1
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Jalilvand S, Mousavi H. Vibration spectra of DNA and RNA segments. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:95-109. [PMID: 38265690 DOI: 10.1007/s00249-023-01699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/17/2023] [Accepted: 12/23/2023] [Indexed: 01/25/2024]
Abstract
The dispersion curves and density of states are used to analyze the vibrational characteristics of DNA and RNA segments. This is done using a harmonic Hamiltonian and the Green's function technique. Two configurations of DNA and RNA, finite and cyclic, have been investigated and compared to their infinite counterparts. For the DNA molecule, three models, including a fishbone model, a ldder model, and a fishbone ladder model, have been employed, while the RNA molecule has been represented using a half fishbone model. To enhance the realism of DNA and RNA simulations, the unit cells within each infinite system as well as the length of the finite and cyclic cases are gradually enlarged. The connections between the sub-sites have been modeled using linear springs, where the stiffness of the vertical springs exhibits random variations throughout the length of the DNA and RNA models. Shorter DNA and RNA segments exhibit additional peaks in their density of states, resulting in more bands in dispersion curves. This indicates that as the number of building blocks grows in these segments, their curves resemble those of infinite systems. These findings have practical implications for studying the vibration characteristics of similar macro-systems.
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Affiliation(s)
| | - Hamze Mousavi
- Department of Physics, Razi University, Kermanshah, Iran.
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2
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Bindu Ramesan A, Vittala SK, Joseph J. DNA condensation and formation of ultrathin nanosheets via DNA assisted self-assembly of an amphiphilic fullerene derivative. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 226:112352. [PMID: 34798504 DOI: 10.1016/j.jphotobiol.2021.112352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022]
Abstract
DNA nanotechnology propose various assembly strategies to develop novel functional nanostructures utilizing unique interactions of DNA with small molecules, nanoparticles, polymers, and other biomolecules. Although, well defined nanostructures of DNA and amphiphilic small molecules were achieved through hybridization of covalently modified DNA, attaining precise organization of functional moieties through non-covalent interactions remain as a challenging task. Herein, we report mutually assisted assembly of an amphiphilic fullerene derivative and various DNA structures through non-covalent interactions, which leads to initial DNA condensation and subsequent assembly yielding ordered fullerene-DNA nanosheets. The molecular design of the cationic, amphiphilic fullerene derivative (FPy) ensures molecular solubility in the 10% DMSO-PBS buffer system and facile interactions with DNA through groove binding and electrostatic interactions of fullerene moiety and positively charged pyridinium moiety, respectively. The formation of FPy/DNA nanostructures were thoroughly investigated in the presence of λ-DNA, pBR322 plasmid DNA, and single and double stranded 20-mer oligonucleotides using UV-visible spectroscopy, AFM and TEM analysis. λ-DNA and pBR322 plasmid DNA readily condense in presence of FPy leading to micrometer sized few layer nanosheets with significant crystallinity due to ordered arrangement of fullerenes. Similarly, single and double stranded 20-mer oligonucleotides also interact efficiently with FPy and form highly crystalline nanosheets, signifying the role of electrostatic interaction and subsequent charge neutralization in the condensation triggered assembly. However, there is significant differences in the crystallinity and ordered arrangements of fullerenes between these two cases, where longer DNA form condensed structures and less ordered nanosheets while short oligonucleotides lead to more ordered and highly crystalline nanosheets, which could be attributed to the differential DNA condensation. Finally, we have demonstrated the addressability of the assembly using a cyanine modified single strand DNA, which also forms highly crystalline nanosheets and exhibit efficient quenching of the cyanine fluorescence upon self-assembly. These results open up new prospects in the development of functional DNA nanostructures through non-covalent interactions and hence have potential applications in the context of DNA nanotechnology.
