1
|
Wang K, Deng P, Lin H, Sun W, Shen J. DNA-Based Conductors: From Materials Design to Ultra-Scaled Electronics. SMALL METHODS 2024:e2400694. [PMID: 39049716 DOI: 10.1002/smtd.202400694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/04/2024] [Indexed: 07/27/2024]
Abstract
Photolithography has been the foundational fabrication paradigm in current high-performance electronics. However, due to the limitation in fabrication resolution, scaling beyond a 20-nm critical dimension for metal conductors presents a significant challenge for photolithography. Structural DNA nanotechnology emerges as a promising alternative to photolithography, allowing for the site-specific assembly of nano-materials at single-molecule resolution. Substantial progresses have been achieved in the ultra-scaled DNA-based conductors, exhibiting novel transport characteristics and small critical dimensions. This review highlights the structure-transport property relationship for various DNA-based conductors and their potential applications in quantum /semiconductor electronics, going beyond the conventional scope focusing mainly on the shape diversity of DNA-templated metals. Different material synthesis methods and their morphological impacts on the conductivities are discussed in detail, with particular emphasis on the conducting mechanisms, such as insulating, metallic conducting, quantum tunneling, and superconducting. Furthermore, the ionic gating effect of self-assembled DNA structures in electrolyte solutions is examined. This review also suggests potential solutions to address current challenges in DNA-based conductors, encouraging multi-disciplinary collaborations for the future development of this exciting area.
Collapse
Affiliation(s)
- Kexin Wang
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Pu Deng
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Huili Lin
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
- Zhangjiang Laboratory, Shanghai, 201210, China
| | - Jie Shen
- School of Materials Science and Engineering, Peking University, Beijing, 100871, China
| |
Collapse
|
2
|
Wang S, Lin PA, DeLuca M, Zauscher S, Arya G, Ke Y. Controlling Silicification on DNA Origami with Polynucleotide Brushes. J Am Chem Soc 2024; 146:358-367. [PMID: 38117542 PMCID: PMC10785815 DOI: 10.1021/jacs.3c09310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.
Collapse
Affiliation(s)
- Shuang Wang
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Po-An Lin
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Marcello DeLuca
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Stefan Zauscher
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
3
|
Martynenko IV, Erber E, Ruider V, Dass M, Posnjak G, Yin X, Altpeter P, Liedl T. Site-directed placement of three-dimensional DNA origami. NATURE NANOTECHNOLOGY 2023; 18:1456-1462. [PMID: 37640908 PMCID: PMC7616159 DOI: 10.1038/s41565-023-01487-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023]
Abstract
The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.
Collapse
Affiliation(s)
- Irina V Martynenko
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| | - Elisabeth Erber
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Veronika Ruider
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Mihir Dass
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Gregor Posnjak
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Xin Yin
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Philipp Altpeter
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität, Munich, Germany.
| |
Collapse
|
4
|
Mao D, Liu L, Zhang C, Liu H, Mao C. Molecular Lithography on Silicon Wafers Guided by Porous, Extended Arrays of Small DNA Tiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11782-11787. [PMID: 37562139 DOI: 10.1021/acs.langmuir.3c01422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Tile-based DNA self-assembly is a cost-effective fabrication method for large-scale nanopatterns. Herein, we report a protocol to directly assemble DNA 2D arrays on silicon wafers and then use the DNA nanostructures as molds to fabricate the corresponding nanostructures on the silicon wafers by hydrogen fluoride (HF) etching. Similar HF etching has been used with robust large DNA origami structures as templates. This work demonstrates that DNA nanostructures assembled from small tiles are sufficiently stable for this process. The resulting feature size (∼8.6 nm) approaches the sizes of e-beam lithography. While the reported method is parallel and inexpensive, e-beam lithography is a serial method and is expensive. We expect that this method will be very useful for preparing fine nanopatterns in large areas.
Collapse
Affiliation(s)
- Dake Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Longfei Liu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
5
|
Pothineni BK, Grundmeier G, Keller A. Cation-dependent assembly of hexagonal DNA origami lattices on SiO 2 surfaces. NANOSCALE 2023; 15:12894-12906. [PMID: 37462427 DOI: 10.1039/d3nr02926c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.
Collapse
Affiliation(s)
- Bhanu Kiran Pothineni
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| |
Collapse
|
6
|
Tarannum T, Ahmed S. Recent development in antiviral surfaces: Impact of topography and environmental conditions. Heliyon 2023; 9:e16698. [PMID: 37260884 PMCID: PMC10227326 DOI: 10.1016/j.heliyon.2023.e16698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023] Open
Abstract
The transmission of viruses is largely dependent on contact with contaminated virus-laden communal surfaces. While frequent surface disinfection and antiviral coating techniques are put forth by researchers as a plan of action to tackle transmission in dire situations like the Covid-19 pandemic caused by SARS-CoV-2 virus, these procedures are often laborious, time-consuming, cost-intensive, and toxic. Hence, surface topography-mediated antiviral surfaces have been gaining more attention in recent times. Although bioinspired hydrophobic antibacterial nanopatterned surfaces mimicking the natural sources is a very prevalent and successful strategy, the antiviral prospect of these surfaces is yet to be explored. Few recent studies have explored the potential of nanopatterned antiviral surfaces. In this review, we highlighted surface properties that have an impact on virus attachment and persistence, particularly focusing and emphasizing on the prospect of the nanotextured surface with enhanced properties to be used as antiviral surface. In addition, recent developments in surface nanopatterning techniques depending on the nano-scaled dimensions have been discussed. The impacts of environments and surface topology on virus inactivation have also been reviewed.
Collapse
|
7
|
Kabusure KM, Piskunen P, Yang J, Linko V, Hakala TK. Raman enhancement in bowtie-shaped aperture-particle hybrid nanostructures fabricated with DNA-assisted lithography. NANOSCALE 2023; 15:8589-8596. [PMID: 37097163 DOI: 10.1039/d3nr00616f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We report on efficient surface-enhanced Raman spectroscopy (SERS) supporting substrates, which are based on deoxyribonucleic acid (DNA)-assisted lithography (DALI) and a layered configuration of materials. In detail, we used nanoscopic DNA origami bowtie templates to form hybrid nanostructures consisting of aligned silver bowtie-shaped particles and apertures of similar shape in a silver film. We hypothesized that this particular geometry could facilitate a four-fold advantage in Raman enhancement compared to common particle-based SERS substrates, and further, we verified these hypotheses experimentally and by finite difference time domain simulations. In summary, our DALI-fabricated hybrid structures suppress the background emission, allow emission predominantly from the areas of high field enhancement, and support additional resonances associated with the nanoscopic apertures. Finally, these nanoapertures also enhance the fields associated with the resonances of the underlying bowtie particles. The versatility and parallel nature of our DNA origami-based nanofabrication scheme and all of the above-mentioned features of the hybrid structures therefore make our optically resonant substrates attractive for various SERS-based applications.
