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Barinov NA, Ivanov DA, Dubrovin EV, Klinov DV. Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface. Int J Biol Macromol 2024; 267:131630. [PMID: 38631581 DOI: 10.1016/j.ijbiomac.2024.131630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.
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Affiliation(s)
- Nikolay A Barinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France
| | - Evgeniy V Dubrovin
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Dmitry V Klinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation.
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2
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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3
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Xing Y, Zhang Y, Zhu X, Wang C, Zhang T, Cheng F, Qu J, Peijnenburg WJGM. A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167615. [PMID: 37806581 DOI: 10.1016/j.scitotenv.2023.167615] [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: 08/22/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.
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Affiliation(s)
- Yi Xing
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yanan Zhang
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Xiaolin Zhu
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Chengzhi Wang
- Center for Water Research, Beijing Normal University, Beijing 100875, China
| | - Tingting Zhang
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Fangyuan Cheng
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Jiao Qu
- School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Bilthoven, the Netherlands
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4
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Ehlert C, Piras A, Gryn’ova G. CO 2 on Graphene: Benchmarking Computational Approaches to Noncovalent Interactions. ACS OMEGA 2023; 8:35768-35778. [PMID: 37810719 PMCID: PMC10551916 DOI: 10.1021/acsomega.3c03251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023]
Abstract
Designing and optimizing graphene-based gas sensors in silico entail constructing appropriate atomistic representations for the physisorption complex of an analyte on an infinite graphene sheet, then selecting accurate yet affordable methods for geometry optimizations and energy computations. In this work, diverse density functionals (DFs), coupled cluster theory, and symmetry-adapted perturbation theory (SAPT) in conjunction with a range of finite and periodic surface models of bare and supported graphene were tested for their ability to reproduce the experimental adsorption energies of CO2 on graphene in a low-coverage regime. Periodic results are accurately reproduced by the interaction energies extrapolated from finite clusters to infinity. This simple yet powerful scheme effectively removes size dependence from the data obtained using finite models, and the latter can be treated at more sophisticated levels of theory relative to periodic systems. While for small models inexpensive DFs such as PBE-D3 afford surprisingly good agreement with the gold standard of quantum chemistry, CCSD(T), interaction energies closest to experiment are obtained by extrapolating the SAPT results and with nonlocal van der Waals functionals in the periodic setting. Finally, none of the methods and models reproduce the experimentally observed CO2 tilted adsorption geometry on the Pt(111) support, calling for either even more elaborate theoretical approaches or a revision of the experiment.
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Affiliation(s)
- Christopher Ehlert
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing (IWR), Heidelberg
University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Anna Piras
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing (IWR), Heidelberg
University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Ganna Gryn’ova
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing (IWR), Heidelberg
University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
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5
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Hoshikawa Y, Kanno Y, Tawata H, Sagae T, Ishii T, Imoto S, Hagihara S, Wada T, Nagatsugi F, Aziz A, Nishihara H, Kyotani T, Itoh T. Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules. Chemistry 2023; 29:e202301422. [PMID: 37392079 DOI: 10.1002/chem.202301422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/02/2023]
Abstract
Water-dispersible carbon nano-test tubes (CNTTs) with an inner and outer diameter of about 25 and 35 nm, respectively, were prepared by the template technique and then their inner carbon surface was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was examined in the presence of Ca2+ cations. Many DNA molecules are attracted to the inner space of Ox-CNTTs based on the Ca2+ -mediated electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface. Moreover, the total net charge of the DNA adsorbed was found to be equal to the total charge of the carboxylate anions. This selective adsorption into the interior of Ox-CNTTs can be explained from the fact that the electrostatic interaction onto the inner concave surface is much stronger than that on the outer convex surface. On the other hand, the desorption of DNA easily occurs whenever Ca2+ cations are removed by washing with deionized water. Thus, each of Ox-CNTTs works well as a nano-container for a large amount of DNA molecules, thereby resulting in the occurrence of DNA enrichment in the nanospace.
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Affiliation(s)
- Yasuto Hoshikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Yasuyuki Kanno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hanako Tawata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takuya Sagae
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takafumi Ishii
- International Research and Education Center for Element Science, Faculty of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Shuhei Imoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Alex Aziz
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hirotomo Nishihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takashi Kyotani
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Tetsuji Itoh
- National Institute of Advanced Industrial Science Technology (AIST), 4-2-1, Nigatake, Miyagino-ku, Sendai, Miyagi, 983-8551, Japan
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6
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Tang X, Chen T, Li W, Mao D, Liu C, Wu Q, Huang N, Hu S, Sun F, Pan Q, Zhu X. Throwing and manipulating and cheating with a DNA nano-dice. Nat Commun 2023; 14:2440. [PMID: 37117228 PMCID: PMC10147716 DOI: 10.1038/s41467-023-38164-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/18/2023] [Indexed: 04/30/2023] Open
Abstract
Artificial molecular machines have captured the imagination of researchers, given their clear potential to mimic and influence human life. Key to behavior simulation is to reproduce the specific properties of physical or abstract systems. Dice throwing, as a stochastic model, is commonly used for result judgment or plan decision in real life. In this perspective we utilize DNA cube framework for the design of a dice device at the nanoscale to reproduce probabilistic events in different situations: equal probability, high probability, and low probability. We first discuss the randomness of DNA cube, or dice, adsorbing on graphene oxide, or table, and then explore a series of events that change the probability through the way in which the energy released from entropy-driven strand displacement reactions or changes in intermolecular forces. As such, the DNA nano-dice system provides guideline and possibilities for the design, engineering, and quantification of behavioral probability simulation, a currently emerging area of molecular simulation research.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Wenxing Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Dongsheng Mao
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Qi Wu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China.
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China.
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China.
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China.
