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Mukhopadhyay T, Ghosh A, Datta A. Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook. ACS PHYSICAL CHEMISTRY AU 2024; 4:97-121. [PMID: 38560753 PMCID: PMC10979489 DOI: 10.1021/acsphyschemau.3c00053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 04/04/2024]
Abstract
Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.
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Affiliation(s)
- Titas
Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Anupam Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road,
Jadavpur, Kolkata 700032, West Bengal, India
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2
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Liu Z, Zhou J, Wang X, Zhao J, Zhao P, Ma Y, Zhang S, Huo D, Hou C, Ren K. Graphene oxide mediated CdSe quantum dots fluorescent aptasensor for high sensitivity detection of fluoroquinolones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123497. [PMID: 37813087 DOI: 10.1016/j.saa.2023.123497] [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: 07/04/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023]
Abstract
In view of the urgent need for fluoroquinolones contamination detection in the fields of food safety, a novel aptasensor based on the fluorescence quenching property of graphene oxide (GO) and the fluorescence characteristic of cadmium selenide quantum dots (CdSe QDs) was developed for fluoroquinolones highly sensitive detection in this work. The CdSe QDs with carboxyl-rich surface were synthesized successfully and fluoresced at 525 nm under the optimal excitation light of 366 nm. Based on the hydrophobic and π-π stacking between GO and aptamer, aptamer labeled by CdSe QDs fluorescence (CdSe QDs-apt) were adsorbed by GO and the fluorescence of CdSe QDs was quenched. After the aptamer combined specifically with fluoroquinolones, greater specific force lead to the desorption of CdSe QDs-apt from GO and fluorescence recovery. Represented by Ciprofloxacin (CIP), a member of fluoroquinolones, the fluorescence emission increased with the increasing of CIP concentrations from 8 nM to 500 nM, and the detection limit was 0.42 nM. The spiked recoveries in real samples of honey and milk were 91.5-96.9 % and 90.3-95.2 %, respectively, indicating that the aptasensor was reliable. Moreover, the fluorescence responses of multiple members of fluoroquinolones were found to be consistent, denoting that the fluorescence aptasensor can be used to detect the total amount of multiple members of fluoroquinolones. These results showed that the aptasensor can be used as a promising platform for fluoroquinolones detection.
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Affiliation(s)
- Zhenping Liu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; Chongqing Vocational Institute of Safety Technology, Chongqing 404000, PR China; Sichuan 'DingDianEr' Food Development Co., Ltd, Chengdu 611732, PR China
| | - Jun Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou Laojiao Group Co. Ltd., Luzhou 646000, PR China
| | - Xianfeng Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Jinsong Zhao
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yibin 644000, PR China
| | - Peng Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Yi Ma
- Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yibin 644000, PR China.
| | - Suyi Zhang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; National Engineering Research Center of Solid-State Brewing, Luzhou Laojiao Group Co. Ltd., Luzhou 646000, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China; Liquor Making Biology Technology and Application of Key Laboratory of Sichuan Province, College of Bioengineering, Sichuan University of Science and Engineering, 188 University Town, Yibin 644000, PR China.
| | - Kang Ren
- Sichuan 'DingDianEr' Food Development Co., Ltd, Chengdu 611732, PR China
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3
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H H, Mallajosyula SS. Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55095-55108. [PMID: 37965826 DOI: 10.1021/acsami.3c12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.
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Affiliation(s)
- Hemanth H
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
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4
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Wang H, Sun Y, Zhou Y, Liu Y, Chen S, Sun W, Zhang Z, Guo J, Yang C, Li Z, Chen L. Unamplified system for sensitive and typing detection of ASFV by the cascade platform that CRISPR-Cas12a combined with graphene field-effect transistor. Biosens Bioelectron 2023; 240:115637. [PMID: 37669587 DOI: 10.1016/j.bios.2023.115637] [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: 05/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
At present, the 100% case fatality and the cross-infection of virus strains make the ASFV 's harm to society continue to expand. The absence of an effective commercial vaccine poses early detection remains the most effective means of curbing ASFV infection. Here, we report a cascaded detection platform based on the CRISPR-Cas12a system combined with graphene field-effect transistor sensors. The cascade platform could detect ASFV as low as 0.5 aM within 30 min and achieve typing of wild and vaccine strains of ASFV in a single detection system. The evaluation of 16 clinical samples proved that, compared with the gold standard Real-time PCR method, this platform has outstanding advantages in sensitivity, specificity and typing. Combining CRISPR-Cas12a's high specificity with the bipolar electric field effect of graphene field-effect transistor, the cascade platform is expected to achieve clinical application in the field of DNA disease detection, and provides a new direction for multi-strain disease typing.
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Affiliation(s)
- Hua Wang
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Yang Sun
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
| | - Yuan Zhou
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Yujie Liu
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Shuo Chen
- Department of Physics and Electronics, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Wenbo Sun
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, PR China
| | - Zidong Zhang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Shandong University, No. 17923 Jing Shi Road, Jinan, 250061, PR China
| | - Junqing Guo
- Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, 116 Huayuan Road, Zhengzhou, 450099, PR China
| | - Cheng Yang
- Department of Physics and Electronics, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
| | - Zhengping Li
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
| | - Lei Chen
- Department of Life Sciences, Shandong Normal University, 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
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5
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Richter L, Szalai AM, Manzanares-Palenzuela CL, Kamińska I, Tinnefeld P. Exploring the Synergies of Single-Molecule Fluorescence and 2D Materials Coupled by DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303152. [PMID: 37670535 DOI: 10.1002/adma.202303152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2023] [Indexed: 09/07/2023]
Abstract
The world of 2D materials is steadily growing, with numerous researchers attempting to discover, elucidate, and exploit their properties. Approaches relying on the detection of single fluorescent molecules offer a set of advantages, for instance, high sensitivity and specificity, that allow the drawing of conclusions with unprecedented precision. Herein, it is argued how the study of 2D materials benefits from fluorescence-based single-molecule modalities, and vice versa. A special focus is placed on DNA, serving as a versatile adaptor when anchoring single dye molecules to 2D materials. The existing literature on the fruitful combination of the two fields is reviewed, and an outlook on the additional synergies that can be created between them provided.
