151
|
Swenson CS, Velusamy A, Argueta-Gonzalez HS, Heemstra JM. Bilingual Peptide Nucleic Acids: Encoding the Languages of Nucleic Acids and Proteins in a Single Self-Assembling Biopolymer. J Am Chem Soc 2019; 141:19038-19047. [PMID: 31711285 DOI: 10.1021/jacs.9b09146] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nucleic acids and proteins are the fundamental biopolymers that support all life on Earth. Nucleic acids store large amounts of information in nucleobase sequences while peptides and proteins utilize diverse amino acid functional groups to adopt complex structures and perform wide-ranging activities. Although nature has evolved machinery to read the nucleic acid code and translate it into amino acid code, the extant biopolymers are restricted to encoding amino acid or nucleotide sequences separately, limiting their potential applications in medicine and biotechnology. Here we describe the design, synthesis, and stimuli-responsive assembly behavior of a bilingual biopolymer that integrates both amino acid and nucleobase sequences into a single peptide nucleic acid (PNA) scaffold to enable tunable storage and retrieval of tertiary structural behavior and programmable molecular recognition capabilities. Incorporation of a defined sequence of amino acid side-chains along the PNA backbone yields amphiphiles having a "protein code" that directs self-assembly into micellar architectures in aqueous conditions. However, these amphiphiles also carry a "nucleotide code" such that subsequent introduction of a complementary RNA strand induces a sequence-specific disruption of assemblies through hybridization. Together, these properties establish bilingual PNA as a powerful biopolymer that combines two information systems to harness structural responsiveness and sequence recognition. The PNA scaffold and our synthetic system are highly generalizable, enabling fabrication of a wide array of user-defined peptide and nucleotide sequence combinations for diverse future biomedical and nanotechnology applications.
Collapse
Affiliation(s)
- Colin S Swenson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Arventh Velusamy
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | | | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| |
Collapse
|
152
|
Platnich CM, Hariri AA, Sleiman HF, Cosa G. Advancing Wireframe DNA Nanostructures Using Single-Molecule Fluorescence Microscopy Techniques. Acc Chem Res 2019; 52:3199-3210. [PMID: 31675207 DOI: 10.1021/acs.accounts.9b00424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA nanotechnology relies on the molecular recognition properties of DNA to produce complex architectures through self-assembly. The resulting DNA nanostructures allow scientists to organize functional materials at the nanoscale and have therefore found applications in many domains of materials science over the past several years. These scaffolds have been used to position proteins, nanoparticles, carbon nanotubes, and other nanomaterials with high spatial resolution. In addition to their remarkable performance as frameworks for other species, DNA constructs also possess interesting dynamic properties, which have led to their use in logic circuits, drug delivery vehicles, and molecular walkers. Although DNA nanostructures have become increasingly complex, the development of tools to study them has lagged. Currently, gel electrophoresis, dynamic light scattering, and ensemble fluorescence measurements are widely used to characterize DNA-based assemblies. Unfortunately, ensemble averaging in these methods obscures malformed structures and may mask properties associated with structure, length, and shape in polydisperse samples. While atomic force microscopy allows for the determination of morphology at the single-molecule level, this technique cannot typically be used to assess the dynamic properties of these constructs. To analyze the function of DNA-based devices such as molecular motors and reconfigurable nanostructures in real time, new single-molecule techniques are required. This Account details the work from our laboratories toward developing single-molecule fluorescence (SMF) methodologies for the structural and dynamic characterization of wireframe DNA nanostructures, one at a time. The methods described herein provide us with two separate yet related sets of information: First, we can statically examine the nanostructures one by one to assess their robustness, structural fidelity, and morphology. This is primarily done using two-color stepwise photobleaching, wherein we can examine the subunit stoichiometry of our assemblies before and after various perturbations to the structures. For example, we can introduce length mismatches to cause the nanotube to bend or perform strand displacement reactions to generate single-stranded, flexible analogues of our materials. Second, due to the unmatched spatiotemporal resolution of SMF techniques, we can study the dynamic character of these assemblies by implementing structural changes to the nanotube and monitoring them in real time. With this structural and dynamic information in hand, our groups have additionally developed new tools for the improved construction of DNA nanotubes, inspired by solid-phase DNA synthesis. By assembling the nanotubes in a stepwise manner, highly monodisperse nanostructures of any desired length can be made without a template strand. In this way, unique building blocks can also be added sequence-specifically, allowing for the production of user-defined scaffolds to organize nanoscale materials in three dimensions. This method, in combination with our imaging and analysis protocols, may be extended to assemble and inspect other supramolecular constructs in a controlled manner. Overall, by combining synthesis, characterization, and analysis, these single-molecule techniques hold the potential to advance the study of DNA nanostructures and dynamic DNA-based devices.
Collapse
Affiliation(s)
- Casey M. Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Amani A. Hariri
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
153
|
Peng H, Newbigging AM, Reid MS, Uppal JS, Xu J, Zhang H, Le XC. Signal Amplification in Living Cells: A Review of microRNA Detection and Imaging. Anal Chem 2019; 92:292-308. [DOI: 10.1021/acs.analchem.9b04752] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Ashley M. Newbigging
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Michael S. Reid
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jagdeesh S. Uppal
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| | - X. Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical
Sciences Building, Edmonton, Alberta T6G 2G3, Canada
| |
Collapse
|
154
|
Ngo TA, Dinh H, Nguyen TM, Liew FF, Nakata E, Morii T. Protein adaptors assemble functional proteins on DNA scaffolds. Chem Commun (Camb) 2019; 55:12428-12446. [PMID: 31576822 DOI: 10.1039/c9cc04661e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
Collapse
Affiliation(s)
- Tien Anh Ngo
- Vinmec Biobank, Hi-tech Center, Vinmec Healthcare System, 458 Minh Khai, Ha Noi, Vietnam
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Thang Minh Nguyen
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Fong Fong Liew
- MAHSA University, Faculty of Dentistry, Bandar Saujana Putra, 42610 Jenjarom, Selangor, Malaysia
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan.
| |
Collapse
|
155
|
Li L, Chen X, Cui C, Pan X, Li X, Yazd HS, Wu Q, Qiu L, Li J, Tan W. Aptamer Displacement Reaction from Live-Cell Surfaces and Its Applications. J Am Chem Soc 2019; 141:17174-17179. [PMID: 31539233 DOI: 10.1021/jacs.9b07191] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DNA strand displacement reaction has had sustained scientific interest in building complicated nucleic acid-based networks. However, extending the fundamental mechanism to more diverse biomolecules in a complex environment remains challenging. Aptamers bind with targeted biomolecules with high affinity and selectivity, thus offering a promising route to link the powers of nucleic acid with diverse cues. Here, we describe three methods that allow facile and efficient displacement reaction of aptamers from the living cell surface using complement DNA (cDNA), toehold-labeled cDNA (tcDNA), and single-stranded binding protein (SSB). The kinetics of the DNA strand displacement reaction is severely affected by complex physicochemical properties of the natural membrane. Toehold-mediated and SSB-mediated aptamer displacement exhibited significantly enhanced kinetics, and they completely removed the aptamer quickly to avoid a false signal caused by aptamer internalization. Because of its simplicity, aptamer displacement enabled detection of membrane protein post-translation and improved selection efficiency of cell-SELEX.
Collapse
Affiliation(s)
- Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Xigao Chen
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiaoshu Pan
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Xiaowei Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Hoda Safari Yazd
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Qiong Wu
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China
| | - Juan Li
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences , The Cancer Hospital of the University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences , The Cancer Hospital of the University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
| |
Collapse
|
156
|
Jaekel A, Stegemann P, Saccà B. Manipulating Enzymes Properties with DNA Nanostructures. Molecules 2019; 24:molecules24203694. [PMID: 31615123 PMCID: PMC6832416 DOI: 10.3390/molecules24203694] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids and proteins are two major classes of biopolymers in living systems. Whereas nucleic acids are characterized by robust molecular recognition properties, essential for the reliable storage and transmission of the genetic information, the variability of structures displayed by proteins and their adaptability to the environment make them ideal functional materials. One of the major goals of DNA nanotechnology-and indeed its initial motivation-is to bridge these two worlds in a rational fashion. Combining the predictable base-pairing rule of DNA with chemical conjugation strategies and modern protein engineering methods has enabled the realization of complex DNA-protein architectures with programmable structural features and intriguing functionalities. In this review, we will focus on a special class of biohybrid structures, characterized by one or many enzyme molecules linked to a DNA scaffold with nanometer-scale precision. After an initial survey of the most important methods for coupling DNA oligomers to proteins, we will report the strategies adopted until now for organizing these conjugates in a predictable spatial arrangement. The major focus of this review will be on the consequences of such manipulations on the binding and kinetic properties of single enzymes and enzyme complexes: an interesting aspect of artificial DNA-enzyme hybrids, often reported in the literature, however, not yet entirely understood and whose full comprehension may open the way to new opportunities in protein science.