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7
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Panneer Selvam S, Cho S. Phosphate-driven H 2O 2 decomposition on DNA-bound bio-inspired activated carbon-based sensing platform for biological and food samples. Food Chem 2023; 421:136234. [PMID: 37119688 DOI: 10.1016/j.foodchem.2023.136234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
Hydrogen peroxide (H2O2) is one of the most important reactive oxygen species (ROS). Increased endogenous H2O2 levels indicate oxidative stress and could be a potential marker of many diseases, including Alzheimer's, cardiovascular diseases, and diabetes. However, consuming H2O2-incorporated food has adverse effects on humans and is a serious health concern. We used salmon testes DNA with bio-inspired activated carbon (AC) as an electrocatalyst for developing a novel H2O2 sensor. The phosphate backbone of DNA contains negatively charged oxygen groups that specifically attract protons from H2O2 reduction. We observed a linearity range of 0.01-250.0 μM in the H2O2 reduction peak current with a detection limit of 2.5 and 45.7 nM for chronoamperometric and differential pulse voltammetric studies. High biocompatibility of the sensor was achieved by the DNA, facilitating endogenous H2O2 detection. Moreover, this non-enzymatic sensor could also help in the rapid screening of H2O2-contaminated foods.
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Affiliation(s)
- Sathish Panneer Selvam
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea; Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon 21999, Korea.
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8
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Hasoň S, Ostatná V, Fojt L, Fojta M. Arrangements of DNA purine bases on pyrolytic graphite electrode surface. Electrochemical characterization and atomic force microscopy imaging. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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10
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Liang L, Shen X, Zhou M, Chen Y, Lu X, Zhang L, Wang W, Shen JW. Theoretical Evaluation of Potential Cytotoxicity of Graphene Quantum Dot to Adsorbed DNA. MATERIALS (BASEL, SWITZERLAND) 2022; 15:7435. [PMID: 36363026 PMCID: PMC9654448 DOI: 10.3390/ma15217435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
As a zero-dimensional (0D) nanomaterial, graphene quantum dot (GQD) has a unique physical structure and electrochemical properties, which has been widely used in biomedical fields, such as bioimaging, biosensor, drug delivery, etc. Its biological safety and potential cytotoxicity to human and animal cells have become a growing concern in recent years. In particular, the potential DNA structure damage caused by GQD is of great importance but still obscure. In this study, molecular dynamics (MD) simulation was used to investigate the adsorption behavior and the structural changes of single-stranded (ssDNA) and double-stranded DNA (dsDNA) on the surfaces of GQDs with different sizes and oxidation. Our results showed that ssDNA can strongly adsorb and lay flat on the surface of GQDs and graphene oxide quantum dots (GOQDs), whereas dsDNA was preferentially oriented vertically on both surfaces. With the increase of GQDs size, more structural change of adsorbed ssDNA and dsDNA could be found, while the size effect of GOQD on the structure of ssDNA and dsDNA is not significant. These findings may help to improve the understanding of GQD biocompatibility and potential applications of GQD in the biomedical field.
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Affiliation(s)
- Lijun Liang
- Center for X-Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027, China
- College of Automation, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Xin Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Mengdi Zhou
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yijian Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Xudong Lu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Li Zhang
- Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Wang
- Department of Pharmacy, Hangzhou Third People’s Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, West Lake Road 38, Hangzhou 310009, China
| | - Jia-Wei Shen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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11
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F.G.M. Cimirro N, Lima EC, Cunha MR, Thue PS, Grimm A, dos Reis GS, Rabiee N, Reza Saeb M, Keivanimehr F, Habibzadeh S. Removal of diphenols using pine biochar. Kinetics, equilibrium, thermodynamics, and mechanism of uptake. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119979] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Betulinic acid and 3-o-acetyl-betulinic acid interactions with external and internal surface of boron-nitride nanotubes: A DFT and MD investigation. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Liang Y, Ang WL, Lim RRX, Bonanni A. Exploring graphene oxide intrinsic electroactivity to elucidate the non-covalent interactions with DNA oligonucleotides. Chem Commun (Camb) 2022; 58:2662-2665. [PMID: 35107450 DOI: 10.1039/d1cc06657a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We show here how the electrochemical reduction signal of graphene oxide nanocolloids is inhibited upon the formation of non-covalent interactions with single stranded DNA oligonucleotides. The drop in the reduction current intensity is strongly influenced by the nucleobase sequence, and can therefore be directly correlated to the specific DNA homo-oligonucleotide.
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Affiliation(s)
- Yaquan Liang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Wei Li Ang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Rachel Rui Xia Lim
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Alessandra Bonanni
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
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14
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Wang J, Li H, Du C, Li Y, Ma X, Yang C, Xu W, Sun C. Structure-switching aptamer triggering signal amplification strategy for tobramycin detection based on hybridization chain reaction and fluorescence synergism. Talanta 2022; 243:123318. [PMID: 35217273 DOI: 10.1016/j.talanta.2022.123318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/18/2022] [Accepted: 02/13/2022] [Indexed: 01/13/2023]
Abstract
Based on hybridization chain reaction (HCR) and fluorescence synergism, a novel aptasensor for tobramycin was successfully constructed. Tobramycin competed with cDNA-FAM to bind aptamers immobilized on magnetic beads. After magnetic separation, the released cDNA-FAM acted as initiator to trigger HCR amplification, thus the fluorescence was significantly enhanced due to binding of SYBR Green Ⅰ (SGI) to the formed long double-stranded DNA and the synergistic fluorescence of FAM. In the absence of tobramycin, the initiator was magnetically separated and no HCR occurred, more importantly, graphene oxide can quench the fluorescence of excessive hairpins/SGI and cDNA-FAM, so almost no background signal was detected. This aptasensor can monitor tobramycin in the range of 0.3-50 μM with low detection limit of 17.37 nM. Due to the potential generality of structure-switching aptamers and effectiveness of fluorescence synergism, this enzyme-free amplification strategy can be extended to other applications by rational design of nucleic acid sequences.
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Affiliation(s)
- Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Caiyi Du
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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15
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Adsorption of acetic acid and benzoic acid on pristine and defect containing graphene: A DFT study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Bhai S, Ganguly B. Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study. Phys Chem Chem Phys 2021; 24:829-841. [PMID: 34928284 DOI: 10.1039/d1cp04009j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.
