the field and the challenges to be addressed.
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Affiliation(s)
- Min Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fangfei Yin
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Song
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Fan Li
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Department of Liver Surgery, 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
| | - Qiang Xia
- Institute of Molecular Medicine, Department of Liver Surgery, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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10
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Deng T, Man Z, Wang W. An assembling strategy for DNA cages with minimum strands. Comput Biol Chem 2021; 93:107507. [PMID: 34051660 DOI: 10.1016/j.compbiolchem.2021.107507] [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: 02/10/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/19/2022]
Abstract
DNA polyhedra are artificial cage-like architectures based on interlocked and interlinked DNA double-strands. Using fewer strands to construct DNA cages shows an important role in the design of single-stranded DNA molecules. However, construction methods for DNA polyhedra from topological perspective remains not well understood. In this study, we theoretically propose an assembling strategy for DNA polyhedra with minimum strands based on computer algorithm. The results show that this efficient method could search DNA polyhedra with fewer strands faster. Our research provides new insights into design and synthesis for DNA polyhedra with required topological structures.
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Affiliation(s)
- Tao Deng
- Key Laboratory of China's Ethnic Languages and Information Technology of Ministry of Education, Northwest Minzu University, Lanzhou, 730030, China; Key Laboratory of Streaming Data Computing Technologies and Application, Northwest Minzu University, Lanzhou, 730030, China; School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou, 730030, China.
| | - Zhengxing Man
- Key Laboratory of Streaming Data Computing Technologies and Application, Northwest Minzu University, Lanzhou, 730030, China; School of Mathematics and Computer Science, Northwest Minzu University, Lanzhou, 730030, China
| | - Weilan Wang
- Key Laboratory of China's Ethnic Languages and Information Technology of Ministry of Education, Northwest Minzu University, Lanzhou, 730030, China
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11
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Nicolson F, Ali A, Kircher MF, Pal S. DNA Nanostructures and DNA-Functionalized Nanoparticles for Cancer Theranostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001669. [PMID: 33304747 PMCID: PMC7709992 DOI: 10.1002/advs.202001669] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/27/2020] [Indexed: 05/12/2023]
Abstract
In the last two decades, DNA has attracted significant attention toward the development of materials at the nanoscale for emerging applications due to the unparalleled versatility and programmability of DNA building blocks. DNA-based artificial nanomaterials can be broadly classified into two categories: DNA nanostructures (DNA-NSs) and DNA-functionalized nanoparticles (DNA-NPs). More importantly, their use in nanotheranostics, a field that combines diagnostics with therapy via drug or gene delivery in an all-in-one platform, has been applied extensively in recent years to provide personalized cancer treatments. Conveniently, the ease of attachment of both imaging and therapeutic moieties to DNA-NSs or DNA-NPs enables high biostability, biocompatibility, and drug loading capabilities, and as a consequence, has markedly catalyzed the rapid growth of this field. This review aims to provide an overview of the recent progress of DNA-NSs and DNA-NPs as theranostic agents, the use of DNA-NSs and DNA-NPs as gene and drug delivery platforms, and a perspective on their clinical translation in the realm of oncology.
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Affiliation(s)
- Fay Nicolson
- Department of ImagingDana‐Farber Cancer Institute & Harvard Medical SchoolBostonMA02215USA
- Center for Molecular Imaging and NanotechnologyMemorial Sloan Kettering Cancer CenterNew YorkNY10065USA
| | - Akbar Ali
- Department of ChemistryIndian Institute of Technology‐ BhilaiRaipurChhattisgarh492015India
| | - Moritz F. Kircher
- Department of ImagingDana‐Farber Cancer Institute & Harvard Medical SchoolBostonMA02215USA
- Center for Molecular Imaging and NanotechnologyMemorial Sloan Kettering Cancer CenterNew YorkNY10065USA
- Department of RadiologyBrigham and Women's Hospital & Harvard Medical SchoolBostonMA02215USA
| | - Suchetan Pal
- Department of ChemistryIndian Institute of Technology‐ BhilaiRaipurChhattisgarh492015India
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12
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Rajwar A, Kharbanda S, Chandrasekaran AR, Gupta S, Bhatia D. Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems. ACS APPLIED BIO MATERIALS 2020; 3:7265-7277. [PMID: 35019470 DOI: 10.1021/acsabm.0c00916] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA nanotechnology is a unique field that provides simple yet robust design techniques for self-assembling nanoarchitectures with extremely high potential for biomedical applications. Though the field began to exploit DNA to build various nanoscale structures, it has now taken a different path, diverging from the creation of complex structures to functional DNA nanodevices that explore various biological systems and mechanisms. Here, we present a brief overview of DNA nanotechnology, summarizing the key strategies for construction of various DNA nanodevices, with special focus on three-dimensional (3D) nanocages or polyhedras. We then discuss biological applications of 3D DNA nanocages, particularly tetrahedral DNA cages, in their ability to program and modulate cellular systems, in biosensing, and as tools for targeted therapeutics. We conclude with a final discussion on challenges and perspectives of 3D DNA nanodevices in biomedical applications.