Collapse
Affiliation(s)
- Andreas Jaekel
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Pierre Stegemann
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| | - Barbara Saccà
- ZMB, University Duisburg-Essen, Universitätstraße 2, 45117 Essen, Germany.
| |
Collapse
|
157
|
Jepsen MDE, Sørensen RS, Maffeo C, Aksimentiev A, Kjems J, Birkedal V. Single molecule analysis of structural fluctuations in DNA nanostructures. NANOSCALE 2019; 11:18475-18482. [PMID: 31577314 PMCID: PMC6825326 DOI: 10.1039/c9nr03826d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA origami is an excellent tool for building complex artificial nanostructures. Functionalization of these structures provides the possibility of precise organization of matter at the nanoscale. In practice, efforts in this endeavour can be impeded by electrostatic repulsion or other dynamics at the molecular scale, resulting in uncompliant local structures. Using single molecule FRET microscopy combined with coarse-grained Brownian dynamics simulations, we investigated here the local structure around the lid of a DNA origami box, which can be opened by specific DNA keys. We found that FRET signals for the closed box depend on buffer ion concentrations and small changes to the DNA structure design. Simulations provided a view of the global and local structure and showed that the distance between the box wall and lid undergoes fluctuations. These results provide methods to vizualise and improve the local structure of three-dimensional DNA origami assemblies and offer guidance for exercising control over placement of chemical groups and ligands.
Collapse
Affiliation(s)
- Mette D E Jepsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
| | | | | | | | | | | |
Collapse
|
158
|
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
| |
Collapse
|
159
|
Jin J, Baker EG, Wood CW, Bath J, Woolfson DN, Turberfield AJ. Peptide Assembly Directed and Quantified Using Megadalton DNA Nanostructures. ACS NANO 2019; 13:9927-9935. [PMID: 31381314 PMCID: PMC6764022 DOI: 10.1021/acsnano.9b04251] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/05/2019] [Indexed: 05/02/2023]
Abstract
In nature, co-assembly of polypeptides, nucleic acids, and polysaccharides is used to create functional supramolecular structures. Here, we show that DNA nanostructures can be used to template interactions between peptides and to enable the quantification of multivalent interactions that would otherwise not be observable. Our functional building blocks are peptide-oligonucleotide conjugates comprising de novo designed dimeric coiled-coil peptides covalently linked to oligonucleotide tags. These conjugates are incorporated in megadalton DNA origami nanostructures and direct nanostructure association through peptide-peptide interactions. Free and bound nanostructures can be counted directly from electron micrographs, allowing estimation of the dissociation constants of the peptides linking them. Results for a single peptide-peptide interaction are consistent with the measured solution-phase free energy; DNA nanostructures displaying multiple peptides allow the effects of polyvalency to be probed. This use of DNA nanostructures as identifiers allows the binding strengths of homo- and heterodimeric peptide combinations to be measured in a single experiment and gives access to dissociation constants that are too low to be quantified by conventional techniques. The work also demonstrates that hybrid biomolecules can be programmed to achieve spatial organization of complex synthetic biomolecular assemblies.
Collapse
Affiliation(s)
- Juan Jin
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Christopher W. Wood
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Jonathan Bath
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- Bristol
BioDesign Institute, BrisSynBio, University
of Bristol Research Centre in Synthetic Biology, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Andrew J. Turberfield
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| |
Collapse
|
160
|
Zhan Y, Ma W, Zhang Y, Mao C, Shao X, Xie X, Lin Y. Diversity of DNA Nanostructures and Applications in Oncotherapy. Biotechnol J 2019; 15:e1900094. [PMID: 31464361 DOI: 10.1002/biot.201900094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/04/2019] [Indexed: 02/05/2023]
Abstract
DNA nanotechnology is a new frontier in the field of tumor biotherapy. Simple DNA strands can be precisely constructed for integration into nanostructures of desired shapes and sizes, with excellent stability and biocompatibility. In this review, an account of the wide range of nanostructures composed of DNA sequences and related advances in oncotherapy using aptamers and chemical drugs is given. Functional ligands, including enzymes, antibodies, and agents, have been appended to DNA frameworks based on their external and internal modifiability. Hence, additional functionalities, such as immunogenicity and enzymatic activity, have been obtained, which extend their practical applications. Importantly, aptamers and drugs can be attached to or incorporated into the wireframes, bringing in highly selective targeting and killing abilities for the modified DNA nanostructures (DNs). In conclusion, distinct DNA sequences, various functional molecules, and different interactions and modifications lead to the diversity of DNs. Currently, one of the leading areas is their applications in tumor therapy. But beyond that, DNs should have much wider application prospects.
Collapse
Affiliation(s)
- Yuxi Zhan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Chenchen Mao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Xueping Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| |
Collapse
|
161
|
Wang W, Yu S, Huang S, Bi S, Han H, Zhang JR, Lu Y, Zhu JJ. Bioapplications of DNA nanotechnology at the solid-liquid interface. Chem Soc Rev 2019; 48:4892-4920. [PMID: 31402369 PMCID: PMC6746594 DOI: 10.1039/c8cs00402a] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA nanotechnology engineered at the solid-liquid interface has advanced our fundamental understanding of DNA hybridization kinetics and facilitated the design of improved biosensing, bioimaging and therapeutic platforms. Three research branches of DNA nanotechnology exist: (i) structural DNA nanotechnology for the construction of various nanoscale patterns; (ii) dynamic DNA nanotechnology for the operation of nanodevices; and (iii) functional DNA nanotechnology for the exploration of new DNA functions. Although the initial stages of DNA nanotechnology research began in aqueous solution, current research efforts have shifted to solid-liquid interfaces. Based on shape and component features, these interfaces can be classified as flat interfaces, nanoparticle interfaces, and soft interfaces of DNA origami and cell membranes. This review briefly discusses the development of DNA nanotechnology. We then highlight the important roles of structural DNA nanotechnology in tailoring the properties of flat interfaces and modifications of nanoparticle interfaces, and extensively review their successful bioapplications. In addition, engineering advances in DNA nanodevices at interfaces for improved biosensing both in vitro and in vivo are presented. The use of DNA nanotechnology as a tool to engineer cell membranes to reveal protein levels and cell behavior is also discussed. Finally, we present challenges and an outlook for this emerging field.