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Affiliation(s)
- Surjit Bhai
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
| | - Bishwajit Ganguly
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
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17
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Huang PJJ, Liu J. Signaling Kinetics of DNA and Aptamer Biosensors Revealing Graphene Oxide Surface Heterogeneity. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00201-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Dubrovin EV, Klinov DV. Atomic Force Microscopy of Biopolymers on Graphite Surfaces. POLYMER SCIENCE SERIES A 2021. [DOI: 10.1134/s0965545x2106002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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19
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Almeida C, Neves MC, Freire MG. Towards the Use of Adsorption Methods for the Removal of Purines from Beer. Molecules 2021; 26:molecules26216460. [PMID: 34770869 PMCID: PMC8587081 DOI: 10.3390/molecules26216460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 11/25/2022] Open
Abstract
Beer corresponds to a fermented alcoholic beverage composed of several components, including purine compounds. These molecules, when ingested by humans, can be catabolized into uric acid, contributing to uric acid’s level increase in serum, which may lead to hyperuricemia and gout. To assure a proper management of this disease, physicians recommend restrictive dietary measures, particularly by avoiding the consumption of beer. Therefore, it is of relevance to develop efficient methods to remove purine compounds from alcoholic beverages such as beer. In this review, we provide an introduction on fermented alcoholic beverages, with emphasis on beer, as well as its purine compounds and their role in uric acid metabolism in the human body in relation to hyperuricemia and gout development. The several reported enzymatic, biological and adsorption methods envisaging purine compounds’ removal are then reviewed. Some enzymatic and biological methods present drawbacks, which can be overcome by adsorption methods. Within adsorption methods, adsorbent materials, such as activated carbon or charcoal, have been reported and applied to beer or wort samples, showing an excellent capacity for adsorbing and removing purine compounds. Although the main topic of this review is on the removal of purine compounds from beer, other studies involving other matrices rather than beer or wort that are rich in purines are included, since they provide relevant clues on designing efficient removal processes. By ensuring the selective removal of purine compounds from this beverage, beer can be taken by hyperuricemic and gouty patients, avoiding restrictive dietary measures, while decreasing the related healthcare economic burden.
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20
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Herbert JM. Neat, Simple, and Wrong: Debunking Electrostatic Fallacies Regarding Noncovalent Interactions. J Phys Chem A 2021; 125:7125-7137. [PMID: 34388340 DOI: 10.1021/acs.jpca.1c05962] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multipole moments such as charge, dipole, and quadrupole are often invoked to rationalize intermolecular phenomena, but a low-order multipole expansion is rarely a valid description of electrostatics at the length scales that characterize nonbonded interactions. This is illustrated by examining several common misunderstandings rooted in erroneous electrostatic arguments. First, the notion that steric repulsion originates in Coulomb interactions is easily disproved by dissecting the interaction potential for Ar2. Second, the Hunter-Sanders model of π-π interactions, which is based on quadrupolar electrostatics, is shown to have no basis in accurate calculations. Third, curved "buckybowls" exhibit unusually large dipole moments, but these are ancillary to the forces that control their intermolecular interactions, as illustrated by two examples involving corannulene. Finally, the assumption that interactions between water and small anions are dictated by the dipole moment of H2O is shown to be false in the case of binary halide-water complexes. These examples present a compelling case that electrostatic explanations based on low-order multipole moments are very often counterfactual for nonbonded interactions at close range and should not be taken seriously in the absence of additional justification.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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21
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Kuntip N, Japrung D, Pongprayoon P. Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot. ACS OMEGA 2021; 6:21764-21772. [PMID: 34471778 PMCID: PMC8388069 DOI: 10.1021/acsomega.1c03404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.
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Affiliation(s)
- Nattapon Kuntip
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National
Nanotechnology Center, National Science
and Technology Development Agency, Thailand Science Park, Pathumthani 12120, Thailand
- . Phone:+66-2564-6665. Fax:+66-25647000
| | - Prapasiri Pongprayoon
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
- Center
for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural
Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
- . Phone: +66-2562-5555. Fax:+66-2579-3955
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22
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Sequence-Independent DNA Adsorption on Few-Layered Oxygen-Functionalized Graphene Electrodes: An Electrochemical Study for Biosensing Application. BIOSENSORS 2021; 11:bios11080273. [PMID: 34436075 PMCID: PMC8394360 DOI: 10.3390/bios11080273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/18/2022]
Abstract
DNA is strongly adsorbed on oxidized graphene surfaces in the presence of divalent cations. Here, we studied the effect of DNA adsorption on electrochemical charge transfer at few-layered, oxygen-functionalized graphene (GOx) electrodes. DNA adsorption on the inkjet-printed GOx electrodes caused amplified current response from ferro/ferricyanide redox probe at concentration range 1 aM–10 nM in differential pulse voltammetry. We studied a number of variables that may affect the current response of the interface: sequence type, conformation, concentration, length, and ionic strength. Later, we showed a proof-of-concept DNA biosensing application, which is free from chemical immobilization of the probe and sensitive at attomolar concentration regime. We propose that GOx electrodes promise a low-cost solution to fabricate a highly sensitive platform for label-free and chemisorption-free DNA biosensing.