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Affiliation(s)
- Anjali Bindu Ramesan
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandeepa Kulala Vittala
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Joshy Joseph
- Photosciences and Photonics Section, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram 695 019, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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3
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Fardian-Melamed N, Katrivas L, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules. NANO LETTERS 2021; 21:8987-8992. [PMID: 34694812 DOI: 10.1021/acs.nanolett.1c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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4
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Barreda JL, Hu L, Yu L, Hudis J, Keiper TD, Xia J, Wang Z, Guan J, Xiong P. Controlled Fabrication of DNA Molecular Templates for In Situ Formation and Measurement of Ultrathin Metal Nanostructures. NANO LETTERS 2020; 20:8135-8140. [PMID: 33048550 DOI: 10.1021/acs.nanolett.0c03166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fabrication of ultrathin metal nanostructures usually requires some combination of high-vacuum deposition and postgrowth processing, which precludes access to nanostructures of ultrasmall cross sections for most materials. DNA nanowires (NWs) are versatile insulating templates with intrinsic sub-10 nm line width. Here, we demonstrate a method of DNA template fabrication with precise control over the location and orientation of the DNA NWs. We further demonstrate that this template can be used to support formation of ultrathin metal NWs for derivative nanodevices: a metal is incrementally deposited, and electrical transport measurement is performed in situ at each step. The results show a homogeneous metal NW is obtained at a thickness as small as 0.9 nm with a cross-section of only a few nm2. The high degree of control in the location, separation, and orientation of the DNA NWs affords this method great promise in fabricating complex nanodevices based on metal NWs.
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Affiliation(s)
- Jorge L Barreda
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Longqian Hu
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Liuqi Yu
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Jacob Hudis
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Timothy D Keiper
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
| | - Junfei Xia
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Zhibin Wang
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Jingjiao Guan
- Department of Chemical and Biomedical Engineering, Florida A&M University-Florida State University College of Engineering, Florida State University, Tallahassee, Florida 32310, United States
| | - Peng Xiong
- Department of Physics, Florida State University, Tallahassee, Florida 32306, United States
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5
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Choi JS, Park HB, Tsui JH, Hong B, Kim DH, Kim HJ. Hybrid gold/DNA nanowire circuit with sub-10 nm nanostructure arrays. MICROSYSTEMS & NANOENGINEERING 2020; 6:91. [PMID: 34567701 PMCID: PMC8433371 DOI: 10.1038/s41378-020-00202-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/30/2020] [Accepted: 08/06/2020] [Indexed: 06/13/2023]
Abstract
We report on a simple and efficient method for the selective positioning of Au/DNA hybrid nanocircuits using a sequential combination of electron-beam lithography (EBL), plasma ashing, and a molecular patterning process. The nanostructures produced by the EBL and ashing process could be uniformly formed over a 12.6 in2 substrate with sub-10 nm patterning with good pattern fidelity. In addition, DNA molecules were immobilized on the selectively nanopatterned regions by alternating surface coating procedures of 3-(aminopropyl)triethoxysilane (APS) and diamond like carbon (DLC), followed by deposition of DNA molecules into a well-defined single DNA nanowire. These single DNA nanowires were used not only for fabricating Au/DNA hybrid nanowires by the conjugation of Au nanoparticles with DNA, but also for the formation of Au/DNA hybrid nanocircuits. These nanocircuits prepared from Au/DNA hybrid nanowires demonstrate conductivities of up to 4.3 × 105 S/m in stable electrical performance. This selective and precise positioning method capable of controlling the size of nanostructures may find application in making sub-10 nm DNA wires and metal/DNA hybrid nanocircuits.
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Affiliation(s)
- Jong Seob Choi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Hye Bin Park
- Digital Healthcare Research Center, Gumi Electronics and Information Technology Research Institute (GERI), 350-27, Gumidaero, Gumi, Gyeongbuk, 39253 South Korea
| | - Jonathan H. Tsui
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
| | - Byungyou Hong
- College of Information and Communication Engineering, Sungkyunkwan University, Suwon, 440-746 South Korea
| | - Deok-Ho Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Hyung Jin Kim
- Digital Healthcare Research Center, Gumi Electronics and Information Technology Research Institute (GERI), 350-27, Gumidaero, Gumi, Gyeongbuk, 39253 South Korea
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6
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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.