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Affiliation(s)
- Anjali Rajwar
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sumit Kharbanda
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India.,Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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13
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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14
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Zhou F, Sun W, Zhang C, Shen J, Yin P, Liu H. 3D Freestanding DNA Nanostructure Hybrid as a Low-Density High-Strength Material. ACS NANO 2020; 14:6582-6588. [PMID: 32356966 DOI: 10.1021/acsnano.0c00178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Structural DNA nanotechnology can produce a wide range of 3D nanostructures with programmable structure and size at <5 nm resolution. However, it is challenging to dry these structures without capillary force-induced damage. As a result, the applications of 3D DNA nanostructures have long been limited in aqueous environments. Ready access to free-standing 3D DNA nanostructures in the dry state could revolutionize many research areas, especially in the development of low-density, high-strength materials. Here we report a method to obtain free-standing wireframe 3D DNA tetrahedra in air on a solid substrate, such as SiO2 and mica, by absorbing uranyl acetate and lyophilization. The dried DNA tetrahedron structure, 93 ± 2 nm in height, withstands 42 ± 22 nN of loading force. The effective hardness (9.1 ± 5.1 MPa) and Young's modulus (77 ± 48 MPa) of this low-density (70.7 kg/m3) DNA-inorganic hybrid nanostructure are comparable to other reported low-density high-strength materials.
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Affiliation(s)
- Feng Zhou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Chen Zhang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jie Shen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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15
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Xie N, Wang H, Quan K, Feng F, Huang J, Wang K. Self-assembled DNA-Based geometric polyhedrons: Construction and applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Characterization of 3D DNA Assemblies Using Cryogenic Electron Microscopy. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-9107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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18
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Abstract
Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-submillimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nanoengineering, and related applications in a range of areas.
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Affiliation(s)
- Kai Xia
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qian Li
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hongzhou Gu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences , Fudan University , Shanghai 200032 , China
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19
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Cheng XS, Diao Y. The braid index of DNA double crossover polyhedral links. PLoS One 2020; 15:e0228855. [PMID: 32049974 PMCID: PMC7015418 DOI: 10.1371/journal.pone.0228855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 11/19/2022] Open
Abstract
In this paper, the authors study the mathematical properties of a class of alternating links called polyhedral links which have been used to model DNA polyhedra. The motivation of such studies is to provide guidance and aid in the research of the properties of certain DNA molecules. For example, such studies can provide characterizations of the structural complexity of DNA molecules. In an earlier work, Cheng and Jin studied the mathematical properties of such polyhedral links and were able to determine the braid index of a double crossover polyhedral link with 4 turn. However, the braid index of a double crossover polyhedral link with 4.5 turn remained an unsolved problem to this date, even though the graphs that admit the double crossover polyhedral links with 4.5 turn have been synthesized. In this paper, we provide a complete formulation of the braid index of a double crossover polyhedral link with an arbitrary turn number. Our approach is more general and it allows us to completely determine the braid indices for a much larger class of links. In the case of the double crossover polyhedral links, our formulation of the braid index is a simple formula based on a simpler graph used as a template to build the double crossover polyhedral links.