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23
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Parvin S, Hazra V, Francis AG, Pati SK, Bhattacharyya S. In Situ Cation Intercalation in the Interlayer of Tungsten Sulfide with Overlaying Layered Double Hydroxide in a 2D Heterostructure for Facile Electrochemical Redox Activity. Inorg Chem 2021; 60:6911-6921. [PMID: 33667066 DOI: 10.1021/acs.inorgchem.1c00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The role of electrochemical interfaces in energy conversion and storage is unprecedented and more so the interlayers of two-dimensional (2D) heterostructures, where the physicochemical nature of these interlayers can be adjusted by cation intercalation. We demonstrate in situ intercalation of Ni2+ and Co2+ with similar ionic radii of ∼0.07 nm in the interlayer of 1T-WS2 while electrodepositing NiCo layered double hydroxide (NiCo-LDH) to create a 2D heterostructure. The extent of intercalation varies with the electrodeposition time. Electrodeposition for 90 s results in 22.4-nm-thick heterostructures, and charge transfer ensues from NiCo-LDH to 1T-WS2, which stabilizes the higher oxidation states of Ni and Co. Density functional theory calculations validate the intercalation principle where the intercalated Ni and Co d electrons contribute to the density of states at the Fermi level of 1T-WS2. Water electrolysis is taken as a representative redox process. The 90 s electrodeposited heterostructure needs the relatively lowest overpotentials of 134 ± 14 and 343 ± 4 mV for hydrogen and oxygen evolution reactions, respectively, to achieve a current density of ±10 mA/cm2 along with exceptional durability for 60 h in 1 M potassium hydroxide. The electrochemical parameters are found to correlate with enhanced mass diffusion through the cation and Cl--intercalated interlayer spacing of 1T-WS2 and the number of active sites. While 1T-WS2 is mostly celebrated as a HER catalyst in an acidic medium, with the help of intercalation chemistry, this work explores an unfound territory of this transition-metal dichalcogenide to catalyze both half-reactions of water electrolysis.
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Affiliation(s)
- Sahanaz Parvin
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Vishwadeepa Hazra
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Anita Gemmy Francis
- Theoretical Sciences Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Swapan K Pati
- Theoretical Sciences Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Sayan Bhattacharyya
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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24
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Ahmed I, Shuai Y, Rafique M, Mahar MA, Larik AS. Tailoring spintronic and opto-electronic characteristics of bilayer AlN through MnO x clusters intercalation; an ab initio study. RSC Adv 2021; 11:15167-15176. [PMID: 35424022 PMCID: PMC8698386 DOI: 10.1039/d1ra01532j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/14/2021] [Indexed: 11/21/2022] Open
Abstract
Adopting ab initio density functional theory (DFT) technique, the spintronic and opto-electronic characteristics of MnO x (i.e., Mn, MnO, MnO2, MnO3 and MnO4) clusters intercalated bilayer AlN (BL/AlN) systems are investigated in this paper. In terms of electron transfer, charge transfer occurs from BL/AlN to the MnO x clusters. MnO x clusters intercalation induces magnetic behavior in the non-magnetic AlN system. The splitting of electronic bands occurs, thus producing spintronic trends in the electronic structure of BL/AlN system. Further, MnO x intercalation converts insulating BL/AlN to a half metal/semiconductor material during spin up/down bands depending upon the type of impurity cluster present in its lattice. For instance, Mn, MnO and MnO2 intercalation in BL/AlN produces a half metallic BL/AlN system as surface states are available at the Fermi Energy (E F) level for spin up and down band channels, accordingly. Whereas, MnO3 and MnO4 intercalation produces a conducting BL/AlN system having a 0.5 eV and 0.6 eV band gap during the spin down band channel, respectively. During spin up band channels these systems behave as semiconductors with band gaps of 1.4 eV and 1.2 eV, respectively. In terms of optical characteristics (i.e., absorption coefficient, reflectivity and energy loss spectrum (ELS)), it was found that MnO x intercalation improves the absorption spectrum in the low electron energy range and absorption peaks are observed in the 0-3 eV energy range, which are not present in the absorption spectrum of pure BL/AlN. The static reflectivity parameter of BL/AlN is increased after MnO x intercalation and the ELS parameter obtains significant peak intensities in the 0-2 eV energy range, whereas for pure BL/AlN, ELS contains negligible value in this energy range. Outcomes of this study indicate that, MnO x clusters intercalation in BL/AlN is a suitable technique to tailor its spintronic and opto-electronic trends. Thus, experimental investigation can be carried out on the systems discussed in this work, so as to fabricate practical layered AlN systems that are functional in the field of nano-technology.
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Affiliation(s)
- Irfan Ahmed
- Mehran University of Engineering and Technology, SZAB Campus, Khairpur Mirs' Pakistan
| | - Yong Shuai
- School of Energy Science and Engineering, Harbin Institute of Technology 92 West Dazhi Street Harbin 150001 PR China
| | - Muhammad Rafique
- Mehran University of Engineering and Technology, SZAB Campus, Khairpur Mirs' Pakistan
- School of Energy Science and Engineering, Harbin Institute of Technology 92 West Dazhi Street Harbin 150001 PR China
| | - Mukhtiar Ahmed Mahar
- Mehran University of Engineering and Technology, SZAB Campus, Khairpur Mirs' Pakistan
- Mehran University of Engineering and Technology Jamshoro Sindh Pakistan
| | - Abdul Sattar Larik
- Mehran University of Engineering and Technology, SZAB Campus, Khairpur Mirs' Pakistan
- Mehran University of Engineering and Technology Jamshoro Sindh Pakistan
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25
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Cortés-Arriagada D. Intermolecular driving forces on the adsorption of DNA/RNA nucleobases to graphene and phosphorene: An atomistic perspective from DFT calculations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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26
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H H, Mallajosyula SS. Polarization influences the evolution of nucleobase-graphene interactions. NANOSCALE 2021; 13:4060-4072. [PMID: 33595570 DOI: 10.1039/d0nr08796c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.
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Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
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27
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Kroeger AA, Karton A. π-π Catalysis in Carbon Flatland-Flipping [8]Annulene on Graphene. Chemistry 2021; 27:3420-3426. [PMID: 33295080 DOI: 10.1002/chem.202004045] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Indexed: 11/10/2022]
Abstract
Noncovalent interactions are an integral part of the modern catalysis toolbox. Although stronger noncovalent interactions such as hydrogen bonding are commonly the main driving force of catalysis, π-π interactions typically provide smaller additional stabilizations, for example, to afford selectivity enhancements. Here, it is shown computationally that pristine graphene flakes may efficiently catalyze the skeletal inversions of various benzannulated cyclooctatetraene derivatives, providing an example of a catalytic process driven solely by π-π stacking interactions. Hereby, the catalytic effect results from disproportionate shape complementarity between catalyst and transition structure compared with catalyst and reactant. An energy decomposition analysis reveals electrostatic and, especially with increasing system size, to a larger extent, dispersion interactions as the origin of stabilization.