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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
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7
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Sun Y, Li L, Shi K. Analog and Digital Bipolar Resistive Switching in Co-Al-Layered Double Hydroxide Memristor. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2095. [PMID: 33105722 PMCID: PMC7690433 DOI: 10.3390/nano10112095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 01/29/2023]
Abstract
We demonstrate a nonvolatile memristor based on Co-Al-layered double hydroxide (Co-Al LDH). We also introduce a memristor that has a hexazinone-adsorbing Co-Al LDH composite active layer. Memristor characteristics could be modulated by adsorbing hexazinone with Co-Al LDHs in the active layer. While different, Co-Al LDH-based memory devices show gradual current changes, and the memory device with small molecules of adsorbed hexazinone undergo abrupt changes. Both devices demonstrate programmable memory peculiarities. In particular, both memristors show rewritable resistive switching with electrical bistability (>105 s). This research manifests the promising potential of 2D nanocomposite materials for adsorbing electroactive small molecules and rectifying resistive switching properties for memristors, paving a way for design of promising 2D nanocomposite memristors for advanced device applications.
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Affiliation(s)
- Yanmei Sun
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Material Science, Heilongjiang University, Harbin 150080, China;
- Key Laboratory of Chemical Engineering Process & Technology for High-efficiency Conversion, School of Chemistry and Material Science, Heilongjiang University, Harbin 150080, China
- School of Electronic Engineering, Heilongjiang University, Harbin 150080, China
| | - Li Li
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Material Science, Heilongjiang University, Harbin 150080, China;
- Key Laboratory of Chemical Engineering Process & Technology for High-efficiency Conversion, School of Chemistry and Material Science, Heilongjiang University, Harbin 150080, China
| | - Keying Shi
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Material Science, Heilongjiang University, Harbin 150080, China;
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8
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Dai X, Li Q, Aldalbahi A, Wang L, Fan C, Liu X. DNA-Based Fabrication for Nanoelectronics. NANO LETTERS 2020; 20:5604-5615. [PMID: 32787185 DOI: 10.1021/acs.nanolett.0c02511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The bottom-up DNA-templated nanoelectronics exploits the unparalleled self-assembly properties of DNA molecules and their amenability with various types of nanomaterials. In principle, nanoelectronic devices can be bottom-up assembled with near-atomic precision, which compares favorably with well-established top-down fabrication process with nanometer precision. Over the past decade, intensive effort has been made to develop DNA-based nanoassemblies including DNA-metal, DNA-polymer, and DNA-carbon nanotube complexes. This review introduces the history of DNA-based fabrication for nanoelectronics briefly and summarizes the state-of-art advances of DNA-based nanoelectronics. In particular, the most widely applied characterization techniques to explore their unique electronic properties at the nanoscale are described and discussed, including scanning tunneling microscopy, conductive atomic force microscopy, and Kelvin probe force microscopy. We also provide a perspective on potential applications of DNA-based nanoelectronics.
