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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Zhu X, Yan X, Yang S, Wang Y, Wang S, Tian Y. DNA-Mediated Assembly of Carbon Nanomaterials. Chempluschem 2022; 87:e202200089. [PMID: 35589623 DOI: 10.1002/cplu.202200089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/26/2022] [Indexed: 02/18/2024]
Abstract
Carbon nanomaterials (CNMs) have attracted extensive attentions on account of their superior electrical, mechanical, optical, and biological properties. However, the dimensional limit and irregular arrangement have hampered their further application. It is necessary to find an easy, efficient and controllable way to assemble CNMs into well-ordered array. DNA nanotechnology, owning to the advantages of precise programmability, highly structural predictability and spatial addressability, has been widely applied in the assembly of CNMs. Summarizing the progress and achievements in this field will be of great value to related studies. Herein, based on the different dimensions of CNMs containing 0-dimensional (0D) carbon dots (CDs), fullerenes, 1-dimensional (1D) carbon nanotubes (CNTs) and 2-dimensional (2D) graphene, we introduced the conjugation strategies between DNA and CNMs, their different assembly methods and their applications. In addition, we also discuss the existing challenges and future opportunities in the field.
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Affiliation(s)
- Xurong Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Xuehui Yan
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Sichang Yang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Yong Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
| | - Shuang Wang
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, 518055, Shenzhen, P. R. China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210023, Nanjing, P. R. China
- Shenzhen Research Institute, Nanjing University, 518000, Shenzhen, P. R. China
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Rahman M, Boggs Z, Neff D, Norton M. The Sapphire (0001) Surface: A Transparent and Ultraflat Substrate for DNA Nanostructure Imaging. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15014-15020. [PMID: 30110549 DOI: 10.1021/acs.langmuir.8b01851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mica is the current substrate of choice for DNA nanostructure imaging, mainly due to its atomically flat surface. However, these mica substrates are often not optically clear. In this work, sapphire has been evaluated as an alternative substrate, with potential to enable parallel optical and AFM studies. Well known for its thermal and chemical properties, sapphire is a hard ionic material with excellent optical properties. Because sapphire lacks the excellent basal cleavage properties of the sheet silicate mica, a process to anneal it at high temperature in water vapor was developed to achieve near atomically smooth (average roughness = 0.141 nm) terraces. AFM imaging was used to determine the dimensions of these terraces and to characterize the morphology of the DNA nanostructures, revealing that their structures were preserved, indicating that annealed c-plane cut (0001) sapphire is a promising substitute for mica as a flat and transparent substrate for DNA nanostructure studies.
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Affiliation(s)
- Masudur Rahman
- Department of Chemistry , Marshall University , Huntington , West Virginia 25755 , United States
| | - Zachary Boggs
- Department of Chemistry , Marshall University , Huntington , West Virginia 25755 , United States
| | - David Neff
- Department of Chemistry , Marshall University , Huntington , West Virginia 25755 , United States
| | - Michael Norton
- Department of Chemistry , Marshall University , Huntington , West Virginia 25755 , United States
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Ricardo KB, Liu H. Graphene-Encapsulated DNA Nanostructure: Preservation of Topographic Features at High Temperature and Site-Specific Oxidation of Graphene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:15045-15054. [PMID: 30336059 DOI: 10.1021/acs.langmuir.8b02129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This paper reports the effect of graphene encapsulation on the thermal stability of DNA nanostructures and the thermal oxidation of graphene in the presence of DNA nanostructures. Triangular-shaped DNA nanostructures were deposited onto a Si/SiO2 substrate and covered with single-layer graphene. The apparent height of the DNA nanostructure significantly decreased upon thermal annealing at 250 °C and higher temperatures. The topographical features of the DNA nanostructure, as measured by atomic force microscopy (AFM), disappeared after annealing at 300 °C for 5 h but reappeared after 23 h. In contrast, in the absence of a graphene coating, the topographical features of DNA nanostructure disappeared after heating at 300 °C for 45 min. After heating at 300 °C for 29 h, oxidation produced nanometer-sized holes on graphene, some of which were triangular and spatially overlapped with DNA nanostructures. These results suggest that the inorganic residues produced by the decomposition of DNA nanostructures enhance the oxidation of graphene in a site-specific manner.
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Affiliation(s)
- Karen B Ricardo
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Haitao Liu
- School of Chemical and Environmental Engineering , Shanghai Institute of Technology , 100 Haiquan Road , Shanghai 201418 , P.R. China
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
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Aptamer Functionalized DNA Hydrogel for Wise-Stage Controlled Protein Release. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8101941] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With the simple functionalization method and good biocompatibility, an aptamer-integrated DNA hydrogel is used as the protein delivery system with an adjustable release rate and time by using complementary sequences (CSs) as the biomolecular trigger. The aptamer-functionalized DNA hydrogel was prepared via a one-pot self-assembly process from two kinds of DNA building blocks (X-shaped and L-shaped DNA units) and a single-stranded aptamer. The gelling process was achieved under physiological conditions within one minute. In the absence of the triggering CSs, the aptamer grafted in the hydrogel exhibited a stable state for protein-specific capture. While hybridizing with the triggering CSs, the aptamer is turned into a double-stranded structure, resulting in the fast dissociation of protein with a wise-stage controlled release program. Further, the DNA hydrogel with excellent cytocompatibility has been successfully applied to human serum, forming a complex matrix. The whole process of protein capture and release were biocompatible and could not refer to any adverse factor of the protein or cells. Thus, the aptamer-functionalized DNA hydrogel will be a good candidate for controlled protein delivery.
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Sidhu A, Ristic D, Sánchez H, Wyman C. The Recombination Mediator BRCA2: Architectural Plasticity of Recombination Intermediates Revealed by Single-Molecule Imaging (SFM/TIRF). Methods Enzymol 2018; 600:347-374. [DOI: 10.1016/bs.mie.2017.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Rahman M, Day BS, Neff D, Norton ML. Origami Arrays as Substrates for the Determination of Reaction Kinetics Using High-Speed Atomic Force Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7389-7392. [PMID: 28679055 DOI: 10.1021/acs.langmuir.7b01556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s. When the the data was fitted with an adsorption-limited kinetic model, a forward rate constant of 5.03 × 105 s-1 was found.
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Affiliation(s)
- Masudur Rahman
- Department of Chemistry, Marshall University , Huntington, West Virginia 25755, United States
| | - B Scott Day
- Department of Chemistry, Marshall University , Huntington, West Virginia 25755, United States
| | - David Neff
- Department of Chemistry, Marshall University , Huntington, West Virginia 25755, United States
| | - Michael L Norton
- Department of Chemistry, Marshall University , Huntington, West Virginia 25755, United States
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