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Affiliation(s)
- Asja A Kroeger
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Amir Karton
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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28
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Stanojević A, Milovanović B, Stanković I, Etinski M, Petković M. The significance of the metal cation in guanine-quartet – metalloporphyrin complexes. Phys Chem Chem Phys 2021; 23:574-584. [DOI: 10.1039/d0cp05798c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The distinct positions of the divalent metal ions with respect to the porphyrin ring are responsible for different interaction energies between metalloporphyrins and the guanine quartet.
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Affiliation(s)
- Ana Stanojević
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | | | - Ivana Stanković
- Institute of Chemistry
- Technology and Metallurgy
- 11 000 Belgrade
- Serbia
| | - Mihajlo Etinski
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
| | - Milena Petković
- University of Belgrade – Faculty of Physical Chemistry
- 11 158 Belgrade
- Serbia
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29
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Devasena T, Francis AP, Ramaprabhu S. Toxicity of Graphene: An Update. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2021; 259:51-76. [PMID: 34611755 DOI: 10.1007/398_2021_78] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Graphene possesses wider biomedical applications including drug delivery, photothermal ablation of tumors, biosensors, and also in the disease diagnosis. The accidental or intentional exposure of the environment including plants, ecosystem, and humans toward graphene is gradually increasing. Therefore, graphene toxicity becomes a critical issue to be addressed despite their diverse applications in multiple fields. In this situation, the scientific community as well as the general public must get awareness about the toxicity of graphene. This article, therefore, reviews the investigations on graphene toxicity. This review reveals the toxicity of graphene in vitro, in vivo models along with the environmental toxicity. The advantages of graphene toxicity in bacterial cells and cancer cells were also reviewed.
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Affiliation(s)
| | | | - Sundara Ramaprabhu
- Alternative Energy and Nanotechnology Laboratory (AENL), Nanofunctional Materials Technology, Centre (NFMTC), Department of Physics, Indian Institute of Technology Madras, Chennai, India
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30
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Kumar A, Kumar D. Interaction of Nucleic Acid Bases (NABs) with Graphene (GR) and Boron Nitride Graphene (BNG). J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Béraud A, Sauvage M, Bazán CM, Tie M, Bencherif A, Bouilly D. Graphene field-effect transistors as bioanalytical sensors: design, operation and performance. Analyst 2020; 146:403-428. [PMID: 33215184 DOI: 10.1039/d0an01661f] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Graphene field-effect transistors (GFETs) are emerging as bioanalytical sensors, in which their responsive electrical conductance is used to perform quantitative analyses of biologically-relevant molecules such as DNA, proteins, ions and small molecules. This review provides a detailed evaluation of reported approaches in the design, operation and performance assessment of GFET biosensors. We first dissect key design elements of these devices, along with most common approaches for their fabrication. We compare possible modes of operation of GFETs as sensors, including transfer curves, output curves and time series as well as their integration in real-time or a posteriori protocols. Finally, we review performance metrics reported for the detection and quantification of bioanalytes, and discuss limitations and best practices to optimize the use of GFETs as bioanalytical sensors.
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Affiliation(s)
- Anouk Béraud
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Canada.
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32
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Tardani F, Casciardi S, Ruzicka B, Sennato S. Salt enhanced sedimentation of halloysite nanotubes for precise determination of DNA adsorption isotherm. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.125400] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ahmadi M, Ahour F. An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4541-4550. [PMID: 32869790 DOI: 10.1039/d0ay01128b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.
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Affiliation(s)
- Mehran Ahmadi
- Nanotechnology Research Center, Faculty of Science, Urmia University, Urmia, Iran.
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34
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DFT study on tailoring the structural, electronic and optical properties of bilayer graphene through metalloids intercalation. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wang Y, Zhang C, Zhao YL, Zhao R, Houk KN. Understand the Specific Regio- and Enantioselectivity of Fluostatin Conjugation in the Post-Biosynthesis. Biomolecules 2020; 10:E815. [PMID: 32466453 PMCID: PMC7355926 DOI: 10.3390/biom10060815] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/22/2022] Open
Abstract
Fluostatins, benzofluorene-containing aromatic polyketides in the atypical angucycline family, conjugate into dimeric and even trimeric compounds in the post-biosynthesis. The formation of the C-C bond involves a non-enzymatic stereospecific coupling reaction. In this work, the unusual regio- and enantioselectivities were rationalized by density functional theory calculations with the M06-2X (SMD, water)/6-311 + G(d,p)//6-31G(d) method. These DFT calculations reproduce the lowest energy C1-(R)-C10'-(S) coupling pathway observed in a nonenzymatic reaction. Bonding of the reactive carbon atoms (C1 and C10') of the two reactant molecules maximizes the HOMO-LUMO interactions and Fukui function involving the highest occupied molecular orbital (HOMO) of nucleophile p-QM and lowest unoccupied molecular orbital (LUMO) of electrophile FST2- anion. In particular, the significant π-π stacking interactions of the low-energy pre-reaction state are retained in the lowest energy pathway for C-C coupling. The distortion/interaction-activation strain analysis indicates that the transition state (TScp-I) of the lowest energy pathway involves the highest stabilizing interactions and small distortion among all possible C-C coupling reactions. One of the two chiral centers generated in this step is lost upon aromatization of the phenol ring in the final difluostatin products. Thus, the π-π stacking interactions between the fluostatin 6-5-6 aromatic ring system play a critical role in the stereoselectivity of the nonenzymatic fluostatin conjugation.
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Affiliation(s)
- Yuanqi Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resource and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China;
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Rosalinda Zhao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
| | - Kendall N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; (R.Z.); (K.N.H.)