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Affiliation(s)
- Lars Richter
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Alan M Szalai
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - C Lorena Manzanares-Palenzuela
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
| | - Izabela Kamińska
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
- Institute of Physical Chemistry of the Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, Haus E, 81377, München, Germany
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6
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Chen S, Bashir R. Advances in field-effect biosensors towards point-of-use. NANOTECHNOLOGY 2023; 34:492002. [PMID: 37625391 PMCID: PMC10523595 DOI: 10.1088/1361-6528/acf3f0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/11/2023] [Accepted: 08/25/2023] [Indexed: 08/27/2023]
Abstract
The future of medical diagnostics calls for portable biosensors at the point of care, aiming to improve healthcare by reducing costs, improving access, and increasing quality-what is called the 'triple aim'. Developing point-of-care sensors that provide high sensitivity, detect multiple analytes, and provide real time measurements can expand access to medical diagnostics for all. Field-effect transistor (FET)-based biosensors have several advantages, including ultrahigh sensitivity, label-free and amplification-free detection, reduced cost and complexity, portability, and large-scale multiplexing. They can also be integrated into wearable or implantable devices and provide continuous, real-time monitoring of analytesin vivo, enabling early detection of biomarkers for disease diagnosis and management. This review analyzes advances in the sensitivity, parallelization, and reusability of FET biosensors, benchmarks the limit of detection of the state of the art, and discusses the challenges and opportunities of FET biosensors for future healthcare applications.
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Affiliation(s)
- Sihan Chen
- Holonyak Micro and Nanotechnology Laboratory, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Rashid Bashir
- Holonyak Micro and Nanotechnology Laboratory, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
- Department of Bioengineering, The Grainger College of Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States of America
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7
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Yang Y, Kong D, Wu Y, Chen Y, Dai C, Chen C, Zhao J, Luo S, Liu W, Liu Y, Wei D. Catalytic Hairpin Assembly-Enhanced Graphene Transistor for Ultrasensitive miRNA Detection. Anal Chem 2023; 95:13281-13288. [PMID: 37610301 DOI: 10.1021/acs.analchem.3c02433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
MicroRNAs (miRNAs) have emerged as powerful biomarkers for disease diagnosis and screening. Traditional miRNA analytical techniques are inadequate for point-of-care testing due to their reliance on specialized expertise and instruments. Graphene field-effect transistors (GFETs) offer the prospect of simple and label-free diagnostics. Herein, a GFET biosensor based on tetrahedral DNA nanostructure (TDN)-assisted catalytic hairpin assembly (CHA) reaction (TCHA) has been fabricated and applied to the sensitive and specific detection of miRNA-21. TDN structures are assembled to construct the biosensing interface, facilitating CHA reaction by providing free space and preventing unwanted entanglements, aggregation, and adsorption of probes on the graphene channel. Owing to synergistic effects of TDN-assisted in situ nucleic acid amplification on the sensing surface, as well as inherent signal sensitization of GFETs, the biosensor exhibits ultrasensitive detection of miRNA-21 down to 5.67 × 10-19 M, approximately three orders of magnitude lower than that normally achieved by graphene transistors with channel functionalization of single-stranded DNA probes. In addition, the biosensor demonstrates excellent analytical performance regarding selectivity, stability, and reproducibility. Furthermore, the practicability of the biosensor is verified by analyzing targets in a complex serum environment and cell lysates, showing tremendous potential in bioanalysis and clinical diagnosis.
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Affiliation(s)
- Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Chang Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Junhong Zhao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Shi Luo
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Wentao Liu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai 200433, China
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8
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Devémy J, Dequidt A, Malfreyt P. A Consistent Thermodynamic Characterization of the Adsorption Process through the Calculation of Free Energy Contributions. J Phys Chem B 2023. [PMID: 37279165 DOI: 10.1021/acs.jpcb.3c01947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We apply in this study different methodologies based on thermodynamic integration (TI), free energy perturbation (FEP), and potential of mean force (PMF) to address the challenging issue of the calculation of the free energy of adsorption. A model system composed of a solid substrate, an adsorbate, and solvent particles is specifically designed to reduce the dependence of our free energy results on the sampling of the phase space and the choice of the pathway. The reliability and efficiency of these alchemical free energy simulations are established through the closure of a thermodynamic cycle describing the adsorption process in solution and in a vacuum. We complete this study by the calculation of free energy contributions related to phenomena of desorption of solvent molecules and desolvation of the adsorbate upon adsorption. This calculation relies on the work of adhesion, the interfacial tension of the liquid-vapor of the solvent, and the free energy of solvation of the substrate. The different ways of calculating the free energy of adsorption are in excellent agreement and could complete experiments in the field of adsorption by giving quantitative data on the different energy contributions involved in the process.
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Affiliation(s)
- Julien Devémy
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Alain Dequidt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Université Clermont Auvergne, CNRS, Clermont Auvergne INP, Institut de Chimie de Clermont-Ferrand, F-63000 Clermont-Ferrand, France
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9
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Sun Y, Yang C, Jiang X, Zhang P, Chen S, Su F, Wang H, Liu W, He X, Chen L, Man B, Li Z. High-intensity vector signals for detecting SARS-CoV-2 RNA using CRISPR/Cas13a couple with stabilized graphene field-effect transistor. Biosens Bioelectron 2023; 222:114979. [PMID: 36463654 PMCID: PMC9710152 DOI: 10.1016/j.bios.2022.114979] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
False detection of SARS-CoV-2 is detrimental to epidemic prevention and control. The scalar nature of the detected signal and the imperfect target recognition property of developed methods are the root causes of generating false signals. Here, we reported a collaborative system of CRISPR-Cas13a coupling with the stabilized graphene field-effect transistor, providing high-intensity vector signals for detecting SARS-CoV-2. In this collaborative system, SARS-CoV-2 RNA generates a "big subtraction" signal with a right-shifted feature, whereas any untargets cause the left-shifted characteristic signal. Thus, the false detection of SARS-CoV-2 is eliminated. High sensitivity with 0.15 copies/μL was obtained. In addition, the wide concerned instability of the graphene field-effect transistor for biosensing in solution environment was solved by the hydrophobic treatment to its substrate, which should be a milestone in advancing it's engineering application. This collaborative system characterized by the high-intensity vector signal and amazing stability significantly advances the accurate SARS-CoV-2 detection from the aspect of signal nature.