Collapse
Affiliation(s)
- Wenjing Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | | | | | | | | | | | | | | |
Collapse
|
162
|
Kogikoski S, Kubota LT. Electron transfer in superlattice films based on self-assembled DNA-Gold nanoparticle. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.06.091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
163
|
Linear, self-assembled patterns appearing spontaneously as a result of DNA-CTMA lipoplex Langmuir-Blodgett deposition on a solid surface. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.121643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
164
|
Wu T, Liu J, Liu M, Liu S, Zhao S, Tian R, Wei D, Liu Y, Zhao Y, Xiao H, Ding B. A Nanobody‐Conjugated DNA Nanoplatform for Targeted Platinum‐Drug Delivery. Angew Chem Int Ed Engl 2019; 58:14224-14228. [DOI: 10.1002/anie.201909345] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
| | - Manman Liu
- CAS Key Laboratory of Soft Matter Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuai Zhao
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Dengshuai Wei
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Polymer Physics and Chemistry Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Yangzhong Liu
- CAS Key Laboratory of Soft Matter Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Polymer Physics and Chemistry Institute of Chemistry Chinese Academy of Sciences 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 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
165
|
Wu T, Liu J, Liu M, Liu S, Zhao S, Tian R, Wei D, Liu Y, Zhao Y, Xiao H, Ding B. A Nanobody‐Conjugated DNA Nanoplatform for Targeted Platinum‐Drug Delivery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909345] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tiantian Wu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
| | - Manman Liu
- CAS Key Laboratory of Soft Matter Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Shaoli Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Shuai Zhao
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Run Tian
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology 11 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Dengshuai Wei
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Polymer Physics and Chemistry Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Yangzhong Liu
- CAS Key Laboratory of Soft Matter Chemistry University of Science and Technology of China Hefei Anhui 230026 China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences CAS Key Laboratory of Analytical Chemistry for Living Biosystems Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Sciences State Key Laboratory of Polymer Physics and Chemistry Institute of Chemistry Chinese Academy of Sciences 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 BeiYiTiao ZhongGuanCun Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
166
|
Zhang T, Nong J, Alzahrani N, Wang Z, Oh SW, Meier T, Yang DG, Ke Y, Zhong Y, Fu J. Self-Assembly of DNA-Minocycline Complexes by Metal Ions with Controlled Drug Release. ACS APPLIED MATERIALS & INTERFACES 2019; 11:29512-29521. [PMID: 31397552 DOI: 10.1021/acsami.9b08126] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we reported a study of metal ions-assisted assembly of DNA-minocycline (MC) complexes and their potential application for controlling MC release. In the presence of divalent cations of magnesium or calcium ions (M2+), MC, a zwitterionic tetracycline analogue, was found to bind to phosphate groups of nucleic acids via an electrostatic bridge of phosphate (DNA)-M2+-MC. We investigated multiple parameters for affecting the formation of DNA-Mg2+-MC complex, including metal ion concentrations, base composition, DNA length, and single- versus double-stranded DNA. For different nitrogen bases, single-stranded poly(A)20 and poly(T)20 showed a higher MC entrapment efficiency of DNA-Mg2+-MC complex than poly(C)20 and poly(G)20. Single-stranded DNA was also found to form a more stable DNA-Mg2+-MC complex than double-stranded DNA. Between different divalent metal ions, we observed that the formation of DNA-Ca2+-MC complex was more stable and efficient than the formation of DNA-Mg2+-MC complex. Toward drug release, we used agarose gel to encapsulate DNA-Mg2+-MC complexes and monitored MC release. Some DNA-Mg2+-MC complexes could prolong MC release from agarose gel to more than 10 days as compared with the quick release of free MC from agarose gel in less than 1 day. The released MC from DNA-Mg2+-MC complexes retained the anti-inflammatory bioactivity to inhibit nitric oxide production from pro-inflammatory macrophages. The reported study of metal ion-assisted DNA-MC assembly not only increased our understanding of biochemical interactions between tetracycline molecules and nucleic acids but also contributed to the development of a highly tunable drug delivery system to mediate MC release for clinical applications.
Collapse
Affiliation(s)
- Ting Zhang
- Center for Computational and Integrative Biology , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
- Department of Chemistry , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
| | - Jia Nong
- School of Biomedical Engineering, Science and Health Systems , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
| | - Nouf Alzahrani
- Department of Chemistry , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
| | - Zhicheng Wang
- School of Biomedical Engineering, Science and Health Systems , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
| | - Sung Won Oh
- Center for Computational and Integrative Biology , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
| | - Tristan Meier
- Eastern Regional High School , 1401 Laurel Oak Road , Voorhees , New Jersey 08043 , United States
| | - Dong Gyu Yang
- Department of Chemistry , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering , Emory School of Medicine , 1760 Haygood Drive , Atlanta , Georgia 30322 , United States
| | - Yinghui Zhong
- School of Biomedical Engineering, Science and Health Systems , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
| | - Jinglin Fu
- Center for Computational and Integrative Biology , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
- Department of Chemistry , Rutgers University-Camden , 315 Penn Street , Camden , New Jersey 08102 , United States
| |
Collapse
|
167
|
Yang L, Meng L, Song J, Xiao Y, Wang R, Kang H, Han D. Dynamic colloidal nanoparticle assembly triggered by aptamer-receptor interactions on live cell membranes. Chem Sci 2019; 10:7466-7471. [PMID: 31489169 PMCID: PMC6713859 DOI: 10.1039/c9sc02693b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/21/2019] [Indexed: 12/24/2022] Open
Abstract
Cells use dynamic systems such as enzyme cascades and signaling networks to control cellular functions. Synthetic dynamic systems that can be target-responsive have great potential to be applied for biomedical applications but the operation of such dynamic systems in complex cellular environments remains challenging. Here, we engineered an aptamer and DNA displacement reaction-based dynamic system that can transform its nanostructure in response to the epithelial cell adhesion molecule (EpCAM) on live cell membranes. The dynamic system consisted of a core nanoparticle and small satellite nanoparticles. With the modifications of different DNA hairpin strands and swing arm strands partially hybridized with an aptamer that specifically recognizes the EpCAM, the two separated particles can dynamically assemble into a core-satellite assembly by aptamer-receptor interactions on the cell membrane surface. The structural change of the system from separated particles to a core-satellite assembly generated plasmonic coupled hot spots for surface-enhanced Raman scattering (SERS) for sensitively capturing the dynamic structural change of the nanoassembly in the cellular environment. These concepts provide strategies for engineering dynamic nanotechnology systems for biological and biomedical applications in complex biological environments.
Collapse
Affiliation(s)
- Linlin Yang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology , Xiamen University , Xiamen , Fujian 361005 , China .
| | - Lingyan Meng
- College of Chemistry and Chemical Engineering , Xiamen University , Xiamen , Fujian 361005 , China
| | - Jiaying Song
- Pen-Tung Sah Institute of Micro-Nano Science and Technology , Xiamen University , Xiamen , Fujian 361005 , China .
| | - Yue Xiao
- Pen-Tung Sah Institute of Micro-Nano Science and Technology , Xiamen University , Xiamen , Fujian 361005 , China .
| | - Ruowen Wang
- Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai , 200127 , China .
| | - Huaizhi Kang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology , Xiamen University , Xiamen , Fujian 361005 , China . .,Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai , 200127 , China .
| | - Da Han
- Institute of Molecular Medicine , Renji Hospital , School of Medicine , Shanghai Jiao Tong University , Shanghai , 200127 , China .
| |
Collapse
|
168
|
Li W, Lin J, Wang T, Huang P. Photo-triggered Drug Delivery Systems for Neuron-related Applications. Curr Med Chem 2019; 26:1406-1422. [PMID: 29932026 DOI: 10.2174/0929867325666180622121801] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022]
Abstract
The development of materials, chemistry and genetics has created a great number of systems for delivering antibiotics, neuropeptides or other drugs to neurons in neuroscience research, and has also provided important and powerful tools in neuron-related applications. Although these drug delivery systems can facilitate the advancement of neuroscience studies, they still have limited applications due to various drawbacks, such as difficulty in controlling delivery molecules or drugs to the target region, and trouble of releasing them in predictable manners. The combination of optics and drug delivery systems has great potentials to address these issues and deliver molecules or drugs to the nervous system with extraordinary spatiotemporal selectivity triggered by light. In this review, we will introduce the development of photo-triggered drug delivery systems in neuroscience research and their neuron-related applications including regulating neural activities, treating neural diseases and inducing nerve regenerations.
Collapse
Affiliation(s)
- Wei Li
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Laboratory of Evolutionary Theranostics, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China.,School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Jing Lin
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Laboratory of Evolutionary Theranostics, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Tianfu Wang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Laboratory of Evolutionary Theranostics, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Peng Huang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Laboratory of Evolutionary Theranostics, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
169
|
Chang Y, Wu Z, Sun Q, Zhuo Y, Chai Y, Yuan R. Simply Constructed and Highly Efficient Classified Cargo-Discharge DNA Robot: A DNA Walking Nanomachine Platform for Ultrasensitive Multiplexed Sensing. Anal Chem 2019; 91:8123-8128. [DOI: 10.1021/acs.analchem.9b00363] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuanyuan Chang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhongyu Wu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Qianxin Sun
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| |
Collapse
|
170
|
Kizer ME, Linhardt RJ, Chandrasekaran AR, Wang X. A Molecular Hero Suit for In Vitro and In Vivo DNA Nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805386. [PMID: 30985074 DOI: 10.1002/smll.201805386] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Precise control of DNA base pairing has rapidly developed into a field full of diverse nanoscale structures and devices that are capable of automation, performing molecular analyses, mimicking enzymatic cascades, biosensing, and delivering drugs. This DNA-based platform has shown the potential of offering novel therapeutics and biomolecular analysis but will ultimately require clever modification to enrich or achieve the needed "properties" and make it whole. These modifications total what are categorized as the molecular hero suit of DNA nanotechnology. Like a hero, DNA nanostructures have the ability to put on a suit equipped with honing mechanisms, molecular flares, encapsulated cargoes, a protective body armor, and an evasive stealth mode.