Collapse
Affiliation(s)
- Kabusure M Kabusure
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| | - Jiaqi Yang
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia.
| | - Tommi K Hakala
- Center for Photonics Sciences, University of Eastern Finland, Yliopistokatu 2, P.O. Box 111, FI-80101, Joensuu, Finland.
| |
Collapse
|
8
|
Manuguri S, Nguyen MK, Loo J, Natarajan AK, Kuzyk A. Advancing the Utility of DNA Origami Technique through Enhanced Stability of DNA-Origami-Based Assemblies. Bioconjug Chem 2022; 34:6-17. [PMID: 35984467 PMCID: PMC9853507 DOI: 10.1021/acs.bioconjchem.2c00311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Since its discovery in 2006, the DNA origami technique has revolutionized bottom-up nanofabrication. This technique is simple yet versatile and enables the fabrication of nanostructures of almost arbitrary shapes. Furthermore, due to their intrinsic addressability, DNA origami structures can serve as templates for the arrangement of various nanoscale components (small molecules, proteins, nanoparticles, etc.) with controlled stoichiometry and nanometer-scale precision, which is often beyond the reach of other nanofabrication techniques. Despite the multiple benefits of the DNA origami technique, its applicability is often restricted by the limited stability in application-specific conditions. This Review provides an overview of the strategies that have been developed to improve the stability of DNA-origami-based assemblies for potential biomedical, nanofabrication, and other applications.
Collapse
Affiliation(s)
- Sesha Manuguri
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet St., Dist. 10, Ho Chi Minh
City 70000, Vietnam,Vietnam
National University Ho Chi Minh City, Linh Trung Ward, Thu Duc Dist., Ho Chi Minh
City 756100, Vietnam
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Ashwin Karthick Natarajan
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland,
| |
Collapse
|
9
|
Kabusure KM, Piskunen P, Yang J, Kataja M, Chacha M, Ojasalo S, Shen B, Hakala TK, Linko V. Optical characterization of DNA origami-shaped silver nanoparticles created through biotemplated lithography. NANOSCALE 2022; 14:9648-9654. [PMID: 35718875 DOI: 10.1039/d1nr06256e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Here, we study optically resonant substrates fabricated using the previously reported BLIN (biotemplated lithography of inorganic nanostructures) technique with single triangle and bowtie DNA origami as templates. We present the first optical characterization of BLIN-fabricated origami-shaped silver nanoparticle patterns on glass surfaces, comprising optical transmission measurements and surface-enhanced Raman spectroscopy. The formed nanoparticle patterns are examined by optical transmission measurements and used for surface enhanced Raman spectroscopy (SERS) of Rhodamine 6G (R6G) dye molecules. Polarization-resolved simulations reveal that the higher SERS enhancement observed for the bowties is primarily due to spectral overlap of the optical resonances with the Raman transitions of R6G. The results manifest the applicability of the BLIN method and substantiate its potential in parallel and high-throughput substrate manufacturing with engineered optical properties. While the results demonstrate the crucial role of the formed nanogaps for SERS, the DNA origami may enable even more complex nanopatterns for various optical applications.
Collapse
Affiliation(s)
- Kabusure M Kabusure
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Jiaqi Yang
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mikko Kataja
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Mwita Chacha
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
| | - Boxuan Shen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Tommi K Hakala
- Department of Physics and Mathematics, University of Eastern Finland, Yliopistokatu 2, P.O Box 111, FI-80101, Joensuu, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland.
- LIBER Center of Excellence, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| |
Collapse
|
10
|
Zhou Y, Deng J, Zhang Y, Li C, Wei Z, Shen J, Li J, Wang F, Han B, Chen D, Fan C, Zhang H, Liu K, Wei Y. Engineering DNA-Guided Hydroxyapatite Bulk Materials with High Stiffness and Outstanding Antimicrobial Ability for Dental Inlay Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202180. [PMID: 35488765 DOI: 10.1002/adma.202202180] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Programmable base pair interactions at the nanoscale make DNA an attractive scaffold for forming hydroxyapatite (HAP) nanostructures. However, engineering macroscale HAP mineralization guided by DNA molecules remains challenging. To overcome this issue, a facile strategy is developed for the fabrication of ultrastiff DNA-HAP bulk composites. The electrostatic complexation of DNA and a surfactant with a quaternary ammonium salt group enables the formation of long-range ordered scaffolds using electrospinning. The growth of 1D and 2D HAP minerals is thus realized by this DNA template at a macroscale. Remarkably, the as-prepared DNA-HAP composites exhibit an ultrahigh Young's modulus of ≈25 GPa, which is comparable to natural HAP and superior to most artificial mineralized composites. Furthermore, a new type of dental inlay with outstanding antibacterial properties is developed using the stiff DNA-HAP. The encapsulated quaternary ammonium group within the dense HAP endows the composite with long-lasting and local antibacterial activity. Therefore, this new type of super-stiff biomaterial holds great potential for oral prosthetic applications.
Collapse
Affiliation(s)
- Yusai Zhou
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jingjing Deng
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Cong Li
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Institute of Translational Medicine and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zheng Wei
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Institute of Translational Medicine and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Bing Han
- Department of Orthodontics, Cranial-Facial Growth and Development Center, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Dong Chen
- Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, 310027, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Centre for Transformative Molecules, Institute of Translational Medicine and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun, Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yan Wei
- Department of Geriatric Dentistry, Beijing Laboratory of Biomedical Materials, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| |
Collapse
|
11
|
Chen Y, Yang C, Zhu Z, Sun W. Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays. Nat Commun 2022; 13:2707. [PMID: 35577805 PMCID: PMC9110747 DOI: 10.1038/s41467-022-30441-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 04/25/2022] [Indexed: 11/17/2022] Open
Abstract
While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.
Collapse
Affiliation(s)
- Yahong Chen
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Wei Sun
- Key Laboratory for the Physics and Chemistry of Nanodevices and Center for Carbon-Based Electronics, School of Electronics, Peking University, Beijing, 100871, China.
| |
Collapse
|
12
|
Heuer-Jungemann A, Linko V. Engineering Inorganic Materials with DNA Nanostructures. ACS CENTRAL SCIENCE 2021; 7:1969-1979. [PMID: 34963890 PMCID: PMC8704036 DOI: 10.1021/acscentsci.1c01272] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 05/25/2023]
Abstract
Nucleic acid nanotechnology lays a foundation for the user-friendly design and synthesis of DNA frameworks of any desirable shape with extreme accuracy and addressability. Undoubtedly, such features make these structures ideal modules for positioning and organizing molecules and molecular components into complex assemblies. One of the emerging concepts in the field is to create inorganic and hybrid materials through programmable DNA templates. Here, we discuss the challenges and perspectives of such DNA nanostructure-driven materials science engineering and provide insights into the subject by introducing various DNA-based fabrication techniques including metallization, mineralization, lithography, casting, and hierarchical self-assembly of metal nanoparticles.