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Affiliation(s)
- Yang Sun
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Cheng Yang
- Department of Physics and Electronics, Shandong Normal University 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Xiaolin Jiang
- Shandong Provincial Key Laboratory of Communicable Disease Control and Prevention, Shandong Center for Disease Control and Prevention, 16992 Jingshi Road, Lixia District, Jinan, Shandong Province, 250014, PR China
| | - Pengbo Zhang
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Shuo Chen
- Department of Physics and Electronics, Shandong Normal University 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China
| | - Fengxia Su
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Hui Wang
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Weiliang Liu
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Xiaofei He
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China
| | - Lei Chen
- Department of of Life Sciences, Shandong Normal University 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
| | - Baoyuan Man
- Department of Physics and Electronics, Shandong Normal University 1 Daxue Road, Changqing District, Jinan, Shandong Province, 250014, PR China.
| | - Zhengping Li
- Department of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District, Beijing, 100083, PR China.
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10
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Jiang H, Xia Q, Zheng J, Bu J, Li R, Cai Z, Ling K. Mn 2+ modified black phosphorus nanosheets with enhanced DNA adsorption and affinity for robust sensing. Biosens Bioelectron 2022; 216:114622. [PMID: 35973273 DOI: 10.1016/j.bios.2022.114622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/17/2022] [Accepted: 08/03/2022] [Indexed: 02/05/2023]
Abstract
To develop various biosensors, several 2D nanomaterials adsorb DNA probes (aptamers) via π-π stacking interactions. However, interference from DNA displacement by external non-targeted ligands has precluded their practical applications for specific detection and imaging at high protein concentrations. Metal coordination is an attractive strategy for biomolecular crosslinking and functional molecular self-assembly. Herein, a robust 2D biosensor nanoplatform was developed to enhance DNA adsorption and affinity using Mn2+-modified black phosphorus nanosheets (BPNS@Mn2+) via metal coordination. The Mn2+ can simultaneously coordinate with the lone pair electrons (π bonds) of the BPNS and nucleotide bases to provide binding sites for DNA nucleobases on the BPNS surface, which greatly enhances the stability of the inner BPNS and improves DNA adsorption and affinity. The DNA adsorption mechanism of BPNS@Mn2+ was also characterized, and is extensively discussed. Without any further modification, this BPNS@Mn2+/DNA biosensor specifically detected single-stranded DNA (linear range: 10-200 nM, detection limit: 5.76 nM) and thrombin (linear range: 20-180 nM, detection limit: 2.39 nM) in 100 nM bovine serum albumin solution. The nonspecific ligands in the environment did not affect the detection performance of the robust biosensor. In addition, the expression levels of microRNA-21 can be imaged and analyzed in living cells using this biosensor, which is consistent with the results of the polymerase chain reaction. This study highlights the potential of metal coordination in surface modification and provides new opportunities for biomedical applications of 2D nanomaterials with superior DNA-adsorption capacity, facilitating the development of biosensor design and nucleic acid/drug delivery.
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Affiliation(s)
- Hongyan Jiang
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Qing Xia
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Jintao Zheng
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Jianlan Bu
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Rui Li
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Zehong Cai
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
| | - Kai Ling
- Department of Pharmacy and Department of Radiology (The First Affiliated Hospital), Shantou University Medical College, Shantou, 515041, China
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11
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Isolation and Characterization of a ssDNA Aptamer against Major Soluble Antigen of Renibacterium salmoninarum. Molecules 2022; 27:molecules27061853. [PMID: 35335217 PMCID: PMC8951219 DOI: 10.3390/molecules27061853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/29/2022] Open
Abstract
Bacterial kidney disease (BKD) is a major health problem of salmonids, affecting both wild and cultured salmon. The disease is caused by Renibacterium salmoninarum (Rs), a fastidious, slow-growing and strongly Gram-positive diplobacillus that produces chronic, systemic infection characterized by granulomatous lesions in the kidney and other organs, often resulting in death. Fast detection of the pathogen is important to limit the spread of the disease, particularly in hatcheries or aquaculture facilities. Aptamers are increasingly replacing conventional antibodies as platforms for the development of rapid diagnostic tools. In this work, we describe the first instance of isolating and characterizing a ssDNA aptamer that binds with high affinity to p57 or major soluble antigen (MSA), the principal antigen found on the cell wall surface of Rs. Specifically, in this study a construct of the full-length protein containing a DNA binding domain (MSA-R2c) was utilized as target. Aptamers were isolated from a pool of random sequences using GO-SELEX (graphene oxide-systematic evolution of ligands by exponential enrichment) protocol. The selection generated multiple aptamers with conserved motifs in the random region. One aptamer with high frequency of occurrence in different clones was characterized and found to display a strong binding affinity to MSA-R2c with a Kd of 3.0 ± 0.6 nM. The aptamer could be potentially utilized for the future development of a sensor for rapid and onsite detection of Rs in water or in infected salmonids, replacing time-consuming and costly lab analyses.
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12
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Wang L, Wang X, Wu Y, Guo M, Gu C, Dai C, Kong D, Wang Y, Zhang C, Qu D, Fan C, Xie Y, Zhu Z, Liu Y, Wei D. Rapid and ultrasensitive electromechanical detection of ions, biomolecules and SARS-CoV-2 RNA in unamplified samples. Nat Biomed Eng 2022. [PMID: 35132229 DOI: 10.1038/s41551-41021-00833-41557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The detection of samples at ultralow concentrations (one to ten copies in 100 μl) in biofluids is hampered by the orders-of-magnitude higher amounts of 'background' biomolecules. Here we report a molecular system, immobilized on a liquid-gated graphene field-effect transistor and consisting of an aptamer probe bound to a flexible single-stranded DNA cantilever linked to a self-assembled stiff tetrahedral double-stranded DNA structure, for the rapid and ultrasensitive electromechanical detection (down to one to two copies in 100 μl) of unamplified nucleic acids in biofluids, and also of ions, small molecules and proteins, as we show for Hg2+, adenosine 5'-triphosphate and thrombin. We implemented an electromechanical biosensor for the detection of SARS-CoV-2 into an integrated and portable prototype device, and show that it detected SARS-CoV-2 RNA in less than four minutes in all nasopharyngeal samples from 33 patients with COVID-19 (with cycle threshold values of 24.9-41.3) and in none of the 54 COVID-19-negative controls, without the need for RNA extraction or nucleic acid amplification.