Collapse
Affiliation(s)
- Megan E Kizer
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | | | - Xing Wang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| |
Collapse
|
171
|
Zeng J, Fu W, Qi Z, Zhu Q, He H, Huang C, Zuo H, Mao C. Self-Assembly of Microparticles by Supramolecular Homopolymerization of One Component DNA Molecule. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805552. [PMID: 30734479 DOI: 10.1002/smll.201805552] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/18/2019] [Indexed: 06/09/2023]
Abstract
DNA is a superb molecule for self-assembly of nanostructures. Often many DNA strands are required for the assembly of one DNA nanostructure. For lowering the cost of synthesizing DNA strands and facilitating the assembly process, it is highly desirable to use a minimal number of unique strands for potential technological applications. Herein, a strategy is reported to assemble a series of DNA microparticles (DNAµPs) from one component DNA strand. As a demonstration of the application of the resulting DNAµPs, the design and assembled DNAµPs are modified to carry additional single-stranded tails on their surfaces. The modified DNAµPs can either capture other nucleic acids or display CpG motifs to stimulate immune responses.
Collapse
Affiliation(s)
- Jie Zeng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Wenhao Fu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Zhenping Qi
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Qiushuang Zhu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Huawei He
- Biological Science Research Center, Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, 400716, China
| | - Chengzhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Hua Zuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
| | - Chengde Mao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, China
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
172
|
Mehmood S, Khan A, Bilal M, Sohail A, Iqbal H. Aptamer-based biosensors: a novel toolkit for early diagnosis of cancer. MATERIALS TODAY CHEMISTRY 2019. [DOI: 10.1016/j.mtchem.2019.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
173
|
Ortelli S, Malucelli G, Blosi M, Zanoni I, Costa AL. NanoTiO2@DNA complex: a novel eco, durable, fire retardant design strategy for cotton textiles. J Colloid Interface Sci 2019; 546:174-183. [DOI: 10.1016/j.jcis.2019.03.055] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 02/03/2023]
|
174
|
Wang T, Shan J, Wang L, Zhang X, Li G. On the kinetics of catalytic hydrogenation over Pd nanoparticles regulated by various nucleosides. Chem Eng Sci 2019. [DOI: 10.1016/j.ces.2019.02.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
175
|
Kim HW, Rhee YM, Shin SK. Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Phys Chem Chem Phys 2019; 20:21068-21074. [PMID: 30074033 DOI: 10.1039/c8cp03050b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.
Collapse
Affiliation(s)
- Hyun Woo Kim
- Center for Molecular Modeling and Simulation, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
| | | | | |
Collapse
|
176
|
Agarwal S, Franco E. Enzyme-Driven Assembly and Disassembly of Hybrid DNA-RNA Nanotubes. J Am Chem Soc 2019; 141:7831-7841. [PMID: 31042366 DOI: 10.1021/jacs.9b01550] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Living cells have the ability to control the dynamics of responsive assemblies such as the cytoskeleton by temporally activating and deactivating inert precursors. While DNA nanotechnology has demonstrated many synthetic supramolecular assemblies that rival biological ones in size and complexity, dynamic control of their formation is still challenging. Taking inspiration from nature, we developed a DNA-RNA nanotube system whose assembly and disassembly can be temporally controlled at physiological temperature using transcriptional programs. Nanotubes assemble when inert DNA monomers are directly and selectively activated by RNA molecules that become embedded in the structure, producing hybrid DNA-RNA assemblies. The reactions and molecular programs controlling nanotube formation are fueled by enzymes that produce or degrade RNA. We show that the speed of assembly and disassembly of the nanotubes can be controlled by tuning various reaction parameters in the transcriptional programs. We anticipate that these hybrid structures are a starting point to build integrated biological circuits and functional scaffolds inside natural and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid components on demand.
Collapse
Affiliation(s)
- Siddharth Agarwal
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
| | - Elisa Franco
- Department of Mechanical Engineering , University of California at Riverside , Riverside , California 90095 , United States
| |
Collapse
|
177
|
Mathur D, Medintz IL. The Growing Development of DNA Nanostructures for Potential Healthcare-Related Applications. Adv Healthc Mater 2019; 8:e1801546. [PMID: 30843670 PMCID: PMC9285959 DOI: 10.1002/adhm.201801546] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/17/2019] [Indexed: 12/21/2022]
Abstract
DNA self-assembly has proven to be a highly versatile tool for engineering complex and dynamic biocompatible nanostructures from the bottom up with a wide range of potential bioapplications currently being pursued. Primary among these is healthcare, with the goal of developing diagnostic, imaging, and drug delivery devices along with combinatorial theranostic devices. The path to understanding a role for DNA nanotechnology in biomedical sciences is being approached carefully and systematically, starting from analyzing the stability and immune-stimulatory properties of DNA nanostructures in physiological conditions, to estimating their accessibility and application inside cellular and model animal systems. Much remains to be uncovered but the field continues to show promising results toward developing useful biomedical devices. This review discusses some aspects of DNA nanotechnology that makes it a favorable ingredient for creating nanoscale research and biomedical devices and looks at experiments undertaken to determine its stability in vivo. This is presented in conjugation with examples of state-of-the-art developments in biomolecular sensing, imaging, and drug delivery. Finally, some of the major challenges that warrant the attention of the scientific community are highlighted, in order to advance the field into clinically relevant applications.
Collapse
Affiliation(s)
- Divita Mathur
- Center for Bio/Molecular Science and EngineeringU.S. Naval Research Laboratory Code 6910WashingtonDC20375USA
- College of ScienceGeorge Mason UniversityFairfaxVA22030USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and EngineeringU.S. Naval Research Laboratory Code 6907WashingtonDC20375USA
| |
Collapse
|
178
|
Su Y, Li D, Liu B, Xiao M, Wang F, Li L, Zhang X, Pei H. Rational Design of Framework Nucleic Acids for Bioanalytical Applications. Chempluschem 2019; 84:512-523. [DOI: 10.1002/cplu.201900118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Yuwei Su
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Bingyi Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Fei Wang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Xueli Zhang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
- Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| |
Collapse
|
179
|
Sun GY, Du YC, Cui YX, Wang J, Li XY, Tang AN, Kong DM. Terminal Deoxynucleotidyl Transferase-Catalyzed Preparation of pH-Responsive DNA Nanocarriers for Tumor-Targeted Drug Delivery and Therapy. ACS APPLIED MATERIALS & INTERFACES 2019; 11:14684-14692. [PMID: 30942569 DOI: 10.1021/acsami.9b05358] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Developing a highly efficient carrier for tumor-targeted delivery and site-specific release of anticancer drugs is a good way to overcome the side effects of traditional cancer chemotherapy. Benefiting from the nontoxic and biocompatible characteristics, DNA-based drug carriers have attracted increasing attention. Herein, we reported a novel and readily manipulated strategy to construct spherical DNA nanocarriers. In this strategy, terminal deoxynucleotidyl transferase (TdT)-catalyzed DNA extension reaction is used to prepare a thick DNA layer on a gold nanoparticle (AuNP) surface by extending long poly(C) sequences from DNA primers immobilized on AuNPs. The poly(C) extension products can then hybridize with G-rich oligonucleotides to give CG-rich DNA duplexes (for loading anticancer drug doxorubicin, Dox) and multiple AS1411 aptamers. Via synergic recognition of multiple aptamer units to nucleolin proteins, biomarker of malignant tumors, Dox-loaded DNA carrier can be efficiently internalized in cancer cells and achieve burst release of drugs in acidic organelles because of i-motif formation-induced DNA duplex destruction. An as-prepared pH-responsive drug carrier was demonstrated to be promising for highly efficient delivery of Dox and selective killing of cancer cells in both in vitro and in vivo experiments, thus showing a huge potential in anticancer therapy.