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Affiliation(s)
- Xinpei Dai
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ali Aldalbahi
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Lihua Wang
- CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201800, China
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Luo X, Lachance-Brais C, Bantle A, Sleiman HF. The assemble, grow and lift-off (AGLO) strategy to construct complex gold nanostructures with pre-designed morphologies. Chem Sci 2020; 11:4911-4921. [PMID: 34122947 PMCID: PMC8159246 DOI: 10.1039/d0sc00553c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The construction of metallic nanostructures with customizable morphologies and complex shapes has been an essential pursuit in nanoscience. DNA nanotechnology has enabled the fabrication of increasingly complex DNA nanostructures with unprecedented specificity, programmability and sub-nanometer precision, which makes it an ideal approach to rationally organize metallic nanostructures. Here we report an Assemble, Grow and Lift-Off (AGLO) strategy to construct robust standalone gold nanostructures with pre-designed customizable shapes in solution, using only a simple 2D DNA origami sheet as a versatile transient template. Gold nanoparticle (AuNP) seeds were firstly assembled onto the pre-designed binding sites of the DNA origami template and then additional gold was slowly deposited onto the AuNP seeds. The growing seed surfaces eventually merge with adjacent seeds to generate one continuous gold nanostructure in a pre-designed shape, which can then be lifted off the origami template. Diverse customized patterns of templated AuNP seeds were successfully transformed into corresponding gold nanostructures with the target structure transformation percentage over 80%. Moreover, the AGLO strategy can be incorporated with a magnetic bead separation platform to enable the easy recycling of the excess AuNP seeds and DNA components.
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Affiliation(s)
- Xin Luo
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Christophe Lachance-Brais
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Amy Bantle
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University 801 Sherbrooke Street West Montreal Quebec H3A 0B8 Canada
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10
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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.
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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
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11
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A minimalist's approach for DNA nanoconstructions. Adv Drug Deliv Rev 2019; 147:22-28. [PMID: 30769045 DOI: 10.1016/j.addr.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology takes DNA, a biopolymer, far beyond being the molecule that stores and transmits genetic information in biological systems. DNA has been employed as building blocks for the assembly of designed, nanoscaled, supramolecular DNA architectures for applications in biophysics, structure determination, synthetic biology, diagnostics, and drug delivery. Herein, we review a symmetric approach of tile-based DNA self-assembly. This approach allows the construction of DNA nanostructures from minimal numbers of different types of DNA strands based on sequence and structural symmetries. Some examples of the applications of this approach in siRNA delivery are discussed as well.
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12
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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.
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13
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Maslova AO, Hsing IM. Thiol-free oligonucleotide surface modification of gold nanoparticles for nanostructure assembly. NANOSCALE ADVANCES 2019; 1:430-435. [PMID: 36132480 PMCID: PMC9473237 DOI: 10.1039/c8na00148k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/19/2018] [Indexed: 06/15/2023]
Abstract
Gold nanoparticles (AuNPs) decorated with thiol-modified DNA (HS-DNA) strands are an extensively studied, easily adjustable, and highly controllable material for constructing 3D nanostructures with various shapes and functions. However, few reproducible and robust methods involving DNA templates as a key reagent are available for obtaining 3D nanoparticle assemblies. It is still challenging to strictly control the number and location of DNA strands on the AuNP surface. Here, we introduce an efficient approach for the surface modification of AuNPs using unmodified DNA oligonucleotides by building DNA cages that trap the nanoparticles. This enables us to vary the process of nanostructure assembly and create anisotropic nanoparticles that are necessary for directed structure construction. This developed method simplifies the production process in comparison with conventional HS-DNA modification protocols and helps to precisely control the density and position of functional DNA strands designed for further hybridization with other AuNP conjugates.
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Affiliation(s)
- Anastasia O Maslova
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology Hong Kong China
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology Hong Kong China
| | - I Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology Hong Kong China
- Bioengineering Graduate Program, The Hong Kong University of Science and Technology Hong Kong China
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14
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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.