Collapse
Affiliation(s)
- Amelie Heuer-Jungemann
- Max
Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Center
for Nanoscience, Ludwig-Maximilians University, 80539 Munich, Germany
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| |
Collapse
|
13
|
Zhao Y, Zhang C, Yang L, Xu X, Xu R, Ma Q, Tang Q, Yang Y, Han D. Programmable and Site-Specific Patterning on DNA Origami Templates with Heterogeneous Condensation of Silver and Silica. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2103877. [PMID: 34636168 DOI: 10.1002/smll.202103877] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/15/2021] [Indexed: 06/13/2023]
Abstract
DNA origami has been widely used as a modular platform for condensation of functional molecules to assemble optical, electronic, and biological components. However, the heterogeneous condensation with greater diversities in chemical composition templated with DNA origami is still challenging. Herein, a programmable deposition method is developed to precisely condense silver-silica nanohybrids on DNA origami templates. First, the site-specific metallization of Ag is achieved by thiol group-initiated silver reduction at the designed areas of DNA origami. Next, cysteamine is used to selectively modify the condensed Ag surface with positively charged amino groups for creating an electronically different environment for site-specific placement of silica by a modified Stöber method. Using these strategies, customized patterning of both silver and silica on tubular and rectangular DNA origami nanostructures is successfully achieved with nanoscale spatial resolution. These findings will greatly facilitate the development of DNA nanotechnology-based bottom-up nanofabrication.
Collapse
Affiliation(s)
- Yumeng Zhao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Xuemei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Qian Tang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Yang Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine and State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200120, P. R. China
| |
Collapse
|
14
|
Xin Y, Shen B, Kostiainen MA, Grundmeier G, Castro M, Linko V, Keller A. Scaling Up DNA Origami Lattice Assembly. Chemistry 2021; 27:8564-8571. [PMID: 33780583 PMCID: PMC8252642 DOI: 10.1002/chem.202100784] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 12/31/2022]
Abstract
The surface-assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica-electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot-decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2 , this large-scale nanopatterning technique holds great promise for the fabrication of functional surfaces.
Collapse
Affiliation(s)
- Yang Xin
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Boxuan Shen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Mauri A. Kostiainen
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Guido Grundmeier
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| | - Mario Castro
- Grupo Interdisciplinar de Sistemas Complejos and Instituto de Investigación TecnológicaUniversidad Pontificia Comillas de MadridMadrid28015Spain
| | - Veikko Linko
- Biohybrid MaterialsDepartment of Bioproducts and BiosystemsAalto UniversityP. O. Box 1610000076AaltoFinland
| | - Adrian Keller
- Technical and Macromolecular ChemistryPaderborn UniversityWarburger Str. 10033098PaderbornGermany
| |
Collapse
|
15
|
Shen J, Sun W, Liu D, Schaus T, Yin P. Three-dimensional nanolithography guided by DNA modular epitaxy. NATURE MATERIALS 2021; 20:683-690. [PMID: 33846583 DOI: 10.1038/s41563-021-00930-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Lithographic scaling of periodic three-dimensional patterns is critical for advancing scalable nanomanufacturing. Current state-of-the-art quadruple patterning or extreme-ultraviolet lithography produce a line pitch down to around 30 nm, which might be further scaled to sub-20 nm through complex post-fabrication processes. Herein, we report the use of three-dimensional (3D) DNA nanostructures to scale the line pitch down to 16.2 nm, around 50% smaller than state-of-the-art results. We use a DNA modular epitaxy approach to fabricate 3D DNA masks with prescribed structural parameters (geometry, pitch and critical dimensions) along a designer assembly pathway. Single-run reactive ion etching then transfers the DNA patterns to a Si substrate at a lateral critical dimension of 7 nm and a vertical critical dimension of 2 nm. The nanolithography guided by DNA modular epitaxy achieves a smaller pitch than the projected values for advanced technology nodes in field-effect transistors, and provides a potential complement to the existing lithographic tools for advanced 3D nanomanufacturing.
Collapse
Affiliation(s)
- Jie Shen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Di Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Schaus
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
16
|
Wang W, Liu X, Zheng X, Jin HJ, Li X. Biomineralization: An Opportunity and Challenge of Nanoparticle Drug Delivery Systems for Cancer Therapy. Adv Healthc Mater 2020; 9:e2001117. [PMID: 33043640 DOI: 10.1002/adhm.202001117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/29/2020] [Indexed: 12/12/2022]
Abstract
Biomineralization is a common process in organisms to produce hard biomaterials by combining inorganic ions with biomacromolecules. Multifunctional nanoplatforms are developed based on the mechanism of biomineralization in many biomedical applications. In the past few years, biomineralization-based nanoparticle drug delivery systems for the cancer treatment have gained a lot of research attention due to the advantages including simple preparation, good biocompatibility, degradability, easy modification, versatility, and targeting. In this review, the research trends of biomineralization-based nanoparticle drug delivery systems and their applications in cancer therapy are summarized. This work aims to promote future researches on cancer therapy based on biomineralization. Rational design of nanoparticle drug delivery systems can overcome the bottleneck in the clinical transformation of nanomaterials. At the same time, biomineralization has also provided new research ideas for cancer treatment, i.e., targeted therapy, which has significantly better performance.