Collapse
Affiliation(s)
- Guo-Ying Sun
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Yun-Xi Cui
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Jing Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Xiao-Yu Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| |
Collapse
|
180
|
Green LN, Subramanian HKK, Mardanlou V, Kim J, Hariadi RF, Franco E. Autonomous dynamic control of DNA nanostructure self-assembly. Nat Chem 2019; 11:510-520. [PMID: 31011170 DOI: 10.1038/s41557-019-0251-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
Biological cells routinely reconfigure their shape using dynamic signalling and regulatory networks that direct self-assembly processes in time and space, through molecular components that sense, process and transmit information from the environment. A similar strategy could be used to enable life-like behaviours in synthetic materials. Nucleic acid nanotechnology offers a promising route towards this goal through a variety of sensors, logic and dynamic components and self-assembling structures. Here, by harnessing both dynamic and structural DNA nanotechnology, we demonstrate dynamic control of the self-assembly of DNA nanotubes-a well-known class of programmable DNA nanostructures. Nanotube assembly and disassembly is controlled with minimal synthetic gene systems, including an autonomous molecular oscillator. We use a coarse-grained computational model to capture nanotube length distribution dynamics in response to inputs from nucleic acid circuits. We hope that these results may find use for the development of responsive nucleic acid materials, with potential applications in biomaterials science, nanofabrication and drug delivery.
Collapse
Affiliation(s)
- Leopold N Green
- Bioengineering, University of California, Riverside, CA, USA.,Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Vahid Mardanlou
- Electrical and Computer Engineering, University of California, Riverside, CA, USA
| | - Jongmin Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Rizal F Hariadi
- Department of Physics and the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Elisa Franco
- Mechanical Engineering, University of California, Riverside, CA, USA. .,Samueli School of Engineering, University of California, Los Angeles, CA, USA.
| |
Collapse
|
181
|
Ge Z, Fu J, Liu M, Jiang S, Andreoni A, Zuo X, Liu Y, Yan H, Fan C. Constructing Submonolayer DNA Origami Scaffold on Gold Electrode for Wiring of Redox Enzymatic Cascade Pathways. ACS APPLIED MATERIALS & INTERFACES 2019; 11:13881-13887. [PMID: 30379533 DOI: 10.1021/acsami.8b12374] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advances in biomimetic microelectronics offer a range of patterned assemblies of proteins and cells for in vitro metabolic engineering where coordinated biochemical pathways allow cell metabolism to be characterized and potentially controlled on a chip. To achieve these goals, developing new methods for interfacing biological systems to microelectronic devices has been in urgent demand. Here, we report the assembly of a DNA origami-templated enzymatic cascade (glucose oxidase and horseradish peroxidase) on gold electrodes, where a monolayer of DNA origami is anchored on gold electrodes via Au-S chemistry, to create programmable, electrochemically driven biomimetic device containing both biochemical and electronic components. Upon the posing of a specific electrical potential, substrates/products flow through the enzyme pair and the end product transfers electrons to the electrode. The steady state flux of the distance-dependent enzymatic cascade reactions is translated into a steady state current signal that records the overall enzyme activity. This biological system can be finely tuned by varying the distance between the enzyme pair, which opens new routes to interface microelectronic devices to biological functions.
Collapse
Affiliation(s)
- Zhilei Ge
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Jinglin Fu
- Department of Chemistry, and Center for Computational and Integrative Biology , Rutgers University-Camden , Camden , New Jersey 08102 , United States
| | - Minghui Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Alessio Andreoni
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Xiaolei Zuo
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yan Liu
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Department of Chemistry and Biochemistry , Arizona State University , Tempe , Arizona 85287 , United States
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics , Chinese Academy of Sciences , Shanghai 201800 , China
| |
Collapse
|
182
|
Zhou X, Mandal S, Jiang S, Lin S, Yang J, Liu Y, Whitten DG, Woodbury NW, Yan H. Efficient Long-Range, Directional Energy Transfer through DNA-Templated Dye Aggregates. J Am Chem Soc 2019; 141:8473-8481. [DOI: 10.1021/jacs.9b01548] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xu Zhou
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Sarthak Mandal
- Center for Innovations in Medicine at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- Department of Chemistry, National Institute of Technology, Tiruchirappalli, Tamil Nadu 620015, India
| | - Shuoxing Jiang
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Su Lin
- Center for Innovations in Medicine at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Jianzhong Yang
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Yan Liu
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - David G. Whitten
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Neal W. Woodbury
- Center for Innovations in Medicine at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
183
|
Bui H, Brown CW, Buckhout-White S, Díaz SA, Stewart MH, Susumu K, Oh E, Ancona MG, Goldman ER, Medintz IL. Transducing Protease Activity into DNA Output for Developing Smart Bionanosensors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805384. [PMID: 30803148 DOI: 10.1002/smll.201805384] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/28/2019] [Indexed: 06/09/2023]
Abstract
DNA can process information through sequence-based reorganization but cannot typically receive input information from most biological processes and translate that into DNA compatible language. Coupling DNA to a substrate responsive to biological events can address this limitation. A two-component sensor incorporating a chimeric peptide-DNA substrate is evaluated here as a protease-to-DNA signal convertor which transduces protease activity through DNA gates that discriminate between different input proteases. Acceptor dye-labeled peptide-DNAs are assembled onto semiconductor quantum dot (QD) donors as the input gate. Addition of trypsin or chymotrypsin cleaves their cognate peptide sequence altering the efficiency of Förster resonance energy transfer (FRET) with the QD and frees a DNA output which interacts with a tetrahedral output gate. Downstream output gate rearrangement results in FRET sensitization of a new acceptor dye. Following characterization of component assembly and optimization of individual steps, sensor ability to discriminate between the two proteases is confirmed along with effects from joint interactions where potential for cross-talk is highest. Processing multiple bits of information for a sensing outcome provides more confidence than relying on a single change especially for the discrimination between different targets. Coupling other substrates to DNA that respond similarly could help target other types of enzymes.
Collapse
Affiliation(s)
- Hieu Bui
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- National Research Council, 500 Fifth Street NW, Keck 576, Washington, DC, 20001, USA
| | - Carl W Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- College of Science, George Mason University, Fairfax, VA, 22030, USA
| | - Susan Buckhout-White
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Michael H Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
- KeyW Corporation, Hanover, MD, 21076, USA
| | - Mario G Ancona
- Electronic Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Ellen R Goldman
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| |
Collapse
|
184
|
Wang L, Zhu Z, Li B, Shao F. One-Dimensional Assemblies of a DNA Tetrahedron: Manipulations on the Structural Conformation and Single-Molecule Behaviors. ACS APPLIED BIO MATERIALS 2019; 2:1278-1285. [PMID: 35021375 DOI: 10.1021/acsabm.8b00834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
DNA nanotechnology can construct various nanostructures with diverse functionalities. However, conformation fluctuations due to the structural flexibility of duplex DNA compromise the efficiency to realize the functionality and reactivity of DNA nanostructures. To understand and control the structural deviation from the design represents a major challenge as well as an opportunity for DNA nanotechnology. In the present work, two series of one-dimensional assemblies of DNA tetrahedrons (DTHs) were fabricated and applied to demonstrate the manipulations of conformation dynamics of a one-dimensional DTH assembly by simple variation on linkage styles at single-molecule resolution. A stepwise strategy allows both nanoassembly with a high fidelity in the number and sequence of DTH units to be assembled with a minimum number of linkage sequences. The characterization for these nanostructures with atomic force microscope (AFM) and a solid-state nanopore technique indicates the difference in conformation dynamics and bending stiffness between two analogous nanoassemblies both in the immobilized state on the surface and free state in solution. This work showed the power of fine-tuning the dynamic conformation of the nanostructures and could see the applications in single-molecule biosensing and functionalization of DNA nanostructures.