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Affiliation(s)
- Liqian Wang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chenjian Gu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Yao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cong Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China
- Department of Macromolecular Science, Fudan University, Shanghai, China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai, China.
- Department of Macromolecular Science, Fudan University, Shanghai, China.
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, China.
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13
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Wang L, Wang X, Wu Y, Guo M, Gu C, Dai C, Kong D, Wang Y, Zhang C, Qu D, Fan C, Xie Y, Zhu Z, Liu Y, Wei D. Rapid and ultrasensitive electromechanical detection of ions, biomolecules and SARS-CoV-2 RNA in unamplified samples. Nat Biomed Eng 2022; 6:276-285. [DOI: 10.1038/s41551-021-00833-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/17/2021] [Indexed: 12/21/2022]
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14
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Faikhruea K, Choopara I, Somboonna N, Assavalapsakul W, Kim BH, Vilaivan T. Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects. ACS APPLIED BIO MATERIALS 2022; 5:789-800. [PMID: 35119822 DOI: 10.1021/acsabm.1c01177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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15
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Wang X, Kong D, Guo M, Wang L, Gu C, Dai C, Wang Y, Jiang Q, Ai Z, Zhang C, Qu D, Xie Y, Zhu Z, Liu Y, Wei D. Rapid SARS-CoV-2 Nucleic Acid Testing and Pooled Assay by Tetrahedral DNA Nanostructure Transistor. NANO LETTERS 2021; 21:9450-9457. [PMID: 34734737 DOI: 10.1021/acs.nanolett.1c02748] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Affiliation(s)
- Xuejun Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Liqian Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Chenjian Gu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Yao Wang
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qunfeng Jiang
- Department of Physics, Fudan University, Shanghai 200433, China
| | - Zhaolin Ai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Cong Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
| | - Di Qu
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youhua Xie
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhaoqin Zhu
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yunqi Liu
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
- Institute of Molecular Materials and Devices, Department of Material Science, Fudan University, Shanghai 200433, China
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16
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Kim DM, Go MJ, Lee J, Na D, Yoo SM. Recent Advances in Micro/Nanomaterial-Based Aptamer Selection Strategies. Molecules 2021; 26:5187. [PMID: 34500620 PMCID: PMC8434002 DOI: 10.3390/molecules26175187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are artificial nucleic acid ligands that have been employed in various fundamental studies and applications, such as biological analyses, disease diagnostics, targeted therapeutics, and environmental pollutant detection. This review focuses on the recent advances in aptamer discovery strategies that have been used to detect various chemicals and biomolecules. Recent examples of the strategies discussed here are based on the classification of these micro/nanomaterial-mediated systematic evolution of ligands by exponential enrichment (SELEX) platforms into three categories: bead-mediated, carbon-based nanomaterial-mediated, and other nanoparticle-mediated strategies. In addition to describing the advantages and limitations of the aforementioned strategies, this review discusses potential strategies to develop high-performance aptamers.
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Affiliation(s)
- Dong-Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon 34158, Korea;
| | - Myeong-June Go
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
| | - Seung-Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul 06974, Korea; (M.-J.G.); (J.L.)
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17
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Nandu N, Smith CW, Uyar TB, Chen YS, Kachwala MJ, He M, Yigit MV. Machine-Learning Single-Stranded DNA Nanoparticles for Bacterial Analysis. ACS APPLIED NANO MATERIALS 2020; 3:11709-11714. [PMID: 34095773 PMCID: PMC8174836 DOI: 10.1021/acsanm.0c03001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
A two-dimensional nanoparticle-single-stranded DNA (ssDNA) array has been assembled for the detection of bacterial species using machine-learning (ML) algorithms. Out of 60 unknowns prepared from bacterial lysates, 54 unknowns were predicted correctly. Furthermore, the nanosensor array, supported by ML algorithms, was able to distinguish wild-type Escherichia coli from its mutant by a single gene difference. In addition, the nanosensor array was able to distinguish untreated wild-type E. coli from those treated with antimicrobial drugs. This work demonstrates the potential of nanoparticle-ssDNA arrays and ML algorithms for the discrimination and identification of complex biological matrixes.
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Affiliation(s)
- Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Taha Bilal Uyar
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Yu-Sheng Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Muhan He
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
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18
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Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13708-13715. [PMID: 33161721 DOI: 10.1021/acs.langmuir.0c02761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yu Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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19
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Sensing and Interaction of His-Tagged CA19-9 Antigen with Graphene-Modified Electrodes. CHEMOSENSORS 2020. [DOI: 10.3390/chemosensors8040112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The electrochemical oxidation of CA19-9 tagged with L-Histidine (CA199-His) was investigated for the first time with screen-printed electrodes (DS) modified with graphene oxide (DS/GO) or thermally reduced graphene oxide (DS/TRGO). Successive cyclic voltammograms (CV) measurements performed with bare and DS/TRGO electrodes proved that the intensity of the oxidation peak (I peak) is time-dependent. In fact, the oxidation signal increased over time, reached a maximum and then decreased due to the saturation of the surface with CA199-His molecules. The interaction of CA199-His with GO, TRGO, or graphite was additionally studied by isothermal calorimetry, a useful tool for accessing information regarding the biomolecule adsorption on graphene surface. The adsorption of CA199-His on TRGO was generating a higher heat, suggesting quantitative and efficient interactions. At the same time, in the case of TRGO, the saturation was not reached, indicating the existence of more free binding sites than in the case of GO and graphite. As such, the carbohydrate marker CA199-His showed a higher affinity for the TRGO surface than for the graphite or GO surfaces. The lack of saturation in the case of TRGO may indicate a continuous structural modification of the antigen when interacting with the graphene surface.