Collapse
Affiliation(s)
- Weicai Wang
- Collaborative Innovation Center of Tumor Marker Detection Technology Equipment and Diagnosis‐Therapy Integration in Universities of Shandong Shandong Province Key Laboratory of Detection Technology for Tumor Makers School of Chemistry and Chemical Engineering Linyi University Linyi Shandong 276005 China
| | - Xiaofan Liu
- Collaborative Innovation Center of Tumor Marker Detection Technology Equipment and Diagnosis‐Therapy Integration in Universities of Shandong Shandong Province Key Laboratory of Detection Technology for Tumor Makers School of Chemistry and Chemical Engineering Linyi University Linyi Shandong 276005 China
| | - Xiangjiang Zheng
- Collaborative Innovation Center of Tumor Marker Detection Technology Equipment and Diagnosis‐Therapy Integration in Universities of Shandong Shandong Province Key Laboratory of Detection Technology for Tumor Makers School of Chemistry and Chemical Engineering Linyi University Linyi Shandong 276005 China
| | - Hyung Jong Jin
- Department of Bioscience and Biotechnology The University of Suwon Hwaseong Gyeonggi‐Do 18323 Republic of Korea
| | - Xuemei Li
- Collaborative Innovation Center of Tumor Marker Detection Technology Equipment and Diagnosis‐Therapy Integration in Universities of Shandong Shandong Province Key Laboratory of Detection Technology for Tumor Makers School of Chemistry and Chemical Engineering Linyi University Linyi Shandong 276005 China
| |
Collapse
|
17
|
Hui L, Nixon R, Tolman N, Mukai J, Bai R, Wang R, Liu H. Area-Selective Atomic Layer Deposition of Metal Oxides on DNA Nanostructures and Its Applications. ACS NANO 2020; 14:13047-13055. [PMID: 33048526 DOI: 10.1021/acsnano.0c04493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We demonstrate area-selective atomic layer deposition (ALD) of oxides on DNA nanostructures. Area-selective ALD of Al2O3, TiO2, and HfO2 was successfully achieved on both 2D and 3D DNA nanostructures deposited on a polystyrene (PS) substrate. The resulting DNA-inorganic hybrid structure was used as a hard mask to achieve deep etching of a Si wafer for antireflection applications. ALD is a widely used process in coating and thin film deposition; our work points to a way to pattern oxide materials using DNA templates and to enhance the chemical/physical stability of DNA nanostructures for applications in surface engineering.
Collapse
Affiliation(s)
- Liwei Hui
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Rachel Nixon
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Nathan Tolman
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jason Mukai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ruobing Bai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
18
|
Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
Collapse
Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| |
Collapse
|
19
|
Sun W, Shen J, Zhao Z, Arellano N, Rettner C, Tang J, Cao T, Zhou Z, Ta T, Streit JK, Fagan JA, Schaus T, Zheng M, Han SJ, Shih WM, Maune HT, Yin P. Precise pitch-scaling of carbon nanotube arrays within three-dimensional DNA nanotrenches. Science 2020; 368:874-877. [DOI: 10.1126/science.aaz7440] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 04/09/2020] [Indexed: 01/18/2023]
Abstract
Precise fabrication of semiconducting carbon nanotubes (CNTs) into densely aligned evenly spaced arrays is required for ultrascaled technology nodes. We report the precise scaling of inter-CNT pitch using a supramolecular assembly method called spatially hindered integration of nanotube electronics. Specifically, by using DNA brick crystal-based nanotrenches to align DNA-wrapped CNTs through DNA hybridization, we constructed parallel CNT arrays with a uniform pitch as small as 10.4 nanometers, at an angular deviation <2° and an assembly yield >95%.
Collapse
Affiliation(s)
- Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Shen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhao Zhao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Noel Arellano
- IBM Almaden Research Center, San Jose, CA 95120, USA
| | | | - Jianshi Tang
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Tianyang Cao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Zhiyu Zhou
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Toan Ta
- IBM Almaden Research Center, San Jose, CA 95120, USA
| | - Jason K. Streit
- Materials Science and Engineering Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Jeffrey A. Fagan
- Materials Science and Engineering Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Thomas Schaus
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Shu-Jen Han
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - William M. Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
20
|
Shang Y, Li N, Liu S, Wang L, Wang ZG, Zhang Z, Ding B. Site-Specific Synthesis of Silica Nanostructures on DNA Origami Templates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2000294. [PMID: 32301202 DOI: 10.1002/adma.202000294] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/20/2020] [Accepted: 03/30/2020] [Indexed: 06/11/2023]
Abstract
DNA origami has been widely investigated as a template for the organization of various functional elements, leading to potential applications in many fields such as biosensing, nanoelectronics, and nanophotonics. However, the synthesis of inorganic nonmetallic nanomaterials with predesigned patterns using DNA origami templates has seldom been explored. Here, a novel method is reported to site-specifically synthesize silica nanostructures with designed patterns on DNA origami templates. The molecular dynamic simulation confirms that the positively charged silica precursors have a stronger electrostatic affinity to protruding double-stranded DNA (dsDNA) than DNA origami surfaces. The work describes a novel strategy to fabricate silica nanostructures with nanoscale precision. Moreover, the site-specific silicification of DNA nanoarchitectures expands the scope of customized synthesis of inorganic nonmetallic nanomaterials.
Collapse
Affiliation(s)
- Yingxu Shang
- 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
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- 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
| | - Shengbo 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
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhen-Gang Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology 11 BeiYiTiao, ZhongGuanCun, Beijing, 100190, China
| | - Zhong Zhang
- 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
| | - 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
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou, 450001, China
| |
Collapse
|
21
|
Vittala SK, Han D. DNA-Guided Assemblies toward Nanoelectronic Applications. ACS APPLIED BIO MATERIALS 2020; 3:2702-2722. [PMID: 35025404 DOI: 10.1021/acsabm.9b01178] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeepa Kulala Vittala
- 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
|
22
|
Kim F, Chen T, Burgess T, Rasie P, Selinger TL, Greschner A, Rizis G, Carneiro K. Functionalized DNA nanostructures as scaffolds for guided mineralization. Chem Sci 2019; 10:10537-10542. [PMID: 32055376 PMCID: PMC6988742 DOI: 10.1039/c9sc02811k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022] Open
Abstract
The field of DNA nanotechnology uses synthetic DNA strands as building blocks for designing complex shapes in one-, two- and three-dimensions. Here, we investigate whether DNA nanostructures are feasible platforms for the precise organization of polyaspartic acid (pAsp), a known mineral carrier, with a goal towards biomimetic mineralization for enamel regeneration. We describe the preparation of DNA-pAsp conjugates and their subsequent assembly into ordered nanostructures. Covalent attachment of pAsp to DNA was noted to hinder DNA nanostructure formation past a certain threshold (50% pAsp) when tested on a previously published DNA system. However, a simplified double stranded DNA system (3sDH system) was more robust and efficient in its pAsp incorporation. In addition, the 3sDH system was successful in organizing mineral inducing groups in one dimension at repeating intervals of 28.7 ± 4.0 nm, as determined by atomic force microscopy. Our results demonstrate that DNA nanostructures can be functionalized with pAsp and act as a platform to investigate guided mineralization.