Collapse
Affiliation(s)
- Liying Wang
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining 314400, People's Republic of China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| | - Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Science, Changchun, Jilin 130022, People's Republic of China
| | - Fangwei Shao
- Zhejiang University-University of Illinois at Urbana-Champaign Institute, Zhejiang University, Haining 314400, People's Republic of China.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371
| |
Collapse
|
185
|
Whitehouse WL, Noble JE, Ryadnov MG, Howorka S. Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures. Bioconjug Chem 2019; 30:1836-1844. [PMID: 30821443 DOI: 10.1021/acs.bioconjchem.9b00036] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanostructures constitute a rapidly advancing tool-set for exploring cell-membrane functions and intracellular sensing or advancing delivery of biomolecular cargo into cells. Chemical conjugation with lipid anchors can mediate binding of DNA nanostructures to synthetic lipid bilayers, yet how such structures interact with biological membranes and internalize cells has not been shown. Here, an archetypal 6-duplex nanobundle is used to investigate how lipid conjugation influences DNA cell binding and internalization kinetics. Cellular interactions of DNA nanobundles modified with one and three cholesterol anchors were assessed using flow cytometry and confocal microscopy. Nuclease digestion was used to distinguish surface-bound DNA, which is nuclease accessible, from internalized DNA. Three cholesterol anchors were found to enhance cellular association by up to 10-fold when compared with unmodified DNA. The bundles were endocytosed efficiently within 24 h. The results can help design controlled DNA binding and trafficking into cells.
Collapse
Affiliation(s)
- William L Whitehouse
- Department of Chemistry, Institute of Structural and Molecular Biology , University College London , London WC1H 0AJ , United Kingdom
| | - James E Noble
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| | - Stefan Howorka
- National Physical Laboratory , Hampton Road , Teddington TW11 0LW , United Kingdom
| |
Collapse
|
186
|
Zhu Z, Wu R, Li B. Exploration of solid-state nanopores in characterizing reaction mixtures generated from a catalytic DNA assembly circuit. Chem Sci 2019; 10:1953-1961. [PMID: 30881624 PMCID: PMC6385554 DOI: 10.1039/c8sc04875d] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022] Open
Abstract
Recent advances have proven that using solid-state nanopores is a promising single molecular technique to enrich the DNA assembly signaling library. Other than using them for distinguishing structures, here we innovatively adapt solid-state nanopores for use in analyzing assembly mixtures, which is usually a tougher task for either traditional characterization techniques or nanopores themselves. A trigger induced DNA step polymerization (SP-CHA), producing three-way-DNA concatemers, is designed as a model. Through counting and integrating the translocation-induced current block when each concatemer passes through a glass conical glass nanopore, we propose an electrophoresis-gel like, but homogeneous, quantitative method that can comprehensively profile the "base-pair distribution" of SP-CHA concatemer mixtures. Due to the higher sensitivity, a number of super long concatemers that were previously difficult to detect via gel electrophoresis are also revealed. These ultra-concatemers, longer than 2 kbp, could provide a much enhanced signal-to-noise ratio for nanopores and are thus believed to be more accurate indicators for the existence of a trigger, which may be of benefit for further applications, such as molecular machines or biosensors.
Collapse
Affiliation(s)
- Zhentong Zhu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
- University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Science , Changchun , Jilin 130022 , P. R. China .
| |
Collapse
|
187
|
He H, Dai J, Dong G, Shi H, Wang F, Qiu Y, Liao R, Zhou C, Guo Y, Xiao D. Self-Replication-Assisted Rapid Preparation of DNA Nanowires at Room Temperature and Its Biosensing Application. Anal Chem 2019; 91:3043-3047. [PMID: 30667217 DOI: 10.1021/acs.analchem.8b05431] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A rapid room-temperature DNA nanowires preparation strategy on the basis of self-replicating catalyzed hairpin assembly (SRCHA) was reported. In this system, three hairpin probes (P1, P2, and P3) were well-designed and partially hybridize to each other, and two split trigger DNA sequences were integrated into P1 and P3, respectively. When the SRCHA was initiated by the trigger DNA, a series of DNA assembly steps based on the toehold-mediated DNA strand displacement were activated, and the Y shaped DNA (P1-P2-P3) was formed. In that case, the two split trigger DNA sequences will come into close-enough proximity to form the trigger DNA replicas, which can initiate the additional SRCHA reaction cycles for DNA nanowire preparation, and eventually a rapid room-temperature DNA nanowires preparation strategy without need of fuel strands was successfully developed. Furthermore, the prepared DNA nanowires have been used to develop a rapid and signal amplified sensing platform for sensitive adenosine triphosphate (ATP) detection.
Collapse
Affiliation(s)
- Hongfei He
- College of Chemistry , Sichuan University , Chengdu 610064 , China.,College of Life Sciences , Sichuan University , Chengdu 610065 , China
| | - Jianyuan Dai
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Guixiu Dong
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Hongli Shi
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Fang Wang
- College of Chemical Engineering , Sichuan University , Chengdu 610065 , China
| | - Yunran Qiu
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Ruoxing Liao
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Cuisong Zhou
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Yong Guo
- College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Dan Xiao
- College of Chemistry , Sichuan University , Chengdu 610064 , China.,College of Chemical Engineering , Sichuan University , Chengdu 610065 , China
| |
Collapse
|
188
|
Hofsäβ R, Ensslen P, Wagenknecht HA. Control of helical chirality in supramolecular chromophore-DNA architectures. Chem Commun (Camb) 2019; 55:1330-1333. [PMID: 30638231 DOI: 10.1039/c8cc08887j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Four different d- and l-configured chromophore-2'-deoxyuridine conjugates were applied to elucidate the helical chirality of their non-covalent assemblies along the d- and l-configured DNA templates by optical spectroscopy. There is no configuration-selective recognition between these nucleosides and the DNA templates. The helicity of the DNA assemblies is either controlled by the configuration of the DNA template or by the nucleoside configuration.
Collapse
Affiliation(s)
- Robert Hofsäβ
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | | | | |
Collapse
|
189
|
Li N, Du M, Tian S, Ji X, He Z. The behavior of a bipedal DNA walker moving on the surface of magnet microparticles and its application in DNA detection. Anal Bioanal Chem 2019; 411:4055-4061. [PMID: 30693369 DOI: 10.1007/s00216-019-01604-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/16/2018] [Accepted: 01/11/2019] [Indexed: 12/26/2022]
Abstract
In this work, a three-dimensional DNA machine based on the isothermal strand-displacement polymerase reaction (ISDPR) has been constructed. The walking behavior of a DNA walker on the obstructive surface of magnetic beads has also been studied by adding different nucleic acid blocks. The "leg" of the DNA walker could hybridize with a hairpin structure DNA named H1 and lead to the opening of it. And the newly exposed stem would interact with a primer. A strand exchange has happened with the assistance of polymerase and dNTPs, so that the "leg" has been displaced and the DNA walker could be pushed to move on the surface. But the nucleic acid blocks could increase steric hindrance and obstruct this process, which is similar to the behavior of human beings walking on craggy paths. Through changing these blocks, such as the structure, the amount, and the length of blocks, the movement of the DNA walker has been controlled. What's more, the results of its application for DNA detection are satisfactory. The limit of detection is 21.6 pM. Also, this method has been successfully applied in complex biological samples. Graphical abstract ᅟ.
Collapse
Affiliation(s)
- Ningxing Li
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Mingyuan Du
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Songbai Tian
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinghu Ji
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhike He
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
| |
Collapse
|
190
|
Huang D, Patel K, Perez-Garrido S, Marshall JF, Palma M. DNA Origami Nanoarrays for Multivalent Investigations of Cancer Cell Spreading with Nanoscale Spatial Resolution and Single-Molecule Control. ACS NANO 2019; 13:728-736. [PMID: 30588806 DOI: 10.1021/acsnano.8b08010] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We present a strategy for the fabrication of biomimetic nanoarrays, based on the use of DNA origami, that permits the multivalent investigation of ligand-receptor molecule interactions in cancer cell spreading, with nanoscale spatial resolution and single-molecule control. We employed DNA origami to control the nanoscale spatial organization of integrin- and epidermal growth factor (EGF)-binding ligands that modulate epidermal cancer cell behavior. By organizing these multivalent DNA nanostructures in nanoarray configurations on nanopatterned surfaces, we demonstrated the cooperative behavior of integrin and EGF ligands in the spreading of human cutaneous melanoma cells: this cooperation was shown to depend on both the number and ratio of the selective ligands employed. Notably, the multivalent biochips we have developed allowed for this cooperative effect to be demonstrated with single-molecule control and nanoscale spatial resolution. By and large, the platform presented here is of general applicability for the study, with molecular control, of different multivalent interactions governing biological processes from the function of cell-surface receptors to protein-ligand binding and pathogen inhibition.
