1
|
Lu X, Hou J, Yang K, Zhu L, Xing B, Lin D. Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:9305-9316. [PMID: 34138538 DOI: 10.1021/acs.est.1c02047] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO2) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min-1) and capacity (4.29 mg/g) for ARGs than nTiO2 (0.05 min-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO2-adsorbed ARGs were effectively desorbed in NaOH and NaH2PO4 solutions, respectively. Molecular dynamics simulation revealed that nTiO2 mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO43- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO2 remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO43-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.
Collapse
Affiliation(s)
- Xinye Lu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Hou
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
- The Institute of Zhejiang Ecological Civilization, Anji 313300, China
| |
Collapse
|
2
|
Troha T, Drevenšek-Olenik I, Webba da Silva M, Spindler L. Surface-Adsorbed Long G-Quadruplex Nanowires Formed by G:C Linkages. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7056-63. [PMID: 27392201 DOI: 10.1021/acs.langmuir.6b01222] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
G-quadruplexes connected into long, continuous nanostructures termed G-wires show properties superior to dsDNA when applied in nanotechnology. Using AFM imaging, we systematically studied surface adsorption of a set of G-rich oligonucleotides with GC-termini for their ability to form long G-wires through G:C pairing. We investigated the effects of increasing sequence length, the type of nucleotide in the side loops, and removal of the CG-3' terminus. We found that sequences with adenine in the side loops most readily form G-wires. The role of magnesium as an efficient surface-anchoring ion was also confirmed. Conversely, as resolved from dynamic light scattering measurements, magnesium had no ability to promote G-quadruplex formation in solution. These insights may help in selecting prosperous candidates for construction of G-quadruplex based nanowires and to explore them for their electronic properties.
Collapse
Affiliation(s)
- Tinkara Troha
- Faculty of Mathematics and Physics, University of Ljubljana , Jadranska 19, 1000 Ljubljana, Slovenia
| | - Irena Drevenšek-Olenik
- Faculty of Mathematics and Physics, University of Ljubljana , Jadranska 19, 1000 Ljubljana, Slovenia
- Department of Complex Matter, "Jožef Stefan" Institute , Jamova 39, 1000 Ljubljana, Slovenia
| | - Mateus Webba da Silva
- Biomedical Sciences Research Institute, University of Ulster , Coleraine BT51 2SA, United Kingdom
| | - Lea Spindler
- Department of Complex Matter, "Jožef Stefan" Institute , Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Mechanical Engineering, University of Maribor , Smetanova 17, 2000 Maribor, Slovenia
| |
Collapse
|
3
|
Zhang S, Ding Y, Wei H. Ruthenium polypyridine complexes combined with oligonucleotides for bioanalysis: a review. Molecules 2014; 19:11933-87. [PMID: 25116805 PMCID: PMC6271144 DOI: 10.3390/molecules190811933] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/17/2014] [Accepted: 07/28/2014] [Indexed: 02/01/2023] Open
Abstract
Ruthenium complexes are among the most interesting coordination complexes and they have attracted great attention over the past decades due to their appealing biological, catalytic, electronic and optical properties. Ruthenium complexes have found a unique niche in bioanalysis, as demonstrated by the substantial progress made in the field. In this review, the applications of ruthenium complexes coordinated with polypyridine ligands (and analogues) in bioanalysis are discussed. Three main detection methods based on electrochemistry, electrochemiluminescence, and photoluminscence are covered. The important targets, including DNA and other biologically important targets, are detected by specific biorecognition with the corresponding oligonucleotides as the biorecognition elements (i.e., DNA is probed by its complementary strand and other targets are detected by functional nucleic acids, respectively). Selected examples are provided and thoroughly discussed to highlight the substantial progress made so far. Finally, a brief summary with perspectives is included.