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Affiliation(s)
- Xiao-Sheng Cheng
- School of Mathematics and Statistics, Huizhou University, Huizhou, Guangdong, P. R. China
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Yuanan Diao
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
- * E-mail:
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20
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Fu X, Peng F, Lee J, Yang Q, Zhang F, Xiong M, Kong G, Meng HM, Ke G, Zhang XB. Aptamer-Functionalized DNA Nanostructures for Biological Applications. Top Curr Chem (Cham) 2020; 378:21. [PMID: 32030541 DOI: 10.1007/s41061-020-0283-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022]
Abstract
DNA nanostructures hold great promise for various applications due to their remarkable properties, including programmable assembly, nanometric positional precision, and dynamic structural control. The past few decades have seen the development of various kinds of DNA nanostructures that can be employed as useful tools in fields such as chemistry, materials, biology, and medicine. Aptamers are short single-stranded nucleic acids that bind to specific targets with excellent selectivity and high affinity and play critical roles in molecular recognition. Recently, many attempts have been made to integrate aptamers with DNA nanostructures for a range of biological applications. This review starts with an introduction to the features of aptamer-functionalized DNA nanostructures. The discussion then focuses on recent progress (particularly during the last five years) in the applications of these nanostructures in areas such as biosensing, bioimaging, cancer therapy, and biophysics. Finally, challenges involved in the practical application of aptamer-functionalized DNA nanostructures are discussed, and perspectives on future directions for research into and applications of aptamer-functionalized DNA nanostructures are provided.
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Affiliation(s)
- Xiaoyi Fu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Fangqi Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Jungyeon Lee
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Qi Yang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Fei Zhang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ, 07102, USA
| | - Mengyi Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Gezhi Kong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hong-Min Meng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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21
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Lin H, Li J, Liu S. The calculation of topological structures of strands-based DNA trigonal bipyramids. J Mol Graph Model 2019; 95:107492. [PMID: 31794933 DOI: 10.1016/j.jmgm.2019.107492] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/22/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022]
Abstract
With the rapid development of DNA nanotechnology, strands-based DNA polyhedra have been reported and widely applied in chemical biology, drug delivery and materials science. A fundamental problem is to determine which topological structures such a DNA polyhedron will allow. Our goal in this paper is to determine all permissible nontrivial topological structures for DNA trigonal bipyramids with double-helical edges, which have been partially realized by one-step self-assembly of multiple DNA single-strands designed rationally. Here oriented trigonal bipyramid links (OTB links) are constructed as the mathematical models for DNA trigonal bipyramids and are further classified into 451 link types. In this process, an OTBL program is designed in the Python programming language to generate all OTB link diagrams and also to remove the same topological structures produced by the rotational symmetry of trigonal bipyramid. Our result gives a list of candidates for further synthesized DNA trigonal bipyramid prisms with required topological structures.
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Affiliation(s)
- Haoyu Lin
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, 250100, China
| | - Jia Li
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, 250100, China
| | - Shuya Liu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Jinan, 250100, China.
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22
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23
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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24
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Wang B, Song L, Jin B, Deng N, Wu X, He J, Deng Z, Li Y. Base‐Sequence‐Independent Efficient Redox Switching of Self‐Assembled DNA Nanocages. Chembiochem 2019; 20:2743-2746. [DOI: 10.1002/cbic.201900253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Bang Wang
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Lei Song
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Bang Jin
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Ning Deng
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Xiaojing Wu
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Jianbo He
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter ChemistryDepartment of ChemistryUniversity of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Yulin Li
- Anhui Province Key Laboratory of Advanced Catalytic Materials and Reaction EngineeringSchool of Chemistry and Chemical EngineeringHefei University of Technology Hefei Anhui 230009 P. R. China
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25
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A minimalist's approach for DNA nanoconstructions. Adv Drug Deliv Rev 2019; 147:22-28. [PMID: 30769045 DOI: 10.1016/j.addr.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology takes DNA, a biopolymer, far beyond being the molecule that stores and transmits genetic information in biological systems. DNA has been employed as building blocks for the assembly of designed, nanoscaled, supramolecular DNA architectures for applications in biophysics, structure determination, synthetic biology, diagnostics, and drug delivery. Herein, we review a symmetric approach of tile-based DNA self-assembly. This approach allows the construction of DNA nanostructures from minimal numbers of different types of DNA strands based on sequence and structural symmetries. Some examples of the applications of this approach in siRNA delivery are discussed as well.