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Ma H, Xu Z, Fang H, Lei X. Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide. Phys Chem Chem Phys 2020; 22:11740-11746. [PMID: 32409813 DOI: 10.1039/d0cp01066a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A12, C12, G12, and T12) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T12) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T12 was more likely to form a quasi-parallel structure with GO compared to A12, C12, or G12. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T12 and the GO surface enabled T12 to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.
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Affiliation(s)
- Huishu Ma
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai, 201800, China
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Bhai S, Ganguly B. Probing the Interaction of Nucleobases and Fluorophore‐Tagged Nucleobases with Graphene Surface: Adsorption and Fluorescence Studies. ChemistrySelect 2020. [DOI: 10.1002/slct.201904442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Surjit Bhai
- Academy of Scientific and Innovative ResearchComputation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility) CSIR-CSMCRI, Bhavnagar- 364002 Gujarat India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar Gujarat India- 364 002
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Exploring the nature of interaction and stability between DNA/RNA base pairs and defective & defect-dopant graphene sheets. A possible insights on DNA/RNA sequencing. Int J Biol Macromol 2020; 146:387-404. [DOI: 10.1016/j.ijbiomac.2020.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/07/2019] [Accepted: 01/01/2020] [Indexed: 01/29/2023]
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Sajid H, Ullah F, Ayub K, Mahmood T. Cyclic versus straight chain oligofuran as sensor: A detailed DFT study. J Mol Graph Model 2020; 97:107569. [PMID: 32120236 DOI: 10.1016/j.jmgm.2020.107569] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/30/2020] [Accepted: 02/16/2020] [Indexed: 12/24/2022]
Abstract
This study presents a novel approach for exploring the sensitivity and selectivity of cyclic oligofuran (5/6/7CF) toward gaseous analytes and their comparison with straight chain analogues (5/6/7SF). The work is not only vital to understand the superior sensitivity but also for rational design of new sensors based on cyclic ring structures of oligofuran. Interaction of cyclic and straight chain oligofuran with NH3, CO, CO2, N2H4, HCN, H2O2, H2S, CH4, CH3OH, SO2, SO3 and H2O analytes is studied via DFT calculation at B3LYP-D3/6-31++G (d, p) level of theory. The sensitivity and selectivity are illustrated by the thermodynamic parameters (Ebind, SAPT0 energies, NCI analysis), electronic properties (H-L gap, percentage of average energy gap, CHELPG charge transfer, DOS spectra), and UV-Vis analysis. All these properties are simulated at B3LYP/6-31G (d) level of theory while UV-Vis is calculated at TD-DFT method. Cyclic oligofurans have high binding energies with analytes compared to 5/6/7SF which corresponds to higher sensitivity of 5/6/7CF. Furthermore, the cyclization of oligofuran significantly improves the sensitivity and selectivity of the system. Alteration in electronic properties of 5/6/7CF and 5/6/7SF is remarkably high upon complexation with SO2 and SO3. Further the stability of rings (5, 6 and 7 membered cyclic oligofurans) and their SO3 complexes is also confirmed by molecular dynamics calculations. The findings of the work clearly suggest that the cyclic geometry enhances not only sensitivity but also selectivity of conducting polymers (oligofuran).
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Affiliation(s)
- Hasnain Sajid
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Faizan Ullah
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
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40
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Theoretical studies of the paracetamol and phenacetin adsorption on single-wall boron-nitride nanotubes: a DFT and MD investigation. Struct Chem 2020. [DOI: 10.1007/s11224-020-01499-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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41
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Chen SL, Chen CY, Hsieh JCH, Yu ZY, Cheng SJ, Hsieh KY, Yang JW, Kumar PV, Lin SF, Chen GY. Graphene Oxide-Based Biosensors for Liquid Biopsies in Cancer Diagnosis. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E1725. [PMID: 31816919 PMCID: PMC6956293 DOI: 10.3390/nano9121725] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/25/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
Liquid biopsies use blood or urine as test samples, which are able to be continuously collected in a non-invasive manner. The analysis of cancer-related biomarkers such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), microRNA, and exosomes provides important information in early cancer diagnosis, tumor metastasis detection, and postoperative recurrence monitoring assist with clinical diagnosis. However, low concentrations of some tumor markers, such as CTCs, ctDNA, and microRNA, in the blood limit its applications in clinical detection and analysis. Nanomaterials based on graphene oxide have good physicochemical properties and are now widely used in biomedical detection technologies. These materials have properties including good hydrophilicity, mechanical flexibility, electrical conductivity, biocompatibility, and optical performance. Moreover, utilizing graphene oxide as a biosensor interface has effectively improved the sensitivity and specificity of biosensors for cancer detection. In this review, we discuss various cancer detection technologies regarding graphene oxide and discuss the prospects and challenges of this technology.
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Affiliation(s)
- Shiue-Luen Chen
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Chong-You Chen
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Jason Chia-Hsun Hsieh
- Division of Haematology/Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital (Linkou), Taoyuan 333, Taiwan;
| | - Zih-Yu Yu
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
| | - Sheng-Jen Cheng
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Kuan Yu Hsieh
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Jia-Wei Yang
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Priyank V Kumar
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Shien-Fong Lin
- Department of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan; (S.-L.C.); (C.-Y.C.); (Z.-Y.Y.); (S.-J.C.); (K.Y.H.); (J.-W.Y.); (S.-F.L.)