Collapse
Affiliation(s)
- Francesca Kim
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Tong Chen
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Trevor Burgess
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Prakash Rasie
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Tim Luca Selinger
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Andrea Greschner
- Institut National de la Recherche Scientifique (INRS) , EMT Research Center , Varennes , QC J3X 1S2 , Canada
| | - Georgios Rizis
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| | - Karina Carneiro
- Faculty of Dentistry , University of Toronto , Toronto , ON M5G 1G6 , Canada .
| |
Collapse
|
23
|
Li N, Shang Y, Xu R, Jiang Q, Liu J, Wang L, Cheng Z, Ding B. Precise Organization of Metal and Metal Oxide Nanoclusters into Arbitrary Patterns on DNA Origami. J Am Chem Soc 2019; 141:17968-17972. [DOI: 10.1021/jacs.9b09308] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, 11 BeiYiTiao, ZhongGuanCun, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-nano Devices, Department of Physics, Renmin University of China, Beijing 100872, China
| | - Qiao Jiang
- 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
| | - 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
| | - Ling Wang
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhihai Cheng
- Beijing Key Laboratory of Optoelectronic Functional Materials & Micro-nano Devices, Department of Physics, Renmin University of China, Beijing 100872, 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
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
24
|
Hui L, Xu A, Liu H. DNA-Based Nanofabrication for Antifouling Applications. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:12543-12549. [PMID: 31433657 DOI: 10.1021/acs.langmuir.9b01569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This paper reports antifouling properties of nanostructured SiO2 substrates patterned by DNA lithography. We used DNA triangle nanostructures as templates to produce triangular-shaped trenches ca. 130 nm in size on SiO2 surfaces. Using B. subtilis as a bacterial model, we found that such nanopatterned surface showed a 75% reduction in bacterial adhesion and 72% reduction in biofilm density at 35% surface coverage of the nanoscale triangular trenches. DNA-based nanofabrication can produce high-resolution designer patterns, but aligning these patterns has been one of the major technical challenges for its applications in nanoelectronics. This work demonstrates the potential of DNA-based nanofabrication in antifouling applications, where surface patterning of micro/nanostructures is required but not their precise alignment.
Collapse
Affiliation(s)
- Liwei Hui
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Anqin Xu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Haitao Liu
- Department of Chemistry , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| |
Collapse
|
25
|
Solidifying framework nucleic acids with silica. Nat Protoc 2019; 14:2416-2436. [PMID: 31270509 DOI: 10.1038/s41596-019-0184-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022]
Abstract
Soft matter can serve as a template to guide the growth of inorganic components with well-controlled structural features. However, the limited design space of conventional organic and biomolecular templates restricts the complexity and accuracy of templated growth. In past decades, the blossoming of structural DNA nanotechnology has provided us with a large reservoir of delicate-framework nucleic acids with design precision down to a single base. Here, we describe a DNA origami silicification (DOS) approach for generating complex silica composite nanomaterials. By utilizing modified silica sol-gel chemistry, pre-hydrolyzed silica precursor clusters can be uniformly coated onto the surface of DNA frameworks; thus, user-defined DNA-silica hybrid materials with ~3-nm precision can be achieved. More importantly, this method is applicable to various 1D, 2D and 3D DNA frameworks that range from 10 to >1,000 nm. Compared to pure DNA scaffolds, a tenfold increase in the Young's modulus (E modulus) of these composites was observed, owing to their soft inner core and solid silica shell. We further demonstrate the use of solidified DNA frameworks to create 3D metal plasmonic devices. This protocol provides a platform for synthesizing inorganic materials with unprecedented complexity and tailored structural properties. The whole protocol takes ~10 d to complete.
Collapse
|
26
|
Hui L, Zhang Q, Deng W, Liu H. DNA-Based Nanofabrication: Pathway to Applications in Surface Engineering. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805428. [PMID: 30811832 DOI: 10.1002/smll.201805428] [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: 12/21/2018] [Revised: 01/30/2019] [Indexed: 05/28/2023]
Abstract
This Concept provides an overview of recent developments of DNA-based nanofabrication and discusses its potential applications in the area of surface engineering. The first part of the paper discusses the strength and limitations of existing DNA-based nanofabrication methods. The second part highlights several examples of surface engineering applications involving nano- and microscale surface textures. It finishes with a discussion of the opportunities and remaining challenges of applying DNA-based nanofabrication in surface engineering applications.
Collapse
Affiliation(s)
- Liwei Hui
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Qinmei Zhang
- College of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, P. R. China
| | - Wei Deng
- College of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, P. R. China
| | - Haitao Liu
- College of Chemistry and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, P. R. China
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| |
Collapse
|
27
|
Fan S, Wang D, Kenaan A, Cheng J, Cui D, Song J. Create Nanoscale Patterns with DNA Origami. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805554. [PMID: 31018040 DOI: 10.1002/smll.201805554] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/16/2019] [Indexed: 05/21/2023]
Abstract
Structural deoxyribonucleic acid (DNA) nanotechnology offers a robust platform for diverse nanoscale shapes that can be used in various applications. Among a wide variety of DNA assembly strategies, DNA origami is the most robust one in constructing custom nanoshapes and exquisite patterns. In this account, the static structural and functional patterns assembled on DNA origami are reviewed, as well as the reconfigurable assembled architectures regulated through dynamic DNA nanotechnology. The fast progress of dynamic DNA origami nanotechnology facilitates the construction of reconfigurable patterns, which can further be used in many applications such as optical/plasmonic sensors, nanophotonic devices, and nanorobotics for numerous different tasks.
Collapse
Affiliation(s)
- Sisi Fan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dongfang Wang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ahmad Kenaan
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| |
Collapse
|
28
|
Hu S, Huang PJJ, Wang J, Liu J. Phosphorothioate DNA Mediated Sequence-Insensitive Etching and Ripening of Silver Nanoparticles. Front Chem 2019; 7:198. [PMID: 31041302 PMCID: PMC6476897 DOI: 10.3389/fchem.2019.00198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/14/2019] [Indexed: 01/06/2023] Open
Abstract
Many DNA-functionalized nanomaterials and biosensors have been reported, but most have ignored the influence of DNA on the stability of nanoparticles. We observed that cytosine-rich DNA oligonucleotides can etch silver nanoparticles (AgNPs). In this work, we showed that phosphorothioate (PS)-modified DNA (PS-DNA) can etch AgNPs independently of DNA sequence, suggesting that the thio-modifications are playing the major role in etching. Compared to unmodified DNA (e.g., poly-cytosine DNA), the concentration of required PS DNA decreases sharply, and the reaction rate increases. Furthermore, etching by PS-DNA occurs quite independent of pH, which is also different from unmodified DNA. The PS-DNA mediated etching could also be controlled well by varying DNA length and conformation, and the number and location of PS modifications. With a higher activity of PS-DNA, the process of etching, ripening, and further etching was taken place sequentially. The etching ability is inhibited by forming duplex DNA and thus etching can be used to measure the concentration of complementary DNA.
Collapse
Affiliation(s)
- Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Jianxiu Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| |
Collapse
|
29
|
Abstract
The DNA origami technique has made its way into various areas of nanotechnology, materials science, biophysics, and medicine. Among the many applications of DNA origami nanostructures, their use as masks for patterning of organic and inorganic materials by molecular lithography has received great attention. Here, we describe a protocol for the self-assembly of ordered monolayers of DNA origami nanostructures on mica surfaces and the subsequent fabrication of regular protein patterns over large surface areas via directed adsorption through the DNA origami mask. While the geometry of the pattern is determined by the shape of the DNA origami nanostructures, protein coverage inside the holes of the mask can be varied from single proteins to dense monolayers by adjusting the protein concentration and cationic strength of the adsorption buffer.