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26
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Zhang Y, Pan V, Li X, Yang X, Li H, Wang P, Ke Y. Dynamic DNA Structures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900228. [PMID: 30970183 PMCID: PMC7252325 DOI: 10.1002/smll.201900228] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/20/2019] [Indexed: 05/19/2023]
Abstract
Dynamic DNA structures, a type of DNA construct built using programmable DNA self-assembly, have the capability to reconfigure their conformations in response to environmental stimulation. A general strategy to design dynamic DNA structures is to integrate reconfigurable elements into conventional static DNA structures that may be assembled from a variety of methods including DNA origami and DNA tiles. Commonly used reconfigurable elements range from strand displacement reactions, special structural motifs, target-binding DNA aptamers, and base stacking components, to DNA conformational change domains, etc. Morphological changes of dynamic DNA structures may be visualized by imaging techniques or may be translated to other detectable readout signals (e.g., fluorescence). Owing to their programmable capability of recognizing environmental cues with high specificity, dynamic DNA structures embody the epitome of robust and versatile systems that hold great promise in sensing and imaging biological analytes, in delivering molecular cargos, and in building programmable systems that are able to conduct sophisticated tasks.
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Affiliation(s)
- Yingwei Zhang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Xue Li
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Xueqin Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Haofei Li
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
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27
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Li N, Shang Y, Han Z, Wang T, Wang ZG, Ding B. Fabrication of Metal Nanostructures on DNA Templates. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13835-13852. [PMID: 30480424 DOI: 10.1021/acsami.8b16194] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Metal nanoarchitectures fabrication based on DNA assembly has attracted a good deal of attention. DNA nanotechnology enables precise organization of nanoscale objects with extraordinary structural programmability. The spatial addressability of DNA nanostructures and sequence-dependent recognition allow functional elements to be precisely positioned; thus, novel functional materials that are difficult to produce using conventional methods could be fabricated. This review focuses on the recent development of the fabrication strategies toward manipulating the shape and morphology of metal nanoparticles and nanoassemblies based on the rational design of DNA structures. DNA-mediated metallization, including DNA-templated conductive nanowire fabrication and sequence-selective metal deposition, etc., is briefly introduced. The modifications of metal nanoparticles (NPs) with DNA and subsequent construction of heterogeneous metal nanoarchitectures are highlighted. Importantly, DNA-assembled dynamic metal nanostructures that are responsive to different stimuli are also discussed as they allow the design of smart and dynamic materials. Meanwhile, the prospects and challenges of these shape-and morphology-controlled strategies are summarized.
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Affiliation(s)
- Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Zihong Han
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Ting Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience , National Center for NanoScience and Technology , 11 Bei Yi Tiao, Zhong Guan Cun , Beijing 100190 , China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
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28
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Taylor LLK, Riddell IA, Smulders MMJ. Selbstorganisation von funktionellen diskreten dreidimensionalen Architekturen in Wasser. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lauren L. K. Taylor
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL Großbritannien
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen Niederlande
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29
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Taylor LLK, Riddell IA, Smulders MMJ. Self-Assembly of Functional Discrete Three-Dimensional Architectures in Water. Angew Chem Int Ed Engl 2018; 58:1280-1307. [DOI: 10.1002/anie.201806297] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Indexed: 01/01/2023]
Affiliation(s)
| | - Imogen A. Riddell
- School of Chemistry; University of Manchester; Oxford Road M13 9PL UK
| | - Maarten M. J. Smulders
- Laboratory of Organic Chemistry; Wageningen University, P.O. Box 8026; 6700EG Wageningen The Netherlands
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30
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Kim J, Jang D, Park H, Jung S, Kim DH, Kim WJ. Functional-DNA-Driven Dynamic Nanoconstructs for Biomolecule Capture and Drug Delivery. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1707351. [PMID: 30062803 DOI: 10.1002/adma.201707351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The discovery of sequence-specific hybridization has allowed the development of DNA nanotechnology, which is divided into two categories: 1) structural DNA nanotechnology, which utilizes DNA as a biopolymer; and 2) dynamic DNA nanotechnology, which focuses on the catalytic reactions or displacement of DNA structures. Recently, numerous attempts have been made to combine DNA nanotechnologies with functional DNAs such as aptamers, DNAzymes, amplified DNA, polymer-conjugated DNA, and DNA loaded on functional nanoparticles for various applications; thus, the new interdisciplinary research field of "functional DNA nanotechnology" is initiated. In particular, a fine-tuned nanostructure composed of functional DNAs has shown immense potential as a programmable nanomachine by controlling DNA dynamics triggered by specific environments. Moreover, the programmability and predictability of functional DNA have enabled the use of DNA nanostructures as nanomedicines for various biomedical applications, such as cargo delivery and molecular drugs via stimuli-mediated dynamic structural changes of functional DNAs. Here, the concepts and recent case studies of functional DNA nanotechnology and nanostructures in nanomedicine are reviewed, and future prospects of functional DNA for nanomedicine are indicated.