Collapse
Affiliation(s)
- Shuyu Zhang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
| | - Yubin Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
| | - Hui Wei
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210093, China.
| |
Collapse
|
4
|
Wang L, Guo Y, Li P, Song Y. Anion-Specific Effects on the Assembly of Collagen Layers Mediated by Magnesium Ion on Mica Surface. J Phys Chem B 2014; 118:511-8. [DOI: 10.1021/jp405035x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li Wang
- Key Laboratory
of Functional
Small Organic Molecule, Ministry of Education, College of Chemistry
and Chemical Engineering, Jiangxi Normal University, 99 Ziyang
Road, Nanchang 330022, China
| | - Yan Guo
- Key Laboratory
of Functional
Small Organic Molecule, Ministry of Education, College of Chemistry
and Chemical Engineering, Jiangxi Normal University, 99 Ziyang
Road, Nanchang 330022, China
| | - Pengcheng Li
- Key Laboratory
of Functional
Small Organic Molecule, Ministry of Education, College of Chemistry
and Chemical Engineering, Jiangxi Normal University, 99 Ziyang
Road, Nanchang 330022, China
| | - Yonghai Song
- Key Laboratory
of Functional
Small Organic Molecule, Ministry of Education, College of Chemistry
and Chemical Engineering, Jiangxi Normal University, 99 Ziyang
Road, Nanchang 330022, China
| |
Collapse
|
5
|
Ding Y, Shi L, Wei H. Protein-directed approaches to functional nanomaterials: a case study of lysozyme. J Mater Chem B 2014; 2:8268-8291. [DOI: 10.1039/c4tb01235f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Using lysozyme as a model, protein-directed approaches to functional nanomaterials were reviewed, making rational materials design possible in the future.
Collapse
Affiliation(s)
- Yubin Ding
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Leilei Shi
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| | - Hui Wei
- Department of Biomedical Engineering
- Aerosol Bioeffects and Health Research Center
- College of Engineering and Applied Sciences
- Nanjing National Laboratory of Microstructures
- Nanjing University
| |
Collapse
|
6
|
Wang H, Wang X, Li H, Zhang X, Zhang Y, Hu J. Molecular expansion of an individual coiled DNA on a graphite surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2405-2410. [PMID: 21341704 DOI: 10.1021/la104776n] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Direct visualization and manipulation of a single polymer on a solid surface in fluid can greatly contribute to our understanding of polymer dynamics and physics relevant to many practical applications. In this paper, the authors report a novel phenomenon that a randomly coiled DNA molecule can be gradually expanded to form a spiral-like pattern by repeatedly rotating a water droplet on a graphite surface where the DNA molecule was deposited. The process of DNA expansion was traced using atomic force microscopy relocation imaging. A simple theoretical model based on the analysis of centrifugal and resistant forces exerted on the DNA molecule during the manipulation was presented to explain the formation of the spiral-like pattern. This study should provide us insight into the movement of polymers on a solid surface under fluid flow.
Collapse
Affiliation(s)
- Huabin Wang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, People's Republic of China
| | | | | | | | | | | |
Collapse
|
7
|
Sun L, Zhao D, Zhang Z, Li B, Shen D. DNA-based fabrication of density-controlled vertically aligned ZnO nanorod arrays and their SERS applications. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1jm10830a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
8
|
Song Y, Lian W, Zhao S, Wang L, Li Z. Self-assembled monolayers of DNA on cysteamine modified Au(111) surface: Atomic force microscopy study. Microsc Res Tech 2009; 73:51-7. [PMID: 19544534 DOI: 10.1002/jemt.20752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lambda-DNA molecules self-assemble on cysteamine-modified gold (111) surface to form flat-lying self-assembled monolayers (SAMs). The formation kinetics of such DNA SAMs is studied by atomic force microscopy (AFM). AFM results show that DNA molecules do not arrange themselves on cysteamine-modified gold (111) surface into a well-ordered monolayer. It is also found that the surface density of DNA monolayer does not increase as the DNA concentration increases. The high temperature of DNA solution and the immersing in ultrapure water produce some obvious DNA bundles. Whereas divalent cations in DNA solution result in the formation of more compact DNA films. The obtained information may be useful for practical application of the DNA films and further theoretical studies.