Collapse
|
30
|
DNA-Assisted Molecular Lithography. Methods Mol Biol 2019; 1811:299-314. [PMID: 29926461 DOI: 10.1007/978-1-4939-8582-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
During the past decade, DNA origami has become a popular method to build custom two- (2D) and three-dimensional (3D) DNA nanostructures. These programmable structures could further serve as templates for accurate nanoscale patterning, and therefore they could find uses in various biotechnological applications. However, to transfer the spatial information of DNA origami to metal nanostructures has been limited to either direct nanoparticle-based patterning or chemical growth of metallic seed particles that are attached to the DNA objects. Here, we present an alternative way by combining DNA origami with conventional lithography techniques. With this DNA-assisted lithography (DALI) method, we can create plasmonic, entirely metallic nanostructures in a highly accurate and parallel manner on different substrates. We demonstrate our technique by patterning a transparent substrate with discrete bowtie-shaped nanoparticles, i.e., "nanoantennas" or "optical antennas," with a feature size of approximately 10 nm. Owing to the versatility of DNA origami, this method can be effortlessly generalized to other shapes and sizes.
Collapse
|
31
|
Atomic force microscopy study of EDTA induced desorption of metal ions immobilized DNA from mica surface. Ultramicroscopy 2019; 199:7-15. [PMID: 30711717 DOI: 10.1016/j.ultramic.2019.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/26/2019] [Indexed: 01/25/2023]
Abstract
Adsorption of DNA molecules onto substrate, such as mica, is well documented. However, desorption of the immobilized DNA molecules from substrate, which is also an important aspect of DNA behavior on substrate, has not been paid much attention. Here, DNA molecules were first immobilized on mica surface by using divalent metal ions as the bridge agents. Desorption of the immobilized DNA from mica surface was realized via ethylenediamine tetraacetic acid disodium salt (EDTA) treatment. EDTA is a chelating agent; it can remove the bridging metal ions between DNA and mica, which leads to the release of DNA molecules from mica substrate. The divalent metal ions assisted DNA adsorption onto mica surface and the EDTA induced DNA desorption from mica surface were followed by atomic force microscopy (AFM). Randomly dispersed DNA strands and DNA networks are two distinct adsorption morphologies of DNA on mica surface and their desorption processes from mica surface induced by EDTA are also different. Other factors that influence the EDTA-induced DNA desorption, such as type of bridging metal ion and DNA molecule length, have also been systematically studied. Moreover, EDTA treatment has no effect on the integrity of DNA molecule. The EDTA induced desorption of metal ions immobilized DNA from mica surface is simple and effective, which has potential applications in DNA separation and purification, DNA biophysics, and DNA-based nanotechnology.
Collapse
|
32
|
Kielar C, Ramakrishnan S, Fricke S, Grundmeier G, Keller A. Dynamics of DNA Origami Lattice Formation at Solid-Liquid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2018; 10:44844-44853. [PMID: 30501167 DOI: 10.1021/acsami.8b16047] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The self-organized formation of regular patterns is not only a fascinating topic encountered in a multitude of natural and artificial systems, but also presents a versatile and powerful route toward large-scale nanostructure assembly and materials synthesis. The hierarchical, interface-assisted assembly of DNA origami nanostructures into regular, 2D lattices represents a particularly promising example, as the resulting lattices may exhibit an astonishing degree of order and can be further utilized as masks in molecular lithography. Here, we thus investigate the development of order in such 2D DNA origami lattices assembled on mica surfaces by employing in situ high-speed atomic force microscopy imaging. DNA origami lattice formation is found to resemble thin-film growth in several aspects. In particular, the Na+/Mg2+ ratio controls DNA origami adsorption, surface diffusion, and desorption, and is thus equivalent in its effects to substrate temperature which controls adatom dynamics in thin-film deposition. Consequently, we observe a pronounced dependence of lattice order on Na+ concentration. At low Na+ concentrations, lattice formation resembles random deposition and results in unordered monolayers, whereas very high Na+ concentrations are accompanied by rapid diffusion and especially DNA origami desorption, which prevent lattice formation. At intermediate Na+ concentrations, highly ordered DNA origami lattices are obtained that display an intricate symmetry, stemming from the complex shape of the employed Rothemund triangle. Nevertheless, even under such optimized conditions, the lattices display a considerable number of defects, including grain boundaries, point and line defects, and screw-like dislocations. By monitoring the dynamics of selected lattice defects, we identify mechanisms that limit the obtainable degree of lattice order. Possible routes toward further increasing lattice order by postassembly annealing are discussed.
Collapse
Affiliation(s)
- Charlotte Kielar
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Sebastian Fricke
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry , Paderborn University , Warburger Str. 100 , 33098 Paderborn , Germany
| |
Collapse
|
33
|
Shen B, Kostiainen MA, Linko V. DNA Origami Nanophotonics and Plasmonics at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14911-14920. [PMID: 30122051 PMCID: PMC6291805 DOI: 10.1021/acs.langmuir.8b01843] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA nanotechnology provides a versatile toolbox for creating custom and accurate shapes that can serve as versatile templates for nanopatterning. These DNA templates can be used as molecular-scale precision tools in, for example, biosensing, nanometrology, and super-resolution imaging, and biocompatible scaffolds for arranging other nano-objects, for example, for drug delivery applications and molecular electronics. Recently, increasing attention has been paid to their potent use in nanophotonics since these modular templates allow a wide range of plasmonic and photonic ensembles ranging from DNA-directed nanoparticle and fluorophore arrays to entirely metallic nanostructures. This Feature Article focuses on the DNA-origami-based nanophotonics and plasmonics-especially on the methods that take advantage of various substrates and interfaces for the foreseen applications.