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Affiliation(s)
- Jinhwan Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
| | - Donghyun Jang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Hyeongmok Park
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sungjin Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Dae Heon Kim
- Department of Biology, Sunchon National University, Sunchon, 57922, Korea
| | - Won Jong Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang, 37673, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
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32
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Hu Q, Wang S, Wang L, Gu H, Fan C. DNA Nanostructure-Based Systems for Intelligent Delivery of Therapeutic Oligonucleotides. Adv Healthc Mater 2018; 7:e1701153. [PMID: 29356400 DOI: 10.1002/adhm.201701153] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/27/2017] [Indexed: 12/15/2022]
Abstract
In the beginning of the 21st century, therapeutic oligonucleotides have shown great potential for the treatment of many life-threatening diseases. However, effective delivery of therapeutic oligonucleotides to the targeted location in vivo remains a major issue. As an emerging field, DNA nanotechnology is applied in many aspects including bioimaging, biosensing, and drug delivery. With sequence programming and optimization, a series of DNA nanostructures can be precisely engineered with defined size, shape, surface chemistry, and function. Simply with hybridization, therapeutic oligonucleotides including unmethylated cytosine-phosphate-guanine dinucleotide oligos, small interfering RNA (siRNA) or antisense RNA, single guide RNA of the regularly interspaced short palindromic repeat-Cas9 system, and aptamers, are successfully loaded on DNA nanostructures for delivery. In this progress report, the development history of DNA nanotechnology is first introduced, and then the mechanisms and means for cellular uptake of DNA nanostructures are discussed. Next, current approaches to deliver therapeutic oligonucleotides with DNA nanovehicles are summarized. In the end, the challenges and opportunities for DNA nanostructure-based systems for the delivery of therapeutic oligonucleotides are discussed.
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Affiliation(s)
- Qinqin Hu
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Sheng Wang
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and Institutes of Biomedical Sciences; Shanghai Medical College of Fudan University; Fudan University; Shanghai 200032 China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics; Chinese Academy of Sciences; Shanghai 201800 China
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33
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Wang X, Chandrasekaran AR, Shen Z, Ohayon YP, Wang T, Kizer ME, Sha R, Mao C, Yan H, Zhang X, Liao S, Ding B, Chakraborty B, Jonoska N, Niu D, Gu H, Chao J, Gao X, Li Y, Ciengshin T, Seeman NC. Paranemic Crossover DNA: There and Back Again. Chem Rev 2018; 119:6273-6289. [PMID: 29911864 DOI: 10.1021/acs.chemrev.8b00207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Over the past 35 years, DNA has been used to produce various nanometer-scale constructs, nanomechanical devices, and walkers. Construction of complex DNA nanostructures relies on the creation of rigid DNA motifs. Paranemic crossover (PX) DNA is one such motif that has played many roles in DNA nanotechnology. Specifically, PX cohesion has been used to connect topologically closed molecules, to assemble a three-dimensional object, and to create two-dimensional DNA crystals. Additionally, a sequence-dependent nanodevice based on conformational change between PX and its topoisomer, JX2, has been used in robust nanoscale assembly lines, as a key component in a DNA transducer, and to dictate polymer assembly. Furthermore, the PX motif has recently found a new role directly in basic biology, by possibly serving as the molecular structure for double-stranded DNA homology recognition, a prominent feature of molecular biology and essential for many crucial biological processes. This review discusses the many attributes and usages of PX-DNA-its design, characteristics, applications, and potential biological relevance-and aims to accelerate the understanding of PX-DNA motif in its many roles and manifestations.