Collapse
Affiliation(s)
- Da Huang
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
| | - Ketan Patel
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - Sandra Perez-Garrido
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - John F Marshall
- Barts Cancer Institute, Cancer Research UK Centre of Excellence , Queen Mary University of London , Charterhouse Square , London EC1M 6BQ , United Kingdom
| | - Matteo Palma
- School of Biological and Chemical Sciences, Materials Research Institute, Institute of Bioengineering , Queen Mary University of London , Mile End Road , London E1 4NS , United Kingdom
| |
Collapse
|
191
|
Zeng C, Lu N, Wen Y, Liu G, Zhang R, Zhang J, Wang F, Liu X, Li Q, Tang Z, Zhang M. Engineering Nanozymes Using DNA for Catalytic Regulation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:1790-1799. [PMID: 30582796 DOI: 10.1021/acsami.8b16075] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
DNA treatment of metal nanoparticles provides a potent tool for tuning their native properties and constructing advanced materials. However, there have been limited studies on interactions between DNA and nanomaterial-based artificial enzymes (nanozymes) to influence their intrinsic peroxidase-like properties. Here, we present the utilization of DNA as a capping ligand to engineer various bio-nanointerfaces for high-precise and adjustable regulation of catalytic behaviors of nanozymes toward the oxidation of substrates. The treatment of stiff double-stranded DNA only induced a negligible enhancement of the catalytic activity of nanozymes, and both coil-like single-stranded DNA and hairpin DNA-capped nanoparticles produced a medium signal increase. Interestingly, hybridization chain reaction (HCR) product-treated nanoparticles showed the highest peroxidase-like activities among four DNA structures. Furthermore, significant parameters that influence HCR process and the modulation of catalysis, such as the concentration of the hairpin DNA, the ionic strength, and the amount of nanozyme, were also systematically investigated. On the basis of HCR amplification and iron oxide (Fe3O4) nanoparticles, we develop a simple, fast, label-free, and sensitive colorimetric strategy for sensing of a Yersinia pestis-relevant DNA sequence with a detection limit as low as 100 pM as well as single nucleotide polymorphism discrimination. These results highlight DNA engineering as a facile strategy to regulate the catalytic activities of nanozymes and understand the interactions between metallic nanoparticles and nucleic acids for biosensing applications.
Collapse
Affiliation(s)
- Caixia Zeng
- School of Materials Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Na Lu
- School of Materials Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Yanli Wen
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology , Shanghai Institute of Measurement and Testing Technology , Shanghai 201203 , China
| | - Gang Liu
- Laboratory of Biometrology, Division of Chemistry and Ionizing Radiation Measurement Technology , Shanghai Institute of Measurement and Testing Technology , Shanghai 201203 , China
| | - Rui Zhang
- School of Materials Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Jiaxing Zhang
- School of Materials Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Zisheng Tang
- Department of Endodontics, Shanghai Ninth People's Hospital, College of Stomatology , Shanghai Jiao Tong University School of Medicine , Shanghai 200011 , China
- National Clinical Research Center of Oral Diseases , Shanghai 200011 , China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology , Shanghai 200011 , China
| | - Min Zhang
- College of Chemistry and Chemical Engineering , Shanghai University of Engineering Science , Shanghai 201620 , China
| |
Collapse
|
192
|
Electrochemiluminecence nanogears aptasensor based on MIL-53(Fe)@CdS for multiplexed detection of kanamycin and neomycin. Biosens Bioelectron 2019; 129:100-106. [PMID: 30685704 DOI: 10.1016/j.bios.2018.12.050] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/19/2018] [Accepted: 12/28/2018] [Indexed: 01/04/2023]
Abstract
A dual gears electrochemiluminecence (ECL) aptasensing strategy for multiple selective determination of kanamycin and neocycin was designed on the basis of the combination of kanamycin and neocycin induced dual gears conversion, the loading platform of metal-organic frameworks (MOFs), surface plasmon resonance (SPR) and ECL resonance energy transfer (ERET) between CdS QDs and AuNPs (or PtNPs). In the absence of target, the dual gears were "off". Then the B1-AuNP (gear B) and aptamer 1-PtNPs acted as signal quenching elements to quench ECL intensity due to ERET process. Upon addition of kanamycin, the aptamer 1-PtNPs were removed from the gear gradually, the ECL was enhanced due to SPR process between AuNPs and CdS QDs. After the incubation of aptamer 2, the dual gears were "off" again and ECL intensity was decreased by ERET process between AuNPs and CdS QDs. In the presence of neomycin, dual gears were "on" again, the ECL signal was enhanced by SPR process between AuNPs and CdS QDs. Under optimal condition, the proposed aptasensor exhibited wide linear ranges of kanamycin (10-10-10-6 M) and neomycin (10-9-10-5 M), and relatively low detection limits to kanamycin (1.7 × 10-11 M) and neomycin (3.5 × 10-10 M). The developed aptasensor realized the multiple ECL detection of kanamycin and neomycin with single luminophore, and was successfully applied to the detection of kanamycin and neomycin in food samples.
Collapse
|
193
|
Yan Y, Li J, Li W, Wang Y, Song W, Bi S. DNA flower-encapsulated horseradish peroxidase with enhanced biocatalytic activity synthesized by an isothermal one-pot method based on rolling circle amplification. NANOSCALE 2018; 10:22456-22465. [PMID: 30478460 DOI: 10.1039/c8nr07294a] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA nanotechnology has been developed to construct a variety of functional two- and three-dimensional structures for versatile applications. Rolling circle amplification (RCA) has become prominent in the assembly of DNA-inorganic composites with hierarchical structures and attractive properties. Here, we demonstrate a one-pot method to directly encapsulate horseradish peroxidase (HRP) in DNA flowers (DFs) during RCA. The growing DNA strands and Mg2PPi crystals lead to the construction of porous DFs, which provide sufficient interaction sites for spontaneously incorporating HRP molecules into DFs with high loading capacity and good stability. Furthermore, in comparison with free HRP, the DNA flower-encapsulated HRP (termed HRP-DFs) demonstrate enhanced enzymatic activity, which can efficiently biocatalyze the H2O2-mediated etching of gold nanorods (AuNRs) to generate distinct color changes since the longitudinal localized surface plasmon resonance (LSPR) frequency of AuNRs is highly sensitive to the changes in the AuNR aspect ratio. Through rationally incorporating the complementary thrombin aptamer sequence into the circular template, the synthesized HRP-DF composites are readily used as amplified labels for visual and colorimetric detection of thrombin with ultrahigh sensitivity and excellent selectivity. Therefore, our proposed strategy for direct encapsulation of enzyme molecules into DNA structures shows considerable potential applications in biosensing, biocatalysis, and point-of-care diagnostics.
Collapse
Affiliation(s)
- Yongcun Yan
- College of Chemistry and Chemical Engineering, Shandong Demonstration Center for Experimental Chemistry Education, Qingdao University, Qingdao 266071, P. R. China.
| | | | | | | | | | | |
Collapse
|
194
|
Chidchob P, Offenbartl-Stiegert D, McCarthy D, Luo X, Li J, Howorka S, Sleiman HF. Spatial Presentation of Cholesterol Units on a DNA Cube as a Determinant of Membrane Protein-Mimicking Functions. J Am Chem Soc 2018; 141:1100-1108. [DOI: 10.1021/jacs.8b11898] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Pongphak Chidchob
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Daniel Offenbartl-Stiegert
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Dillon McCarthy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Xin Luo
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
195
|
Li Y, Yang S, Zheng J, Zou Z, Yang R, Tan W. "Trojan Horse" DNA Nanostructure for Personalized Theranostics: Can It Knock on the Door of Preclinical Practice? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15028-15044. [PMID: 30295491 DOI: 10.1021/acs.langmuir.8b02008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanotheranostics, combing diagnostic and therapeutic components in an all-in-one nanomaterial, possess exciting potentials for precision nanomedicine. However, a major obstacle for current nanotheranostics to enter preclinical and/or clinical trials is the intrinsic toxicities of these nanomaterials. As an emerging biomaterial, the bioinspired DNA nanostructure shows advantages for constructing better nanotheranostics due to its excellent features, including native biocompatibility, full programmability, and ready accessibility. In this feature article, we highlight recent advances in the design of DNA-nanostructure-based diagnostics and/or therapeutics capable of specifically responding to biological stimuli in a dynamic way, with a particular focus on the design mechanism, responsive performance, and potential for preclinical and/or clinical trials in personalized theranostics.