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20
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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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21
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Interfacing DNA with nanoparticles: Surface science and its applications in biosensing. Int J Biol Macromol 2020; 151:757-780. [DOI: 10.1016/j.ijbiomac.2020.02.217] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/19/2020] [Accepted: 02/19/2020] [Indexed: 12/17/2022]
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22
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Jeong S, Pinals RL, Dharmadhikari B, Song H, Kalluri A, Debnath D, Wu Q, Ham MH, Patra P, Landry MP. Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption. Sci Rep 2020; 10:7074. [PMID: 32341425 PMCID: PMC7184744 DOI: 10.1038/s41598-020-63769-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023] Open
Abstract
Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.
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Affiliation(s)
- Sanghwa Jeong
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Bhushan Dharmadhikari
- Department of Electrical and Computer Engineering & Technology, Minnesota State University, Mankato, MA, 56001, USA
| | - Hayong Song
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Ankarao Kalluri
- Department of Biomedical Engineering, University of Bridgeport, Bridgeport, CT, 06604, USA
| | - Debika Debnath
- Department of Biomedical Engineering, University of Bridgeport, Bridgeport, CT, 06604, USA
| | - Qi Wu
- Department of Biomedical Engineering, University of Bridgeport, Bridgeport, CT, 06604, USA
| | - Moon-Ho Ham
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Prabir Patra
- Department of Biomedical Engineering, University of Bridgeport, Bridgeport, CT, 06604, USA. .,Department of Mechanical Engineering, University of Bridgeport, Bridgeport, CT, 06604, USA.
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Innovative Genomics Institute (IGI), Berkeley, CA, 94720, USA. .,California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, 94720, USA. .,Chan-Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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23
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Lei X, Ma H, Fang H. Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions. NANOSCALE 2020; 12:6699-6707. [PMID: 32186546 DOI: 10.1039/c9nr10170e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.
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Affiliation(s)
- Xiaoling Lei
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China.
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Chang Y, Liu B, Huang Z, Liu Y, Liu M, Liu J. Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1034-1042. [PMID: 31935105 DOI: 10.1021/acs.langmuir.9b02743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y2O3 was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y2O3 and then recovered and even enhanced with higher Y2O3 concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y2O3. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G15 and FAM-C15 adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y2O3 might be useful as a model surface for investigating DNA hybridization on a surface.
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Affiliation(s)
- Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
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Kim KI, Yoon S, Chang J, Lee S, Cho HH, Jeong SH, Jo K, Lee JH. Multifunctional Heterogeneous Carbon Nanotube Nanocomposites Assembled by DNA-Binding Peptide Anchors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905821. [PMID: 31898870 DOI: 10.1002/smll.201905821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/13/2019] [Indexed: 05/25/2023]
Abstract
Although carbon nanotubes (CNTs) are remarkable materials with many exceptional characteristics, their poor chemical functionality limits their potential applications. Herein, a strategy is proposed for functionalizing CNTs, which can be achieved with any functional group (FG) without degrading their intrinsic structure by using a deoxyribonucleic acid (DNA)-binding peptide (DBP) anchor. By employing a DBP tagged with a certain FG, such as thiol, biotin, and carboxyl acid, it is possible to introduce any FG with a controlled density on DNA-wrapped CNTs. Additionally, different types of FGs can be introduced on CNTs simultaneously, using DBPs tagged with different FGs. This method can be used to prepare CNT nanocomposites containing different types of nanoparticles (NPs), such as Au NPs, magnetic NPs, and quantum dots. The CNT nanocomposites decorated with these NPs can be used as reusable catalase-like nanocomposites with exceptional catalytic activities, owing to the synergistic effects of all the components. Additionally, the unique DBP-DNA interaction allows the on-demand detachment of the NPs attached to the CNT surface; further, it facilitates a CNT chirality-specific NP attachment and separation using the sequence-specific programmable characteristics of oligonucleotides. The proposed method provides a novel chemistry platform for constructing new functional CNTs suitable for diverse applications.
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Affiliation(s)
- Kyung-Il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seokyoung Yoon
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Hui Hun Cho
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Sun Hwan Jeong
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Research Center for Advanced Materials Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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Mukhopadhyay TK, Datta A. Screening two dimensional materials for the transportation and delivery of diverse genetic materials. NANOSCALE 2020; 12:703-719. [PMID: 31829380 DOI: 10.1039/c9nr05930j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In spite of several reports of graphene and other 2D materials concerning their capacity for biomolecular adsorption and delivery, recent toxicity evaluations found them to be nanotoxic toward different biomolecules, especially nucleic acids. Therefore, there is urgent demand for the synthesis of 2D materials exhibiting biocompatible and non-nanotoxic features. In this article, employing classical molecular dynamics simulations, we provide a benchmarking of h2D-C2N, graphene and hexagonal boron nitride (h-BN) toward the adsorption, preservation, targeting and delivery of various classes of nucleic acids namely single stranded DNA, double stranded natural as well as unnatural base substituted DNA and two different types of human telomeric guanine quadruplexes, all comprising different secondary structures. Our simulations reveal that, while h2D-C2N preserves the structures of most of the nucleic acids, graphene and h-BN disrupt them through strong π-π stacking with aromatic nucleobases. Interestingly, for the first time we identified a 'quartet-by-quartet' disruption mechanism of guanine quadruplexes, but only on graphene and h-BN. The lateral diffusion of adsorbed nucleic acids over C2N is restricted unlike that over both graphene and h-BN, thereby increasing the targeting efficacy for C2N. Modeling of the delivery phenomena suggests orders of magnitude longer release times from graphene and h-BN compared to C2N, thereby demonstrating the preferential suitability of C2N for all the hierarchical steps of nucleic acid transportation.
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Affiliation(s)
- Titas Kumar Mukhopadhyay
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A and 2B Raja S.C. Mullick Road, Jadavpur, Kolkata-700032, West Bengal, India.