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Affiliation(s)
- Xing Wang
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | | | - Zhiyong Shen
- College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241000 , China
| | - Yoel P Ohayon
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tong Wang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Megan E Kizer
- Department of Chemistry and Chemical Biology and The Center for Biotechnology and Interdisciplinary Studies , Rensselaer Polytechnic Institute , Troy , New York 12180 , United States
| | - Ruojie Sha
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Chengde Mao
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Hao Yan
- Department of Chemistry and Biochemistry and The Biodesign Institute , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaoping Zhang
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Shiping Liao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Baoquan Ding
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Banani Chakraborty
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Natasha Jonoska
- Department of Mathematics and Statistics , University of South Florida , Tampa , Florida 33620 , United States
| | - Dong Niu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Hongzhou Gu
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Jie Chao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Xiang Gao
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Yuhang Li
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Tanashaya Ciengshin
- Department of Chemistry , New York University , New York , New York 10012 , United States
| | - Nadrian C Seeman
- Department of Chemistry , New York University , New York , New York 10012 , United States
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34
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Ke Y, Castro C, Choi JH. Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research. Annu Rev Biomed Eng 2018; 20:375-401. [PMID: 29618223 DOI: 10.1146/annurev-bioeng-062117-120904] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.
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Affiliation(s)
- Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, Georgia 30322, USA;
| | - Carlos Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43214, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
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35
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Hu Q, Li H, Wang L, Gu H, Fan C. DNA Nanotechnology-Enabled Drug Delivery Systems. Chem Rev 2018; 119:6459-6506. [PMID: 29465222 DOI: 10.1021/acs.chemrev.7b00663] [Citation(s) in RCA: 559] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.
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Affiliation(s)
- Qinqin Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China
| | - Hua Li
- Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China.,Research & Development Center, Shandong Buchang Pharmaceutical Company, Limited, Heze 274000 , China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University , Shanghai 200032 , China.,Department of Systems Biology for Medicine , School of Basic Medical Sciences, Fudan University , Shanghai 200032 , China.,Shanghai Institute of Cardiovascular Diseases , Zhongshan Hospital, Fudan University , Shanghai 200032 , China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China.,School of Life Science and Technology , ShanghaiTech University , Shanghai 201210 , China
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36
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Xavier PL, Chandrasekaran AR. DNA-based construction at the nanoscale: emerging trends and applications. NANOTECHNOLOGY 2018; 29:062001. [PMID: 29232197 DOI: 10.1088/1361-6528/aaa120] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.
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Affiliation(s)
- P Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY) and Department of Physics, University of Hamburg, D-22607 Hamburg, Germany. Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, D-22761 Hamburg, Germany
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37
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Li Y, Mao C, Deng Z. Supramolecular Wireframe DNA Polyhedra: Assembly and Applications. CHINESE J CHEM 2017. [DOI: 10.1002/cjoc.201600789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yulin Li
- School of Chemistry and Chemical Engineering; Hefei University of Technology, 193 Tunxi Road; Hefei Anhui 230009 China
| | - Chengde Mao
- Department of Chemistry; Purdue University; West Lafayette Indiana 47907 USA
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Materials Science; University of Science and Technology of China; Hefei Anhui 230026 China
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38
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Wu XR, Wu CW, Ding F, Tian C, Jiang W, Mao CD, Zhang C. Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2017.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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39
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Abstract
Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.
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Affiliation(s)
- Cheng Tian
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Chuan Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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40
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Wu XR, Wu CW, Zhang C. Discrete DNA three-dimensional nanostructures: the synthesis and applications. CHINESE JOURNAL OF POLYMER SCIENCE 2016. [DOI: 10.1007/s10118-017-1871-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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41
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Whitelam S. Minimal Positive Design for Self-Assembly of the Archimedean Tilings. PHYSICAL REVIEW LETTERS 2016; 117:228003. [PMID: 27925733 DOI: 10.1103/physrevlett.117.228003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Indexed: 06/06/2023]
Abstract
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of minimal positive design allows the self-assembly of networks equivalent to the 8 semiregular Archimedean tilings of the plane, structures not previously realized in simulation. This strategy consists of identifying the fewest distinct types of interparticle interaction that appear in the desired structure, and does not require enumeration of the many possible undesired structures. The resulting particles, which self-assemble into the desired networks, possess DNA-like selectivity of their interactions. Assembly of certain molecular networks may therefore require such selectivity.