Collapse
Affiliation(s)
- Yuan Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Sheng Yang
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Jing Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Zhen Zou
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Ronghua Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
- School of Chemistry and Biological Engineering , Changsha University of Science and Technology , Changsha 410004 , P. R. China
| | - Weihong Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| |
Collapse
|
196
|
Sekine T, Kanayama N, Ozasa K, Nyu T, Hayashi T, Maeda M. Stochastic Binding Process of Blunt-End Stacking of DNA Molecules Observed by Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15078-15083. [PMID: 30179510 DOI: 10.1021/acs.langmuir.8b02224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Hydrophobic attraction is often a physical origin of nonspecific and irreversible (uncontrollable) processes observed for colloidal and biological systems, such as aggregation, precipitation, and fouling with biomolecules. On the contrary, blunt-end stacking of complementary DNA duplex chain pairs, which is also mainly driven by hydrophobic interaction, is specific and stable enough to lead to self-assemblies of DNA nanostructures. To understand the reason behind these contradicting phenomena, we measured forces operating between two self-assembled monolayers of duplexed DNA molecules with blunt ends (DNA-SAMs) and analyzed their statistics. We found the high specificity and stability of blunt-end stacking that resulted in the high resemblance between the interaction forces measured on approaching and retracting. The other finding is on the stochastic formation process of blunt-end stacking, which appeared as a significant fluctuation of the interaction forces at separations smaller than 2.5 nm. Based on these results, we discuss the underlying mechanism of the specificity and stability of blunt-end stacking.
Collapse
Affiliation(s)
- Taito Sekine
- Department of Materials Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8502 , Japan
| | - Naoki Kanayama
- Graduate School of Medicine, Science and Technology , Shinshu University , 4-7-1 Wakasato , Nagano , Nagano 380-8553 , Japan
| | | | - Takashi Nyu
- Department of Materials Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8502 , Japan
| | - Tomohiro Hayashi
- Department of Materials Science and Engineering, School of Materials and Chemical Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8502 , Japan
| | | |
Collapse
|
197
|
Xia X, Wang H, Yang H, Deng S, Deng R, Dong Y, He Q. Dual-Terminal Stemmed Aptamer Beacon for Label-Free Detection of Aflatoxin B 1 in Broad Bean Paste and Peanut Oil via Aggregation-Induced Emission. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:12431-12438. [PMID: 30387615 DOI: 10.1021/acs.jafc.8b05217] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aflatoxin B1 (AFB1) contamination ranks as one of the most critical food safety issues, and assays for its on-site monitoring are highly demanded. Herein, we propose a label-free, one-tube, homogeneous, and cheap AFB1 assay based on a finely tunable dual-terminal stemmed aptamer beacon (DS aptamer beacon) and aggregation-induced emission (AIE) effects. The DS aptamer beacon structure could provide terminal protection of the aptamer probe against exonuclease I and confer specific and quick response to target AFB1. In comparison to the conventional molecule beacon structure, the stability of the DS aptamer beacon could be finely tuned by adjusting its two terminal stems, allowing for elaborately optimizing probe affinity and selectivity. By the utilization of an AIE-active fluorophore, which would be lighted up by aggregating to negatively charged DNA, AFB1 could be determined in a label-free manner. The proposed method could quantify AFB1 in one test tube using two unlabeled DNA strands. It has been successfully applied for analyzing AFB1 in peanut oil and broad bean sauce, with total recoveries ranging from 92.75 to 118.70%. Thus, the DS aptamer beacon-based assay could potentially facilitate real-time monitoring and controlling of AFB1 pollution.
Collapse
Affiliation(s)
- Xuhan Xia
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Haibo Wang
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Hao Yang
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Sha Deng
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Ruijie Deng
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Yi Dong
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| | - Qiang He
- College of Light Industry, Textile and Food Engineering, Healthy Food Evaluation Research Center, and Key Laboratory of Food Science and Technology of Ministry of Education of Sichuan Province , Sichuan University , Chengdu , Sichuan 610065 , People's Republic of China
| |
Collapse
|
198
|
Fang L, Liu D, Wang Y, Li Y, Song L, Gong M, Li Y, Deng Z. Nanosecond-Laser-Based Charge Transfer Plasmon Engineering of Solution-Assembled Nanodimers. NANO LETTERS 2018; 18:7014-7020. [PMID: 30281316 DOI: 10.1021/acs.nanolett.8b02965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ability to re-engineer self-assembled functional structures with nanometer accuracy through solution-processing techniques represents a big challenge in nanotechnology. Herein we demonstrate that Ag+-soldered nanodimers with a steric confinement coating of silica can be harnessed to realize an in-solution nanosecond laser reshaping to form interparticle conductive pathway with finely controlled conductance. The high structural purity of the nanodimers, the rigid silica coating, and the uniform (but still adjustable) sub-1-nm interparticle gap together determine the success of the laser reshaping process. This method is applicable to DNA-assembled nanodimers, and thus promises DNA-based programming toward higher structural complexity. The resulting structures exhibit highly tunable charge transfer plasmons at visible and near-infrared frequencies dictated by the fluence of the laser pulses. Our work provides an in-solution, rapid, and nonperturbative route to realize charge transfer plasmonic coupling along prescribed paths defined by self-assembly, conferring great opportunities for functional metamaterials in the context of chemical, biological, and nanophotonic applications. The ability to continuously control a subnm interparticle gap and the nanomeric width of a conductive junction also provides a platform to investigate modern plasmonic theories involving quantum and nonlocal effects.
Collapse
Affiliation(s)
- Lingling Fang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Dilong Liu
- Key Lab of Materials Physics, Institute of Solid State Physics , Chinese Academy of Sciences , Hefei , Anhui 230031 , China
| | - Yueliang Wang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Yanjuan Li
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Lei Song
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Ming Gong
- Engineering and Materials Science Experiment Center , University of Science and Technology of China , Hefei , Anhui 230027 , China
| | - Yue Li
- Key Lab of Materials Physics, Institute of Solid State Physics , Chinese Academy of Sciences , Hefei , Anhui 230031 , China
| | - Zhaoxiang Deng
- CAS Key Laboratory of Soft Matter Chemistry, Department of Chemistry , University of Science and Technology of China , Hefei , Anhui 230026 , China
| |
Collapse
|
199
|
Qi X, Zhang F, Su Z, Jiang S, Han D, Ding B, Liu Y, Chiu W, Yin P, Yan H. Programming molecular topologies from single-stranded nucleic acids. Nat Commun 2018; 9:4579. [PMID: 30389935 PMCID: PMC6214983 DOI: 10.1038/s41467-018-07039-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/12/2018] [Indexed: 12/03/2022] Open
Abstract
Molecular knots represent one of the most extraordinary topological structures in biological polymers. Creating highly knotted nanostructures with well-defined and sophisticated geometries and topologies remains challenging. Here, we demonstrate a general strategy to design and construct highly knotted nucleic acid nanostructures, each weaved from a single-stranded DNA or RNA chain by hierarchical folding in a prescribed order. Sets of DNA and RNA knots of two- or three-dimensional shapes have been designed and constructed (ranging from 1700 to 7500 nucleotides), and they exhibit complex topological features, with high crossing numbers (from 9 up to 57). These single-stranded DNA/RNA knots can be replicated and amplified enzymatically in vitro and in vivo. This work establishes a general platform for constructing nucleic acid nanostructures with complex molecular topologies.
Collapse
Affiliation(s)
- Xiaodong Qi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Fei Zhang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
| | - Zhaoming Su
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Shuoxing Jiang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Dongran Han
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, China, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Liu
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA
| | - Wah Chiu
- Department of Bioengineering and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, 85287, USA.
| |
Collapse
|
200
|
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.
Collapse
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
| |
Collapse
|