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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:
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15
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Tapio K, Shao D, Auer S, Tuppurainen J, Ahlskog M, Hytönen VP, Toppari JJ. A DNA-nanoparticle actuator enabling optical monitoring of nanoscale movements induced by an electric field. NANOSCALE 2018; 10:19297-19309. [PMID: 30209452 DOI: 10.1039/c8nr05535a] [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
Merging biological and non-biological matter to fabricate nanoscale assemblies with controllable motion and function is of great interest due to its potential application, for example, in diagnostics and biosensing. Here, we have constructed a DNA-based bionanoactuator that interfaces with biological and non-biological matter via an electric field in a reversibly controllable fashion. The read-out of the actuator is based on motion-induced changes in the plasmon resonance of a gold nanoparticle immobilized to a gold surface by single stranded DNA. The motion of the gold nanoparticle and thus the conformational changes of the DNA under varying electric field were analyzed by dark field spectroscopy. After this basic characterization, another actuator was built utilizing hairpin-DNA coated gold nanoparticles, where the hairpin-DNA induced discrete transitions between two specific open-loop and folded-loop states. These two states and the transition dynamics between them were clearly visible in the actuator behavior. The demonstrated nanoactuator concept could be readily extended to inspection of conformational changes of other biomolecules as well. Besides, this concept enables other possibilities in applications like surface-enhanced Raman spectroscopy and fluorescence enhancement, since the specific wavelength of the plasmon resonance of the actuator can be tuned by the external voltage.
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Affiliation(s)
- Kosti Tapio
- University of Jyvaskyla, Department of Physics, Nanoscience Center, FI-40014 University of Jyväskylä, P.O. Box 35, Finland.
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16
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Bayrak T, Jagtap NS, Erbe A. Review of the Electrical Characterization of Metallic Nanowires on DNA Templates. Int J Mol Sci 2018; 19:E3019. [PMID: 30282940 PMCID: PMC6213931 DOI: 10.3390/ijms19103019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/24/2018] [Accepted: 09/26/2018] [Indexed: 01/29/2023] Open
Abstract
The use of self-assembly techniques may open new possibilities in scaling down electronic circuits to their ultimate limits. Deoxyribonucleic acid (DNA) nanotechnology has already demonstrated that it can provide valuable tools for the creation of nanostructures of arbitrary shape, therefore presenting an ideal platform for the development of nanoelectronic circuits. So far, however, the electronic properties of DNA nanostructures are mostly insulating, thus limiting the use of the nanostructures in electronic circuits. Therefore, methods have been investigated that use the DNA nanostructures as templates for the deposition of electrically conducting materials along the DNA strands. The most simple such structure is given by metallic nanowires formed by deposition of metals along the DNA nanostructures. Here, we review the fabrication and the characterization of the electronic properties of nanowires, which were created using these methods.
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Affiliation(s)
- Türkan Bayrak
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden, 01062 Dresden, Germany.
| | - Nagesh S Jagtap
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
| | - Artur Erbe
- Institute of Ion Beam Physics and Materials Research, Helmholtz-Zentrum Dresden-Rossendorf, 01328 Dresden, Germany.
- Cluster of Excellence Center for Advancing Electronics Dresden (cfaed), TU Dresden, 01062 Dresden, Germany.
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17
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Sokolowska K, Hulkko E, Lehtovaara L, Lahtinen T. Dithiol-Induced Oligomerization of Thiol-Protected Gold Nanoclusters. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:12524-12533. [PMID: 30258521 PMCID: PMC6150662 DOI: 10.1021/acs.jpcc.8b02988] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/16/2018] [Indexed: 06/08/2023]
Abstract
Controlled synthesis of nanostructure oligomers requires detailed understanding of their wet chemistry and the forces driving the polymerization process. In this paper, we report the main factors affecting the reaction yields of a dithiol-induced synthesis of covalently bound nanocluster dimers and oligomers and present a detailed analysis of possible reaction mechanisms. We synthesize the nanocluster oligomers using monodisperse para-mercaptobenzoic acid (p-MBA)-protected gold nanoclusters with a nominal composition of Au∼250(p-MBA) n to minimize ensemble effects on size, shape, and surface structure. Ligand exchange was performed on the nanoclusters with five different dithiol linkers: 5,5'-bis(mercaptomethyl)-2,2'-bipyridine, 4,4″-thiobisbenzenethiol, benzene-1,4-dithiol, 1,4-benzenedimethanethiol, and dimercaptostilbene. Oligomer yields depend strongly on the used dithiol and on the dithiol-to-nanocluster ratio. Detailed analysis of the reaction yields in combination with simulations suggests that the system reaches a dynamic equilibrium, where ligand exchange happens continuously forming and breaking nanocluster oligomers that are bound together by short chains of disulfide-bridged dithiols. Despite the dynamic nature of the system, dithiol-induced polymerization of nanoclusters is a general and straightforward approach to produce dimers and larger oligomers of thiol-protected nanoclusters. Our work provides physical insight into, offers tools for, and reveals challenges in the controlled synthesis of covalently bound nanoparticle assemblies.