Collapse
Affiliation(s)
- Boxuan Shen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER
Center of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid
Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- E-mail:
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Ge Z, Gu H, Li Q, Fan C. Concept and Development of Framework Nucleic Acids. J Am Chem Soc 2018; 140:17808-17819. [PMID: 30516961 DOI: 10.1021/jacs.8b10529] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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
| | - Hongzhou Gu
- Center for Biotechnology and Biomedical Engineering, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - 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
|
36
|
|
37
|
Ramakrishnan S, Ijäs H, Linko V, Keller A. Structural stability of DNA origami nanostructures under application-specific conditions. Comput Struct Biotechnol J 2018; 16:342-349. [PMID: 30305885 PMCID: PMC6169152 DOI: 10.1016/j.csbj.2018.09.002] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022] Open
Abstract
With the introduction of the DNA origami technique, it became possible to rapidly synthesize almost arbitrarily shaped molecular nanostructures at nearly stoichiometric yields. The technique furthermore provides absolute addressability in the sub-nm range, rendering DNA origami nanostructures highly attractive substrates for the controlled arrangement of functional species such as proteins, dyes, and nanoparticles. Consequently, DNAorigami nanostructures have found applications in numerous areas of fundamental and applied research, ranging from drug delivery to biosensing to plasmonics to inorganic materials synthesis. Since many of those applications rely on structurally intact, well-definedDNA origami shapes, the issue of DNA origami stability under numerous application-relevant environmental conditions has received increasing interest in the past few years. In this mini-review we discuss the structural stability, denaturation, and degradation of DNA origami nanostructures under different conditions relevant to the fields of biophysics and biochemistry, biomedicine, and materials science, and the methods to improve their stability for desired applications.
Collapse
Affiliation(s)
- Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
- University of Jyväskylä, Department of Biological and Environmental Science, P. O. Box 35, FI-40014 Jyväskylä, Finland
| | - Veikko Linko
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany
| |
Collapse
|
38
|
Hossen MM, Bendickson L, Palo PE, Yao Z, Nilsen-Hamilton M, Hillier AC. Creating metamaterial building blocks with directed photochemical metallization of silver onto DNA origami templates. NANOTECHNOLOGY 2018; 29:355603. [PMID: 29877867 DOI: 10.1088/1361-6528/aacb16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA origami can be used to create a variety of complex and geometrically unique nanostructures that can be further modified to produce building blocks for applications such as in optical metamaterials. We describe a method for creating metal-coated nanostructures using DNA origami templates and a photochemical metallization technique. Triangular DNA origami forms were fabricated and coated with a thin metal layer by photochemical silver reduction while in solution or supported on a surface. The DNA origami template serves as a localized photosensitizer to facilitate reduction of silver ions directly from solution onto the DNA surface. The metallizing process is shown to result in a conformal metal coating, which grows in height to a self-limiting value with increasing photoreduction steps. Although this coating process results in a slight decrease in the triangle dimensions, the overall template shape is retained. Notably, this coating method exhibits characteristics of self-limiting and defect-filling growth, which results in a metal nanostructure that maps the shape of the original DNA template with a continuous and uniform metal layer and stops growing once all available DNA sites are exhausted.
Collapse
Affiliation(s)
- Md Mir Hossen
- Division of Materials Sciences and Engineering, Ames Laboratory, Ames, IA, United States of America. Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States of America
| | | | | | | | | | | |
Collapse
|
39
|
Boron-Implanted Silicon Substrates for Physical Adsorption of DNA Origami. Int J Mol Sci 2018; 19:ijms19092513. [PMID: 30149587 PMCID: PMC6165417 DOI: 10.3390/ijms19092513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alternative, we developed an ion implantation process that tailors the surface potential of silicon substrates to facilitate adsorption of DNA nanostructures without the need for chemical functionalization. Industry standard 300 mm silicon wafers were processed, and we showed controlled adsorption of DNA origami onto boron-implanted silicon patterns; selective to a surrounding silicon oxide matrix. The hydrophilic substrate achieves very high surface selectivity by exploiting pH-dependent protonation of silanol-groups on silicon dioxide (SiO₂), across a range of solution pH values and magnesium chloride (MgCl₂) buffer concentrations.
Collapse
|
40
|
Complex silica composite nanomaterials templated with DNA origami. Nature 2018; 559:593-598. [DOI: 10.1038/s41586-018-0332-7] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
|
41
|
Ye K, Kaplan DL, Bao G, Bettinger C, Forgacs G, Dong C, Khademhosseini A, Ke Y, Leong K, Sambanis A, Sun W, Yin P. Advanced Cell and Tissue Biomanufacturing. ACS Biomater Sci Eng 2018; 4:2292-2307. [PMID: 33435095 DOI: 10.1021/acsbiomaterials.8b00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This position paper assesses state-of-the-art advanced biomanufacturing and identifies paths forward to advance this emerging field in biotechnology and biomedical engineering, including new research opportunities and translational and corporate activities. The vision for the field is to see advanced biomanufacturing emerge as a discipline in academic and industrial communities as well as a technological opportunity to spur research and industry growth. To navigate this vision, the paths to move forward and to identify major barriers were a focal point of discussions at a National Science Foundation-sponsored workshop focused on the topic. Some of the major needs include but are not limited to the integration of specific scientific and engineering disciplines and guidance from regulatory agencies, infrastructure requirements, and strategies for reliable systems integration. Some of the recommendations, major targets, and opportunities were also outlined, including some "grand challenges" to spur interest and progress in the field based on the participants at the workshop. Many of these recommendations have been expanded, materialized, and adopted by the field. For instance, the formation of an initial collaboration network in the community was established. This report provides suggestions for the opportunities and challenges to help move the field of advanced biomanufacturing forward. The field is in the early stages of effecting science and technology in biomanufacturing with a bright and important future impact evident based on the rapid scientific advances in recent years and industry progress.
Collapse
Affiliation(s)
- Kaiming Ye
- Department of Biomedical Engineering, Center of Biomanufacturing for Regenerative Medicine, Watson School of Engineering and Applied Science, Binghamton University, State University of New York (SUNY), Binghamton, New York 13902, United States
| | - David L Kaplan
- Department of Biomedical Engineering, School of Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Gang Bao
- Department of Bioengineering, School of Engineering, Rice University, Houston, Texas 77005, United States
| | - Christopher Bettinger
- Department of Materials Science and Engineering, College of Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Gabor Forgacs
- Department of Bioengineering, College of Engineering, University of Missouri, Columbia, Missouri 65211, United States.,Modern Meadow, Inc., 340 Kingsland Street, Nutley, New Jersey 07110, United States
| | - Cheng Dong
- Department of Biomedical Engineering, College of Engineering, Penn State University, University Park, Pennsylvania 16802, United States
| | - Ali Khademhosseini
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Yonggang Ke
- Department of Biomedical Engineering, College of Engineering, Georgia Tech, Atlanta, Georgia 30332, United States
| | - Kam Leong
- Department of Biomedical Engineering, School of Engineering and Applied Science, Columbia University, New York City, New York 10027, United States
| | | | - Wei Sun
- Department of Mechanical Engineering and Mechanics, College of Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States.,Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Peng Yin
- Department of Systems Biology, Harvard Medical School, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
42
|
Liu Y, Kumar S, Taylor RE. Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2018; 10:e1518. [PMID: 29633568 DOI: 10.1002/wnan.1518] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/23/2018] [Accepted: 02/14/2018] [Indexed: 01/04/2023]
Abstract
The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
Collapse
Affiliation(s)
- Ying Liu
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Sriram Kumar
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Rebecca E Taylor
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania
| |
Collapse
|
43
|
Shen B, Linko V, Tapio K, Pikker S, Lemma T, Gopinath A, Gothelf KV, Kostiainen MA, Toppari JJ. Plasmonic nanostructures through DNA-assisted lithography. SCIENCE ADVANCES 2018; 4:eaap8978. [PMID: 29423446 PMCID: PMC5804581 DOI: 10.1126/sciadv.aap8978] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/08/2018] [Indexed: 05/21/2023]
Abstract
Programmable self-assembly of nucleic acids enables the fabrication of custom, precise objects with nanoscale dimensions. These structures can be further harnessed as templates to build novel materials such as metallic nanostructures, which are widely used and explored because of their unique optical properties and their potency to serve as components of novel metamaterials. However, approaches to transfer the spatial information of DNA constructions to metal nanostructures remain a challenge. We report a DNA-assisted lithography (DALI) method that combines the structural versatility of DNA origami with conventional lithography techniques to create discrete, well-defined, and entirely metallic nanostructures with designed plasmonic properties. DALI is a parallel, high-throughput fabrication method compatible with transparent substrates, thus providing an additional advantage for optical measurements, and yields structures with a feature size of ~10 nm. We demonstrate its feasibility by producing metal nanostructures with a chiral plasmonic response and bowtie-shaped nanoantennas for surface-enhanced Raman spectroscopy. We envisage that DALI can be generalized to large substrates, which would subsequently enable scale-up production of diverse metallic nanostructures with tailored plasmonic features.