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Guan-Yu Chen
- Institute of Biomedical Engineering, College of Electrical and Computer Engineering, National Chiao Tung University, Hsinchu 300, Taiwan
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan
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42
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Moore TC, Yang AH, Ogungbesan O, Hartkamp R, Iacovella CR, Zhang Q, McCabe C. Influence of Single-Stranded DNA Coatings on the Interaction between Graphene Nanoflakes and Lipid Bilayers. J Phys Chem B 2019; 123:7711-7721. [PMID: 31405277 DOI: 10.1021/acs.jpcb.9b04042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Using molecular dynamics simulations, it is demonstrated that a partial coating of single-stranded DNA (ssDNA) reduces the penetration depth of a graphene nanoflake (GNF) into a phospholipid bilayer by attenuating the hydrophobic force that drives the penetration. As the GNF penetrates the bilayer, the ssDNA remains adsorbed to the GNF outside of the bilayer where it shields the graphene from the surrounding water. The penetration depth is found to be controlled by the amount of ssDNA coating the GNF, with a sparser coating resulting in a deeper penetration since the ssDNA shields less of the GNF surface. As the coating density is increased, the likelihood of the GNF entering the bilayer is reduced where it instead tends to lie flat on the bilayer surface with the sugar phosphate backbone of ssDNA interacting with the hydrophilic lipid head groups. While no bilayer disruption is observed for a partially inserted ssDNA-coated GNF, a larger, bare, partially inserted GNF is found to preferentially extract phospholipids from the bilayer, offering further evidence of lipid extraction as a main cytotoxicity mechanism of GNFs. Therefore, a coating of ssDNA may reduce the cytotoxicity of GNFs by shielding the unfavorable graphene-water interaction, thus preventing graphene penetration and lipid extraction.
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Affiliation(s)
| | | | - Olu Ogungbesan
- Department of Chemical, Biochemical, and Environmental Engineering , University of Maryland Baltimore County , Baltimore , Maryland 21201 , United States
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Density functional theory study of π-aromatic interaction of benzene, phenol, catechol, dopamine isolated dimers and adsorbed on graphene surface. J Mol Model 2019; 25:302. [PMID: 31486895 DOI: 10.1007/s00894-019-4185-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
We analyze the influence of different groups on the intermolecular energy of aromatic homodimers and on the interaction between a single aromatic molecule and a graphene surface. The analysis is performed for benzene, phenol, catechol, and dopamine. For calculating the energies, we employ density functional theory within the local density approximation (LDA-DFT). Our results show that the lowest intermolecular energies between the aromatic molecules are related to the T-shaped configurations. This lower energy results from the quadrupole interaction. In the case of the interaction between the graphene sheet and the aromatic molecules, the lowest energy configuration is the face to face. The adsorption energy of a molecule on a graphene surface involves π - π interactions that explain the face to face arrangement. These results provide insight into the manner by which substituents can be utilized in crystal engineering, supramolecular chemistry, bioinspired materials, formation of various molecular clusters, parameterization of force fields suitable for classical simulations, and design of novel sensing, drug delivery, and filters based on graphene.
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44
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Influence of the lengths of thymine, cytosine, and adenine stretches on the two-dimensional condensation of oligodeoxynucleotides at mercury and silver amalgam electrode surfaces. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.113364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Putri AD, Murti BT, Kanchi S, Sabela MI, Bisetty K, Tiwari A, Inamuddin, Asiri AM. Computational studies on the molecular insights of aptamer induced poly(N-isopropylacrylamide)-graft-graphene oxide for on/off- switchable whole-cell cancer diagnostics. Sci Rep 2019; 9:7873. [PMID: 31133671 PMCID: PMC6536548 DOI: 10.1038/s41598-019-44378-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 05/13/2019] [Indexed: 01/04/2023] Open
Abstract
This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an "on/off"-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system's π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.
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Affiliation(s)
- Athika Darumas Putri
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
- Semarang College of Pharmaceutical Sciences, Jl. Letnand Jendral Sarwo Edi Wibowo, Semarang City, 50192, Indonesia
| | - Bayu Tri Murti
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
- Semarang College of Pharmaceutical Sciences, Jl. Letnand Jendral Sarwo Edi Wibowo, Semarang City, 50192, Indonesia
| | - Suvardhan Kanchi
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
| | - Myalowenkosi I Sabela
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa
| | - Krishna Bisetty
- Department of Chemistry, Faculty of Applied Science, Durban University of Technology, Durban, 4000, South Africa.
| | - Ashutosh Tiwari
- Institute of Advanced Materials, UCS, Teknikringen 4A, Mjärdevi Science Park, SE-58330, Linköping, Sweden
- Vinoba Bhave Research Institute, Binda-Dhokri Road, Saidabad, Allahabad, 221508, India
| | - Inamuddin
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
- Centre of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Abdullah M Asiri
- Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Centre of Excellence for Advanced Materials Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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Lin TX, Lai PX, Mao JY, Chu HW, Unnikrishnan B, Anand A, Huang CC. Supramolecular Aptamers on Graphene Oxide for Efficient Inhibition of Thrombin Activity. Front Chem 2019; 7:280. [PMID: 31157200 PMCID: PMC6532589 DOI: 10.3389/fchem.2019.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/05/2019] [Indexed: 01/08/2023] Open
Abstract
Graphene oxide (GO), a two-dimensional material with a high aspect ratio and polar functional groups, can physically adsorb single-strand DNA through different types of interactions, such as hydrogen bonding and π-π stacking, making it an attractive nanocarrier for nucleic acids. In this work, we demonstrate a strategy to target exosites I and II of thrombin simultaneously by using programmed hybrid-aptamers for enhanced anticoagulation efficiency and stability. The targeting ligand is denoted as Supra-TBA15/29 (supramolecular TBA15/29), containing TBA15 (a 15-base nucleotide, targeting exosite I of thrombin) and TBA29 (a 29-base nucleotide, targeting exosite II of thrombin), and it is designed to allow consecutive hybridization of TBA15 and TBA29 to form a network of TBAs (i.e., supra-TBA15/29). The programmed hybrid-aptamers (Supra-TBA15/29) were self-assembled on GO to further boost anticoagulation activity by inhibiting thrombin activity, and thus suppress the thrombin-induced fibrin formation from fibrinogen. The Supra-TBA15/29-GO composite was formed mainly through multivalent interaction between poly(adenine) from Supra-TBA15/29 and GO. We controlled the assembly of Supra-TBA15/29 on GO by regulating the preparation temperature and the concentration ratio of Supra-TBA15/29 to GO to optimize the distance between TBA15 and TBA29 units, aptamer density, and aptamer orientation on the GO surfaces. The dose-dependent thrombin clotting time (TCT) delay caused by Supra-TBA15/29-GO was >10 times longer than that of common anticoagulant drugs including heparin, argatroban, hirudin, and warfarin. Supra-TBA15/29-GO exhibits high biocompatibility, which has been proved by in vitro cytotoxicity and hemolysis assays. In addition, the thromboelastography of whole-blood coagulation and rat-tail bleeding assays indicate the anticoagulation ability of Supra-TBA15/29-GO is superior to the most widely used anticoagulant (heparin). Our highly biocompatible Supra-TBA15/29-GO with strong multivalent interaction with thrombin [dissociation constant (K d) = 1.9 × 10-11 M] shows great potential as an effective direct thrombin inhibitor for the treatment of hemostatic disorders.