Collapse
Affiliation(s)
- Yonghai Song
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi Province, People's Republic of China
| | | | | | | | | |
Collapse
|
9
|
SONG Y, WANG L, ZHAO S, LIAN W, LI Z. Disassembly of DNA-ligand on mica surface: atomic force microscopy studies. J Microsc 2009; 234:130-6. [DOI: 10.1111/j.1365-2818.2009.03154.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
10
|
Bombelli FB, Gambinossi F, Lagi M, Berti D, Caminati G, Brown T, Sciortino F, Norden B, Baglioni P. DNA closed nanostructures: a structural and Monte Carlo simulation study. J Phys Chem B 2009; 112:15283-94. [PMID: 18989907 DOI: 10.1021/jp804544u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA nanoconstructs are obtained in solution by using six unique 42-mer DNA oligonucleotides, whose sequences have been designed to form a pseudohexagonal structure. The required flexibility is provided by the insertion of two non-base-paired thymines in the middle of each sequence that work as flexible hinges and constitute the corners of the nanostructure when formed. We show that hexagonally shaped nanostructures of about 7 nm diameter and their corresponding linear open constructs are formed by self-assembly of the specifically designed linear oligonucleotides. The structural and dynamical characterization of the nanostructure is obtained in situ for the first time by using dynamic light scattering (DLS), a noninvasive method that provides a fast dynamic and structural analysis and allows the characterization of the different synthetic DNA nanoconstructs in solution. A validation of the LS results is obtained through Monte Carlo (MC) simulations and atomic force microscopy (AFM). In particular, a mesoscale molecular model for DNA, developed by Knotts et al., is exploited to perform MC simulations and to obtain information about the conformations as well as the conformational flexibilities of these nanostructures, while AFM provides a very detailed particle analysis that yields an estimation of the particle size and size distribution. The structural features obtained by MC and AFM are in good agreement with DLS, showing that DLS is a fast and reliable tool for characterization of DNA nanostructures in solution.
Collapse
Affiliation(s)
- Francesca Baldelli Bombelli
- Department of Chemistry and CSGI, University of Florence, Via della Lastruccia 3 - Sesto Fiorentino, 50019 Florence, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Cui K, Song Y, Wang L. Electrochemical and electrocatalytic behaviors of poly(ferrocenylsilane)/DNA modified glass carbon electrode. Electrochem commun 2008. [DOI: 10.1016/j.elecom.2008.08.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
|
12
|
Yao Y, Song Y, Wang L. Synthesis of CdS nanoparticles based on DNA network templates. NANOTECHNOLOGY 2008; 19:405601. [PMID: 21832621 DOI: 10.1088/0957-4484/19/40/405601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
CdS nanoparticles have been successfully synthesized by using DNA networks as templates. The synthesis was carried out by first dropping a mixture of cadmium acetate and DNA on a mica surface for the formation of the DNA network template and then transferring the sample into a heated thiourea solution. The Cd(2+) reacted with thiourea at high temperature and formed CdS nanoparticles on the DNA network template. UV-vis spectroscopy, photoluminescence, x-ray diffraction and atomic force microscopy (AFM) were used to characterize the CdS nanoparticles in detail. AFM results showed that the resulted CdS nanoparticles were directly aligned on the DNA network templates and that the synthesis and assembly of CdS nanoparticles was realized in one step. CdS nanoparticles fabricated with this method were smaller than those directly synthesized in a thiourea solution and were uniformly aligned on the DNA networks. By adjusting the density of the DNA networks and the concentration of Cd(2+), the size and density of the CdS nanoparticles could be effectively controlled and CdS nanoparticles could grow along the DNA chains into nanowires. The possible growth mechanism has also been discussed in detail.
Collapse
Affiliation(s)
- Yong Yao
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, People's Republic of China
| | | | | |
Collapse
|
13
|
Song Y, Li Z, Wang L, Yao Y, Chen C, Cui K. One-step preparation of hybrid materials of polyacrylamide networks and gold nanoparticles. Microsc Res Tech 2008; 71:409-12. [DOI: 10.1002/jemt.20568] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|