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Affiliation(s)
- Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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42
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Antiparallel d-stable traces and a stronger version of ore problem. J Math Biol 2016; 75:109-127. [PMID: 27853820 DOI: 10.1007/s00285-016-1077-2] [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: 06/08/2015] [Revised: 08/21/2016] [Indexed: 10/20/2022]
Abstract
In 2013 a novel self-assembly strategy for polypeptide nanostructure design which could lead to significant developments in biotechnology was presented in Gradišar et al. (Nat Chem Bio 9:362-366, 2013). It was since observed that a polyhedron P can be realized by interlocking pairs of polypeptide chains if its corresponding graph G(P) admits a strong trace. It was since also demonstrated that a similar strategy can also be expanded to self-assembly of designed DNA (Kočar, Nat commun 7:1-8, 2016). In this direction, in the present paper we characterize graphs which admit closed walk which traverses every edge exactly once in each direction and for every vertex v, there is no subset N of its neighbors, with [Formula: see text], such that every time the walk enters v from N, it also exits to a vertex in N. This extends Thomassen's characterization (Thomassen, J Combin Theory Ser B 50:198-207, 1990) for the case [Formula: see text].
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43
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Wang P, Wu S, Tian C, Yu G, Jiang W, Wang G, Mao C. Retrosynthetic Analysis-Guided Breaking Tile Symmetry for the Assembly of Complex DNA Nanostructures. J Am Chem Soc 2016; 138:13579-13585. [PMID: 27726355 DOI: 10.1021/jacs.6b06074] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | | | | | | | | | - Guansong Wang
- Institute
of Respiratory Diseases, Xinqiao Hospital, Chongqing 400037, China
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44
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Wang W, Lin T, Zhang S, Bai T, Mi Y, Wei B. Self-assembly of fully addressable DNA nanostructures from double crossover tiles. Nucleic Acids Res 2016; 44:7989-96. [PMID: 27484479 PMCID: PMC5027514 DOI: 10.1093/nar/gkw670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 11/23/2022] Open
Abstract
DNA origami and single-stranded tile (SST) are two proven approaches to self-assemble finite-size complex DNA nanostructures. The construction elements appeared in structures from these two methods can also be found in multi-stranded DNA tiles such as double crossover tiles. Here we report the design and observation of four types of finite-size lattices with four different double crossover tiles, respectively, which, we believe, in terms of both complexity and robustness, will be rival to DNA origami and SST structures.
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Affiliation(s)
- Wen Wang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China
| | - Tong Lin
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Suoyu Zhang
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Tanxi Bai
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Yongli Mi
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Depatment of Chemistry, Tongji University, Shanghai 200092, China Department of Chemical and Biomolecular Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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45
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Franch O, Iacovelli F, Falconi M, Juul S, Ottaviani A, Benvenuti C, Biocca S, Ho YP, Knudsen BR, Desideri A. DNA hairpins promote temperature controlled cargo encapsulation in a truncated octahedral nanocage structure family. NANOSCALE 2016; 8:13333-13341. [PMID: 27341703 DOI: 10.1039/c6nr01806h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In the present study we investigate the mechanism behind temperature controlled cargo uptake using a truncated octahedral DNA cage scaffold functionalized with one, two, three or four hairpin forming DNA strands inserted in one corner of the structure. This investigation was inspired by our previous demonstration of temperature controlled reversible encapsulation of the cargo enzyme, horseradish peroxidase, in the cage with four hairpin forming strands. However, in this previous study the mechanism of cargo uptake was not directly addressed (Juul, et al., Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage, ACS Nano, 2013, 7, 9724-9734). In the present study we use a combination of molecular dynamics simulations and in vitro analyses to unravel the mechanism of cargo uptake in hairpin containing DNA cages. We find that two hairpin forming strands are necessary and sufficient to facilitate efficient cargo uptake, which argues against a full opening-closing of one corner of the structure being responsible for encapsulation. Molecular dynamics simulations were carried out to evaluate the atomistic motions responsible for encapsulation and showed that the two hairpin forming strands facilitated extension of at least one of the face surfaces of the cage scaffold, allowing entrance of the cargo protein into the cavity of the structure. Hence, the presented data demonstrate that cargo uptake does not involve a full opening of the structure. Rather, the uptake mechanism represents a feature of increased flexibility integrated in this nanocage structure upon the addition of at least two hairpin-forming strands.
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Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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46
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Sun S, Wang M, Zhang F, Zhu J. DNA polygonal cavities with tunable shapes and sizes. Chem Commun (Camb) 2016; 51:16247-50. [PMID: 26399176 DOI: 10.1039/c5cc06092c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a new and simple angle control strategy to construct shape- and size-tunable DNA polygonal cavities. A monomer with a controlled slope on one end was used for hierarchical assembly into diverse polygons in a single step. Additionally, by simply moving the position of sticky ends on the monomer, the cavity size can be precisely programmed.