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Lopez A, Liu B, Huang Z, Zhang F, Liu J. Fluorescein-Stabilized i-Motif DNA and Its Unfolding Leading to a Stronger Adsorption Affinity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11932-11939. [PMID: 31433649 DOI: 10.1021/acs.langmuir.9b01606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Several previous studies have indicated that polydeoxycytidine (poly-C) DNA has an anomalously high affinity for different types of surfaces. It was hypothesized that the formation of an i-motif structure could be a factor responsible for this enhanced affinity, but this is against the notion that a folded molecule should have fewer interactions with a surface. Herein, the properties of poly-C DNA were examined in detail, focusing on the presence or absence of a FAM (carboxyfluorescein) label and its subsequent adsorption on graphene oxide. Fluorescence and CD spectroscopy studies indicated that FAM can stabilize an i-motif structure in C15 DNA. In particular, the fluorescence of FAM is drastically quenched when the DNA is folded. This structure is irreversibly unfolded upon heating. Furthermore, the unfolded structure has an even higher affinity for graphene oxide than the folded structure. Finally, a large portion of the folded C15 unfolds upon desorption from graphene oxide, and unfolding could happen upon adsorption or desorption of the DNA. This study provides a method to further enhance the adsorption stability of poly-C DNA and calls for care when investigating the potential effects of dye labels on DNA.
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Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Fang Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
- College of Biological Science and Engineering , Fuzhou University , Fuzhou 350108 , People's Republic of China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
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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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Tabunag JS, Guo Y, Yu HZ. Interactions Between Hemin-Binding DNA Aptamers and Hemin–Graphene Nanosheets: Reduced Affinity but Unperturbed Catalytic Activity. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00087-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Nandu N, Hizir MS, Yigit MV. Systematic Investigation of Two-Dimensional DNA Nanoassemblies for Construction of a Nonspecific Sensor Array. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14983-14992. [PMID: 29739192 DOI: 10.1021/acs.langmuir.8b00788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We have performed a systematic study to analyze the effect of ssDNA length, nucleobase composition, and the type of two-dimensional nanoparticles (2D-nps) on the desorption response of 36 two-dimensional nanoassemblies (2D-NAs) against several proteins. The studies were performed using fluorescently labeled polyA, polyC, and polyT with 23, 18, 12, and 7 nucleotide-long sequences. The results suggest that the ssDNAs with polyC and longer sequences are more resistant to desorption, compared to their counterparts. In addition, 2D-NAs assembled using WS2 were least susceptible to desorption by the proteins tested, whereas nGO 2D-NAs were the most susceptible nanoassemblies. Later, the results of these systematic studies were used to construct a sensor array for discrimination of seven model proteins (BSA, lipase, alkaline phosphatase, acid phosphatase, protease, β-galactosidase, and Cytochrome c). Neither the ssDNAs nor the 2D-nps have any specific interaction with the proteins tested. Only the displacement of the ssDNAs from the 2D-np surface was measured upon the disruption of the existing forces within 2D-NAs. A customized sensor array with five 2D-NAs was developed as a result of a careful screening/filtering process. The sensor array was tested against 200 nM of protein targets, and each protein was discriminated successfully. The results suggest that the systematic studies performed using various ssDNAs and 2D-nps enabled the construction of a sensor array without a bind-and-release sensing mechanism. The studies also demonstrate the significance of systematic investigations in the construction of two-dimensional DNA nanoassemblies for functional studies.
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Affiliation(s)
- Nidhi Nandu
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Mustafa Salih Hizir
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
- The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
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31
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Lai PX, Mao JY, Unnikrishnan B, Chu HW, Wu CW, Chang HT, Huang CC. Self-assembled, bivalent aptamers on graphene oxide as an efficient anticoagulant. Biomater Sci 2018; 6:1882-1891. [PMID: 29808843 DOI: 10.1039/c8bm00288f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Graphene oxide (GO) has unique structural properties, can effectively adsorb single-strand DNA through π-π stacking, hydrogen bonding and hydrophobic interactions, and is useful in many biotechnology applications. In this study, we developed a thrombin-binding-aptamers (15- and 29-mer) conjugated graphene oxide (TBA15/TBA29-GO) composite for the efficient inhibition of thrombin activity towards the formation of fibrin from fibrinogen. The TBA15/TBA29-GO composite was simply obtained by the self-assembly of TBA15/TBA29 hybrids on GO. The high density and appropriate orientation of TBA15/TBA29 on the GO surface enabled TBA15/TBA29-GO to acquire an ultrastrong binding affinity for thrombin (dissociation constant = 2.9 × 10-12 M). Compared to bivalent TBA15h20A20/TBA29h20A20 hybrids, the TBA15/TBA29-GO composite exhibited a superior anticoagulant potency (ca. 10-fold) against thrombin-mediated coagulation as a result of steric blocking effects and a higher binding affinity for thrombin. In addition, the prolonged thrombin clotting time, prothrombin time (PT), and activated partial thromboplastin time (aPTT) of TBA15/TBA29-GO were at least 2 times longer than those of commercially available drugs (heparin, argatroban, hirudin, and warfarin). The in vitro cytotoxicity and hemolysis analyses revealed the high biocompatibility of TBA15/TBA29-GO. The rat-tail bleeding assay of the hemostasis time and ex vivo PT and aPTT further revealed that TBA15/TBA29-GO is superior (>2-fold) to heparin, which is commonly used in the treatment and prevention of thrombotic diseases. Our multivalent, oligonucleotide-modified GO nanocomposites are easy to prepare, cost-effective, and highly biocompatible and they show great potential as effective anticoagulants for the treatment of thrombotic disorders.
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Affiliation(s)
- Pei-Xin Lai
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan.