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18
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Nummelin S, Kommeri J, Kostiainen MA, Linko V. Evolution of Structural DNA Nanotechnology. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703721. [PMID: 29363798 DOI: 10.1002/adma.201703721] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/17/2017] [Indexed: 05/24/2023]
Abstract
The research field entitled structural DNA nanotechnology emerged in the beginning of the 1980s as the first immobile synthetic nucleic acid junctions were postulated and demonstrated. Since then, the field has taken huge leaps toward advanced applications, especially during the past decade. This Progress Report summarizes how the controllable, custom, and accurate nanostructures have recently evolved together with powerful design and simulation software. Simultaneously they have provided a significant expansion of the shape space of the nanostructures. Today, researchers can select the most suitable fabrication methods, and design paradigms and software from a variety of options when creating unique DNA nanoobjects and shapes for a plethora of implementations in materials science, optics, plasmonics, molecular patterning, and nanomedicine.
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Affiliation(s)
- Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
| | - Juhana Kommeri
- 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
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, 00076, Aalto, Finland
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19
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Saikia N, Johnson F, Waters K, Pandey R. Dynamics of self-assembled cytosine nucleobases on graphene. NANOTECHNOLOGY 2018; 29:195601. [PMID: 29461252 DOI: 10.1088/1361-6528/aab0ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.
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20
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Julin S, Nummelin S, Kostiainen MA, Linko V. DNA nanostructure-directed assembly of metal nanoparticle superlattices. JOURNAL OF NANOPARTICLE RESEARCH : AN INTERDISCIPLINARY FORUM FOR NANOSCALE SCIENCE AND TECHNOLOGY 2018; 20:119. [PMID: 29950921 PMCID: PMC5997120 DOI: 10.1007/s11051-018-4225-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/13/2018] [Indexed: 05/19/2023]
Abstract
Structural DNA nanotechnology provides unique, well-controlled, versatile, and highly addressable motifs and templates for assembling materials at the nanoscale. These methods to build from the bottom-up using DNA as a construction material are based on programmable and fully predictable Watson-Crick base pairing. Researchers have adopted these techniques to an increasing extent for creating numerous DNA nanostructures for a variety of uses ranging from nanoelectronics to drug-delivery applications. Recently, an increasing effort has been put into attaching nanoparticles (the size range of 1-20 nm) to the accurate DNA motifs and into creating metallic nanostructures (typically 20-100 nm) using designer DNA nanoshapes as molds or stencils. By combining nanoparticles with the superior addressability of DNA-based scaffolds, it is possible to form well-ordered materials with intriguing and completely new optical, plasmonic, electronic, and magnetic properties. This focused review discusses the DNA structure-directed nanoparticle assemblies covering the wide range of different one-, two-, and three-dimensional systems.