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Affiliation(s)
- Sha Sun
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Mingyang Wang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Feifei Zhang
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.
| | - Jin Zhu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing 210093, China.
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47
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Schreck JS, Romano F, Zimmer MH, Louis AA, Doye JPK. Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model. ACS NANO 2016; 10:4236-47. [PMID: 27010928 DOI: 10.1021/acsnano.5b07664] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy
| | - Matthew H Zimmer
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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48
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Schreck JS, Ouldridge TE, Romano F, Louis AA, Doye JPK. Characterizing the bending and flexibility induced by bulges in DNA duplexes. J Chem Phys 2016; 142:165101. [PMID: 25933790 DOI: 10.1063/1.4917199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages, two-dimensional arrays, and ribbons, is a bulged duplex, that is, two helical segments that connect at a bulge loop. We use a coarse-grained model of DNA to characterize such bulged duplexes. We find that this motif can adopt structures belonging to two main classes: one where the stacking of the helices at the center of the system is preserved, the geometry is roughly straight, and the bulge is on one side of the duplex and the other where the stacking at the center is broken, thus allowing this junction to act as a hinge and increasing flexibility. Small loops favor states where stacking at the center of the duplex is preserved, with loop bases either flipped out or incorporated into the duplex. Duplexes with longer loops show more of a tendency to unstack at the bulge and adopt an open structure. The unstacking probability, however, is highest for loops of intermediate lengths, when the rigidity of single-stranded DNA is significant and the loop resists compression. The properties of this basic structural motif clearly correlate with the structural behavior of certain nano-scale objects, where the enhanced flexibility associated with larger bulges has been used to tune the self-assembly product as well as the detailed geometry of the resulting nanostructures. We further demonstrate the role of bulges in determining the structure of a "Z-tile," a basic building block for nanostructures.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolph Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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49
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Li M, Deng Q, Jin X. A general method for computing the Homfly polynomial of DNA double crossover 3-regular links. PLoS One 2015; 10:e0125184. [PMID: 25932998 PMCID: PMC4416910 DOI: 10.1371/journal.pone.0125184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/10/2015] [Indexed: 11/18/2022] Open
Abstract
In the last 20 years or so, chemists and molecular biologists have synthesized some novel DNA polyhedra. Polyhedral links were introduced to model DNA polyhedra and study topological properties of DNA polyhedra. As a very powerful invariant of oriented links, the Homfly polynomial of some of such polyhedral links with small number of crossings has been obtained. However, it is a challenge to compute Homfly polynomials of polyhedral links with large number of crossings such as double crossover 3-regular links considered here. In this paper, a general method is given for computing the chain polynomial of the truncated cubic graph with two different labels from the chain polynomial of the original labeled cubic graph by substitutions. As a result, we can obtain the Homfly polynomial of the double crossover 3-regular link which has relatively large number of crossings.
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Affiliation(s)
- Meilian Li
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian, P. R. China
- School of Mathematics and Computer Sciences, Longyan University, Longyan, Fujian, P. R. China
| | - Qingying Deng
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian, P. R. China
| | - Xian’an Jin
- School of Mathematical Sciences, Xiamen University, Xiamen, Fujian, P. R. China
- * E-mail:
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50
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Li Y, Liu Z, Yu G, Jiang W, Mao C. Self-assembly of molecule-like nanoparticle clusters directed by DNA nanocages. J Am Chem Soc 2015; 137:4320-3. [PMID: 25823595 DOI: 10.1021/jacs.5b01196] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Analogous to the atom-molecule relationship, nanoparticle (NP) clusters (or NP-molecules) with defined compositions and directional bonds could potentially integrate the properties of the component individual NPs, leading to emergent properties. Despite extensive efforts in this direction, no general approach is available for assembly of such NP-molecules. Here we report a general method for building this type of structures by encapsulating NPs into self-assembled DNA polyhedral wireframe nanocages, which serve as guiding agents for further assembly. As a demonstration, a series of NP-molecules have been assembled and validated. Such NP-molecules will, we believe, pave a way to explore new nanomaterials with emergent functions/properties that are related to, but do not belong to the individual component nanoparticles.
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Affiliation(s)
- Yulin Li
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhiyu Liu
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Guimei Yu
- ‡Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Wen Jiang
- ‡Markey Center for Structural Biology and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Chengde Mao
- †Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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