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Vlăsceanu GM, Amărandi RM, Ioniță M, Tite T, Iovu H, Pilan L, Burns JS. Versatile graphene biosensors for enhancing human cell therapy. Biosens Bioelectron 2018; 117:283-302. [DOI: 10.1016/j.bios.2018.04.053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 01/04/2023]
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Augspurger EE, Rana M, Yigit MV. Chemical and Biological Sensing Using Hybridization Chain Reaction. ACS Sens 2018; 3:878-902. [PMID: 29733201 DOI: 10.1021/acssensors.8b00208] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Since the advent of its theoretical discovery more than 30 years ago, DNA nanotechnology has been used in a plethora of diverse applications in both the fundamental and applied sciences. The recent prominence of DNA-based technologies in the scientific community is largely due to the programmable features stored in its nucleobase composition and sequence, which allow it to assemble into highly advanced structures. DNA nanoassemblies are also highly controllable due to the precision of natural and artificial base-pairing, which can be manipulated by pH, temperature, metal ions, and solvent types. This programmability and molecular-level control have allowed scientists to create and utilize DNA nanostructures in one, two, and three dimensions (1D, 2D, and 3D). Initially, these 2D and 3D DNA lattices and shapes attracted a broad scientific audience because they are fundamentally captivating and structurally elegant; however, transforming these conceptual architectural blueprints into functional materials is essential for further advancements in the DNA nanotechnology field. Herein, the chemical and biological sensing applications of a 1D DNA self-assembly process known as hybridization chain reaction (HCR) are reviewed. HCR is a one-dimensional (1D) double stranded (ds) DNA assembly process initiated only in the presence of a specific short ssDNA (initiator) and two kinetically trapped DNA hairpin structures. HCR is considered an enzyme-free isothermal amplification process, which shows substantial promise and offers a wide range of applications for in situ chemical and biological sensing. Due to its modular nature, HCR can be programmed to activate only in the presence of highly specific biological and/or chemical stimuli. HCR can also be combined with different types of molecular reporters and detection approaches for various analytical readouts. While the long dsDNA HCR product may not be as structurally attractive as the 2D and 3D DNA networks, HCR is highly instrumental for applied biological, chemical, and environmental sciences, and has therefore been studied to foster a variety of objectives. In this review, we have focused on nucleic acid, protein, metabolite, and heavy metal ion detection using this 1D DNA nanotechnology via fluorescence, electrochemical, and nanoparticle-based methodologies.
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Mukhopadhyay TK, Bhattacharyya K, Datta A. Gauging the Nanotoxicity of h2D-C 2N toward Single-Stranded DNA: An in Silico Molecular Simulation Approach. ACS APPLIED MATERIALS & INTERFACES 2018; 10:13805-13818. [PMID: 29611415 DOI: 10.1021/acsami.8b00494] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent toxicological assessments of graphene, graphene oxides, and some other two-dimensional (2D) materials have shown them to be substantially toxic at the nanoscale, where they inhibit and eventually disrupt biological processes. These shortfalls of graphene and analogs have resulted in a quest for novel biocompatible 2D materials with minimum cytotoxicity. In this article, we demonstrate C2N (h2D-C2N), a newly synthesized 2D porous graphene analog, to be non-nanotoxic toward genetic materials from an "in-silico" point of view through sequence-dependent binding of different polynucleotide single-stranded DNA (ssDNA) onto it. The calculated binding energy of nucleobases and the free energy of binding of polynucleotides follow the common trait, cytosine > guanine > adenine > thymine, and are well within the limits of physisorption. Ab-initio simulations completely exclude the possibility of any chemical reaction, demonstrating purely noncovalent binding of nucleobases with C2N through a crucial interplay between hydrogen bonding and π-stacking interactions with the surface. Further, we show that the extent of distortion inflicted upon ssDNA by C2N is negligible. Analysis of the density of states of the nucleobase-C2N hybrids confirms minimum electronic perturbation of the bases after adsorption. Most importantly, we demonstrate the potency of C2N in nucleic acid transportation via reversible binding of ssDNA. The plausible use of C2N as a template for DNA repair is illustrated through an example of C2N-assisted complementary ssDNA winding.
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Affiliation(s)
- Titas Kumar Mukhopadhyay
- Department of Spectroscopy , Indian Association for the Cultivation of Science , 2A and 2B Raja S.C.Mullick Road , Jadavpur, Kolkata 700032 West Bengal , India
| | - Kalishankar Bhattacharyya
- Department of Spectroscopy , Indian Association for the Cultivation of Science , 2A and 2B Raja S.C.Mullick Road , Jadavpur, Kolkata 700032 West Bengal , India
| | - Ayan Datta
- Department of Spectroscopy , Indian Association for the Cultivation of Science , 2A and 2B Raja S.C.Mullick Road , Jadavpur, Kolkata 700032 West Bengal , India
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35
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Huang Z, Liu J. Length-Dependent Diblock DNA with Poly-cytosine (Poly-C) as High-Affinity Anchors on Graphene Oxide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1171-1177. [PMID: 28946748 DOI: 10.1021/acs.langmuir.7b02812] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
DNA-functionalized graphene oxide (GO) is a popular system for biosensor development and directed materials assembly. Compared to covalent attachment, simple physisorption of DNA has been more popular, and a DNA sequence with a strong affinity on GO is highly desirable. Recently, we found that poly-cytosine (poly-C) DNA can strongly adsorb on many common nanomaterials, including GO. To identify an optimal length of poly-C DNA, we herein designed a series of diblock DNA sequences containing between 0 and 30 cytosines. The displacement of a random sequenced DNA by poly-C DNA was demonstrated, confirming the desired diblock structure on GO with the poly-C block anchoring on the surface and the other block available for hybridization. The adsorption density of poly-C containing DNA did not vary much as the length of the poly-C block increased, suggesting the conformation of the anchoring DNA on the GO was quite independent of the DNA length. With a longer poly-C block, the efficiency of surface hybridization of the other block increased, while nonspecific adsorption of noncomplementary DNA was inhibited more. Compared to poly-adenine (poly-A)-containing DNAs, which were previously used for the same purpose, poly-C DNA adsorption is more stable. Using four types of 15-mer DNA homopolymers as the intended anchoring sequences, the C15 DNA had the best hybridization efficiency. This work has suggested the optimal length for the poly-C block to be 15-mer or longer, and it has provided interesting insights into the DNA/GO biointerface.