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Affiliation(s)
- Sofia Julin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Sami Nummelin
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
| | - Mauri A. Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
- HYBER Center of Excellence, Department of Applied Physics, Aalto University, Espoo, Finland
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland
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21
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Dai Z, Lo PK. Photo-switchable patterning of gold nanoparticles along 3D DNA nanotubes. NANOSCALE 2018; 10:5431-5435. [PMID: 29516074 DOI: 10.1039/c7nr09650j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We have developed a reversible photoswitching platform based on 3D DNA nanotubes by integrating photoisomerizable azobenzene molecules along the edges. This would allow the reversible conformational changes of the nanotubes between linear and bent features and the switchable patterning of gold nanoparticles in response to UV/Vis irradiation. This work provides a new strategy to create reversibly reconfigurable transformative nanomaterials for potential applications in the fields of renewable energy, sensing, nanorobotics and nanomedicine.
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Affiliation(s)
- Ziwen Dai
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China and Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China.
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China and Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China.
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22
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Rahbani JF, Vengut‐Climent E, Chidchob P, Gidi Y, Trinh T, Cosa G, Sleiman HF. DNA Nanotubes with Hydrophobic Environments: Toward New Platforms for Guest Encapsulation and Cellular Delivery. Adv Healthc Mater 2018; 7:e1701049. [PMID: 29356412 DOI: 10.1002/adhm.201701049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 12/17/2017] [Indexed: 01/13/2023]
Abstract
Natural systems combine different supramolecular interactions in a hierarchical manner to build structures. In contrast, DNA nanotechnology relies almost exclusively on DNA base pairing for structure generation. Introducing other supramolecular interactions can expand the structural and functional range of DNA assemblies, but this requires an understanding of the interplay between these interactions. Here, an economic strategy to build DNA nanotubes functionalized with lipid-like polymers is reported. When these polymers are linked to the nanotube using a spacer, they fold inside to create a hydrophobic environment within the nanotube; the nanotube can encapsulate small molecules and conditionally release them when specific DNA strands are added, as monitored by single-molecule fluorescence microscopy. When the polymers are directly linked to the nanostructure without spacers, they interact intermolecularly to form a network of DNA bundles. This morphological switch can be directly observed using a strand displacement strategy. The two association modes result in different cellular uptake behavior. Nanotubes with internal hydrophobic association show dye-mediated mitochondrial colocalization inside cells; while the bundles disassemble into smaller polymer-coated structures that reduce the extent of nonspecific cellular uptake. This approach uncovers parameters to direct the hierarchical assembly of DNA nanostructures, and produces promising materials for targeted drug delivery.
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Affiliation(s)
- Janane F. Rahbani
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Empar Vengut‐Climent
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Pongphak Chidchob
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Yasser Gidi
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Tuan Trinh
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Gonzalo Cosa
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry, Centre for Self‐Assembled Chemical Structures McGill University 801 Sherbrooke St. West Montreal H3A 0B8 Canada
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Abdalla S, Obaid A, Al-Marzouki FM. Effects of Environmental Factors and Metallic Electrodes on AC Electrical Conduction Through DNA Molecule. NANOSCALE RESEARCH LETTERS 2017; 12:316. [PMID: 28454482 PMCID: PMC5407417 DOI: 10.1186/s11671-017-2076-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/13/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Deoxyribonucleic acid (DNA) is one of the best candidate materials for various device applications such as in electrodes for rechargeable batteries, biosensors, molecular electronics, medical- and biomedical-applications etc. Hence, it is worthwhile to examine the mechanism of charge transport in the DNA molecule, however, still a question without a clear answer is DNA a molecular conducting material (wire), semiconductor, or insulator? The answer, after the published data, is still ambiguous without any confirmed and clear scientific answer. DNA is found to be always surrounded with different electric charges, ions, and dipoles. These surrounding charges and electric barrier(s) due to metallic electrodes (as environmental factors (EFs)) play a substantial role when measuring the electrical conductivity through λ-double helix (DNA) molecule