Collapse
Affiliation(s)
- Boxuan Shen
- Department of Physics, Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
| | - Kosti Tapio
- Department of Physics, Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Siim Pikker
- Department of Physics, Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Tibebe Lemma
- Department of Physics, Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Ashwin Gopinath
- Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kurt V. Gothelf
- Centre for DNA Nanotechnology, Interdisciplinary Nanoscience Center, iNANO, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
- HYBER Centre of Excellence, Department of Applied Physics, Aalto University, 00076 Aalto, Finland
- Corresponding author. (M.A.K.); (J.J.T.)
| | - J. Jussi Toppari
- Department of Physics, Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
- Corresponding author. (M.A.K.); (J.J.T.)
| |
Collapse
|
44
|
Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
Collapse
Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| |
Collapse
|
45
|
Kim H, Arbutina K, Xu A, Liu H. Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al 2O 3 and its application in imprinting lithography. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2363-2375. [PMID: 29181293 PMCID: PMC5687006 DOI: 10.3762/bjnano.8.236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 10/02/2017] [Indexed: 06/01/2023]
Abstract
We present a method to increase the stability of DNA nanostructure templates through conformal coating with a nanometer-thin protective inorganic oxide layer created using atomic layer deposition (ALD). DNA nanotubes and origami triangles were coated with ca. 2 nm to ca. 20 nm of Al2O3. Nanoscale features of the DNA nanostructures were preserved after the ALD coating and the patterns are resistive to UV/O3 oxidation. The ALD-coated DNA templates were used for a direct pattern transfer to poly(L-lactic acid) films.
Collapse
Affiliation(s)
- Hyojeong Kim
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Kristin Arbutina
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Anqin Xu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States of America
| |
Collapse
|
46
|
Green CM, Schutt K, Morris N, Zadegan RM, Hughes WL, Kuang W, Graugnard E. Metrology of DNA arrays by super-resolution microscopy. NANOSCALE 2017; 9:10205-10211. [PMID: 28489095 DOI: 10.1039/c7nr00928c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent results in the assembly of DNA into structures and arrays with nanoscale features and patterns have opened the possibility of using DNA for sub-10 nm lithographic patterning of semiconductor devices. Super-resolution microscopy is being actively developed for DNA-based imaging and is compatible with inline optical metrology techniques for high volume manufacturing. Here, we combine DNA tile assembly with state-dependent super-resolution microscopy to introduce crystal-PAINT as a novel approach for metrology of DNA arrays. Using this approach, we demonstrate optical imaging and characterization of DNA arrays revealing grain boundaries and the temperature dependence of array quality. For finite arrays, analysis of crystal-PAINT images provides further quantitative information of array properties. This metrology approach enables defect detection and classification and facilitates statistical analysis of self-assembled DNA nanostructures.
Collapse
Affiliation(s)
- Christopher M Green
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Kelly Schutt
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Noah Morris
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID 83725, USA.
| | - Reza M Zadegan
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - William L Hughes
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Wan Kuang
- Department of Electrical & Computer Engineering, Boise State University, Boise, ID 83725, USA.
| | - Elton Graugnard
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| |
Collapse
|
47
|
Hong F, Zhang F, Liu Y, Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev 2017; 117:12584-12640. [DOI: 10.1021/acs.chemrev.6b00825] [Citation(s) in RCA: 645] [Impact Index Per Article: 92.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fan Hong
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Yan Liu
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Hao Yan
- The Biodesign Institute and
School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| |
Collapse
|
48
|
Ricardo KB, Xu A, Salim M, Zhou F, Liu H. Deposition of DNA Nanostructures on Highly Oriented Pyrolytic Graphite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3991-3997. [PMID: 28406032 DOI: 10.1021/acs.langmuir.6b03836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO2. This process is potentially useful for a range of applications that include but are not limited to nanostructure fabrication, sensing, and electronic and surface engineering.
Collapse
Affiliation(s)
- Karen B Ricardo
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Anqin Xu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Muhammad Salim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Feng Zhou
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
49
|
|
50
|
Tian C, Kim H, Sun W, Kim Y, Yin P, Liu H. DNA Nanostructures-Mediated Molecular Imprinting Lithography. ACS NANO 2017; 11:227-238. [PMID: 28052196 DOI: 10.1021/acsnano.6b04777] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper describes the fabrication of polymer stamps using DNA nanostructure templates. This process creates stamps having diverse nanoscale features with dimensions ranging from several tens of nanometers to micrometers. DNA nanostructures including DNA nanotubes, stretched λ-DNA, two-dimensional (2D) DNA brick crystals with three-dimensional (3D) features, hexagonal DNA 2D arrays, and triangular DNA origami were used as master templates to transfer patterns to poly(methyl methacrylate) and poly(l-lactic acid) with high fidelity. The resulting polymer stamps were used as molds to transfer the pattern to acryloxy perfluoropolyether polymer. This work establishes an approach to using self-assembled DNA templates for applications in soft lithography.
Collapse
Affiliation(s)
- Cheng Tian
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Hyojeong Kim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Wei Sun
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Yunah Kim
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Boston, Massachusetts 02115, United States
- Department of Systems Biology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Haitao Liu
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|