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Affiliation(s)
- Ting-Xuan Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Pei-Xin Lai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ju-Yi Mao
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
| | - Han-Wei Chu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Binesh Unnikrishnan
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Anisha Anand
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Ching Huang
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan.,Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
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47
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Qin X, Wang Q, Geng L, Shu X, Wang Y. A “signal-on” photoelectrochemical aptasensor based on graphene quantum dots-sensitized TiO2 nanotube arrays for sensitive detection of chloramphenicol. Talanta 2019; 197:28-35. [DOI: 10.1016/j.talanta.2018.12.103] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/26/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023]
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48
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Zhang B, Lu Y, Yang C, Guo Q, Nie G. Simple "signal-on" photoelectrochemical aptasensor for ultrasensitive detecting AFB1 based on electrochemically reduced graphene oxide/poly(5-formylindole)/Au nanocomposites. Biosens Bioelectron 2019; 134:42-48. [PMID: 30954925 DOI: 10.1016/j.bios.2019.03.048] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/23/2023]
Abstract
A simple "signal-on" photoelectrochemical (PEC) aptasensor is constructed for Aflatoxin B1 (AFB1) detection based on electrochemically reduced graphene oxide/poly(5-formylindole)/Au (erGO/P5FIn/Au) nanocomposites. The nanocomposites are synthesized by simple electrochemical deposition method and show good photoelectrochemical performance. Poly(5-formylindole) (P5FIn) can generate electron-hole pairs under light irradiation, leading to the formation of robust cathode photocurrent. Au can be acted as signal amplifier due to the high conductivity. The erGO is used to immobilize AFB1 aptamer chain by π-π stacking interaction between the carbon six-membered ring in graphene and the C-N heterocyclic ring in nucleobases of ssDNA. After the insulating AFB1 aptamer chain is fixed to the electrode, the signal of PEC sensor is "OFF". In the process of AFB1 detection, the aptamer chain detaches from the surface of erGO, which results in "ON" of the sensor signal. Based on this design, this constructed PEC aptasensor shows a high sensitivity for AFB1 with a wide linear detection range (LDR) from 0.01 ng mL-1 to 100 ng mL-1. The limit of detection (LOD) is 0.002 ng mL-1. This PEC sensor also exhibits good stability, selectivity, specificity, and satisfactory practical sample analysis ability. This work may provide a new promising PEC platform for AFB1 detection as well as some other small molecules analysis.
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Affiliation(s)
- Bin Zhang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Yan Lu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Chaonan Yang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Qingfu Guo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Guangming Nie
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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49
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Ajala AO, Voora V, Mardirossian N, Furche F, Paesani F. Assessment of Density Functional Theory in Predicting Interaction Energies between Water and Polycyclic Aromatic Hydrocarbons: from Water on Benzene to Water on Graphene. J Chem Theory Comput 2019; 15:2359-2374. [PMID: 30860827 DOI: 10.1021/acs.jctc.9b00110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The interactions of water with polycyclic aromatic hydrocarbons, from benzene to graphene, are investigated using various exchange-correlation functionals selected across the hierarchy of density functional theory (DFT) approximations. The accuracy of the different functionals is assessed through comparisons with random phase approximation (RPA) and coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] calculations. Diffusion Monte Carlo (DMC) data reported in the literature are also used for comparison. Relatively large variations are found in interaction energies predicted by different DFT models, with GGA functionals underestimating the interaction strength for configurations with the water oxygen pointing toward the aromatic molecules. The meta-GGA B97M-rV and range-separated hybrid, meta-GGA ωB97M-V functionals provide nearly quantitative agreement with CCSD(T) values for the water-benzene, water-coronene, and water-circumcoronene dimers, while RPA and DMC predict interaction energies that differ by up to ∼1 kcal/mol and ∼0.4 kcal/mol from the corresponding CCSD(T) values, respectively. Similar trends among GGA, meta-GGA, and hybrid functionals are observed for larger polycyclic aromatic hydrocarbons. By performing absolutely localized molecular orbital energy decomposition analyses (ALMO-EDA), it is found that, independently of the number of carbon atoms and exchange-correlation functional, the dominant contributions to the interaction energies between water and polycyclic aromatic hydrocarbon molecules are the electrostatic and dispersion terms while polarization and charge transfer effects are negligibly small. Calculations carried out with GGA and meta-GGA functionals indicate that, as the number of carbon atoms increases, the interaction energies slowly converge to the corresponding values obtained for an infinite graphene sheet.
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Affiliation(s)
- Adeayo O Ajala
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , United States
| | - Vamsee Voora
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
| | - Narbe Mardirossian
- Division of Chemistry and Chemical Engineering , California Institute of Technology , 1200 E. California Boulevard , Pasadena , California 91125 , United States
| | - Filipp Furche
- Department of Chemistry , University of California Irvine , Irvine , California 92697 , United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California San Diego , La Jolla , California 92093 , United States.,Materials Science and Engineering , University of California San Diego , La Jolla , California 92093 , United States.,San Diego Supercomputer Center , University of California San Diego , La Jolla , California 92093 , United States
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50
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Affiliation(s)
- Amita Sihag
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
| | - Sairam S. Mallajosyula
- Department of ChemistryIndian Institute of Technology Gandhinagar Palaj, Gandhinagar Gujrat – 382355 India
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