suspended between metallic electrodes. We found that strong frequency dependence of AC-complex conductivity comes from the electrical conduction of EFs. This leads to superimposing serious incorrect experimental data to measured ones. METHODS At 1 MHz, we carried out a first control experiment on electrical conductivity with and without the presence of DNA molecule. If there are possible electrical conduction due to stray ions and contribution of substrate, we will detected them. This control experiment revealed that there is an important role played by the environmental-charges around DNA molecule and any experiment should consider this role. RESULTS AND DISCUSSION We have succeeded to measure both electrical conductivity due to EFs (σ ENV) and electrical conductivity due to DNA molecule (σ DNA) independently by carrying the measurements at different DNA-lengths and subtracting the data. We carried out measurements as a function of frequency (f) and temperature (T) in the ranges 0.1 Hz < f < 1 MHz and 288 K < T < 343 K. The measured conductivity (σ MES) portrays a metal-like behavior at high frequencies near 1 MHz. However, we found that σ DNA was far from this behavior because the conduction due to EFs superimposes σ DNA, in particular at low frequencies. By measuring the electrical conductivity at different lengths: 40, 60, 80, and 100 nm, we have succeeded not only to separate the electrical conduction of the DNA molecule from all EFs effects that surround the molecule, but also to present accurate values of σ DNA and the dielectric constant of the molecule ε'DNA as a function of temperature and frequency. Furthermore, in order to explain these data, we present a model describing the electrical conduction through DNA molecule: DNA is a classical semiconductor with charges, dipoles and ions that result in creation of localized energy-states (LESs) in the extended bands and in the energy gap of the DNA molecule. CONCLUSIONS This model explains clearly the mechanism of charge transfer mechanism in the DNA, and it sheds light on why the charge transfer through the DNA can lead to insulating, semiconducting, or metallic behavior on the same time. The model considers charges on DNA, in the extended bands, either could be free to move under electric field or localized in potential wells/hills. Localization of charges in DNA is an intrinsic structural-property of this solitaire molecule. At all temperatures, the expected increase in thermal-induced charge is attributed to the delocalization of holes (or/and electrons) in potential hills (or/and potential wells) which accurately accounts for the total electric and dielectric behavior through DNA molecule. We succeeded to fit the experimental data to the proposed model with reasonable magnitudes of potential hills/wells that are in the energy range from 0.068 eV.
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Affiliation(s)
- S. Abdalla
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah, 21589 Saudi Arabia
| | - A. Obaid
- Department of Chemistry, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah, 21589 Saudi Arabia
| | - F. M. Al-Marzouki
- Department of Physics, Faculty of Science, King Abdulaziz University Jeddah, P.O. Box 80203, Jeddah, 21589 Saudi Arabia
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Lhermitte JR, Stein A, Tian C, Zhang Y, Wiegart L, Fluerasu A, Gang O, Yager KG. Coherent amplification of X-ray scattering from meso-structures. IUCRJ 2017; 4:604-613. [PMID: 28989716 PMCID: PMC5619852 DOI: 10.1107/s2052252517008107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/31/2017] [Indexed: 05/20/2023]
Abstract
Small-angle X-ray scattering (SAXS) often includes an unwanted background, which increases the required measurement time to resolve the sample structure. This is undesirable in all experiments, and may make measurement of dynamic or radiation-sensitive samples impossible. Here, we demonstrate a new technique, applicable when the scattering signal is background-dominated, which reduces the requisite exposure time. Our method consists of exploiting coherent interference between a sample with a designed strongly scattering 'amplifier'. A modified angular correlation function is used to extract the symmetry of the interference term; that is, the scattering arising from the interference between the amplifier and the sample. This enables reconstruction of the sample's symmetry, despite the sample scattering itself being well below the intensity of background scattering. Thus, coherent amplification is used to generate a strong scattering term (well above background), from which sample scattering is inferred. We validate this method using lithographically defined test samples.
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Affiliation(s)
- Julien R. Lhermitte
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Aaron Stein
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Cheng Tian
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Yugang Zhang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Lutz Wiegart
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Andrei Fluerasu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
| | - Oleg Gang
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027, USA
| | - Kevin G. Yager
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York, NY 11973, USA
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