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Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada
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36
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Hughes ZE, Walsh TR. Structural Disruption of an Adenosine-Binding DNA Aptamer on Graphene: Implications for Aptasensor Design. ACS Sens 2017; 2:1602-1611. [PMID: 29063764 DOI: 10.1021/acssensors.7b00435] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report on the predicted structural disruption of an adenosine-binding DNA aptamer adsorbed via noncovalent interactions on aqueous graphene. The use of surface-adsorbed biorecognition elements on device substrates is needed for integration in nanofluidic sensing platforms. Upon analyte binding, the conformational change in the adsorbed aptamer may perturb the surface properties, which is essential for the signal generation mechanism in the sensor. However, at present, these graphene-adsorbed aptamer structure(s) are unknown, and are challenging to experimentally elucidate. Here we use molecular dynamics simulations to investigate the structure and analyte-binding properties of this aptamer, in the presence and absence of adenosine, both free in solution and adsorbed at the aqueous graphene interface. We predict this aptamer to support a variety of stable binding modes, with direct base-graphene contact arising from regions located in the terminal bases, the centrally located binding pockets, and the distal loop region. Considerable retention of the in-solution aptamer structure in the adsorbed state indicates that strong intra-aptamer interactions compete with the graphene-aptamer interactions. However, in some adsorbed configurations the analyte adenosines detach from the binding pockets, facilitated by strong adenosine-graphene interactions.
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Affiliation(s)
- Zak E. Hughes
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
| | - Tiffany R. Walsh
- Institute for Frontier Materials, Deakin University, Geelong, Victoria 3216, Australia
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37
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Chen AW, Briseno AL, Santore MM. Tunable fluorescence quenching near the graphene-aqueous interface. J Colloid Interface Sci 2017; 506:76-82. [DOI: 10.1016/j.jcis.2017.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/28/2022]
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Hughes ZE, Wei G, Drew KLM, Colombi Ciacchi L, Walsh TR. Adsorption of DNA Fragments at Aqueous Graphite and Au(111) via Integration of Experiment and Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10193-10204. [PMID: 28885033 DOI: 10.1021/acs.langmuir.7b02480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We combine single molecule force spectroscopy measurements with all-atom metadynamics simulations to investigate the cross-materials binding strength trends of DNA fragments adsorbed at the aqueous graphite C(0001) and Au(111) interfaces. Our simulations predict this adsorption at the level of the nucleobase, nucleoside, and nucleotide. We find that despite challenges in making clear, careful connections between the experimental and simulation data, reasonable consistency between the binding trends between the two approaches and two substrates was evident. On C(0001), our simulations predict a binding trend of dG > dA ≈ dT > dC, which broadly aligns with the experimental trend. On Au(111), the simulation-based binding strength trends reveal stronger adsorption for the purines relative to the pyrimadines, with dG ≈ dA > dT ≈ dC. Moreover, our simulations provide structural insights into the origins of the similarities and differences in adsorption of the nucleic acid fragments at the two interfaces. In particular, our simulation data offer an explanation for the differences observed in the relative binding trend between adenosine and guanine on the two substrates.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Gang Wei
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Kurt L M Drew
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
| | - Lucio Colombi Ciacchi
- Hybrid Materials Interface Group, Faculty of Production Engineering, University of Bremen , D-28359 Bremen, Germany
| | - Tiffany R Walsh
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
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tRNA Modification Detection Using Graphene Nanopores: A Simulation Study. Biomolecules 2017; 7:biom7030065. [PMID: 32962315 PMCID: PMC5618246 DOI: 10.3390/biom7030065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/15/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection of RNA modifications requires working with nucleosides in bulk samples. Nanopore detection technology uses a single-molecule approach that has the potential to detect tRNA modifications. To evaluate the feasibility of this approach, we have performed all-atom molecular dynamics (MD) simulation studies of a five-layered graphene nanopore by localizing canonical and modified uridine nucleosides. We found that in a 1 M KCl solution with applied positive and negative biases not exceeding 2 V, nanopores can distinguish U from 5-carbonylmethyluridine (cm5U), 5-methoxycarbonylmethyluridine (mcm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), and 5-methoxycarbonylmethyl-2′-O-methyluridine (mcm5Um) based on changes in the resistance of the nanopore. Specifically, we observed that in nanopores with dimensions less than 3 nm diameter, a localized mcm5Um and mcm5U modifications could be clearly distinguished from the canonical uridine, while the other modifications showed a modest yet detectable decrease in their respective nanopore conductance. We have compared the results between nanopores of various sizes to aid in the design, optimization, and fabrication of graphene nanopores devices for tRNA modification detection.
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Xu Z, Lei X, Tu Y, Tan ZJ, Song B, Fang H. Dynamic Cooperation of Hydrogen Binding and π Stacking in ssDNA Adsorption on Graphene Oxide. Chemistry 2017; 23:13100-13104. [DOI: 10.1002/chem.201701733] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Zhen Xu
- College of Mechanical Engineering; Shanghai University of Engineering Science; Shanghai 201620 P. R. China
| | - Xiaoling Lei
- Division of Interfacial Water and Key Laboratory of Interfacial, Physic and Technology; Shanghai Institute of Applied Physics; Chinese, Academy of Sciences, P.O. Box 800-204; Shanghai 201800 P. R. China
| | - Yusong Tu
- College of Physics Science and Technology; Yangzhou University; Jiangsu 225009 P. R. China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education; School of Physics and Technology; Wuhan University; Hubei 430072 P. R. China
| | - Bo Song
- Division of Interfacial Water and Key Laboratory of Interfacial, Physic and Technology; Shanghai Institute of Applied Physics; Chinese, Academy of Sciences, P.O. Box 800-204; Shanghai 201800 P. R. China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial, Physic and Technology; Shanghai Institute of Applied Physics; Chinese, Academy of Sciences, P.O. Box 800-204; Shanghai 201800 P. R. China
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Hizir MS, Robertson NM, Balcioglu M, Alp E, Rana M, Yigit MV. Universal sensor array for highly selective system identification using two-dimensional nanoparticles. Chem Sci 2017; 8:5735-5745. [PMID: 28989614 PMCID: PMC5621473 DOI: 10.1039/c7sc01522d] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/13/2017] [Indexed: 12/13/2022] Open
Abstract
A typical lock-and-key sensing strategy, relying only on the most dominant interactions between the probe and target, could be too limiting. In reality, the information received upon sensing is much richer. Non-specific events due to various intermolecular forces contribute to the overall received information with different degrees, and when analyzed, could provide a much more powerful detection opportunity. Here, we have assembled a highly selective universal sensor array using water-soluble two-dimensional nanoparticles (nGO, MoS2 and WS2) and fluorescent DNA molecules. The array is composed of 12 fluorescently silent non-specific nanoreceptors (2D-nps) and used for the identification of three radically different systems; five proteins, three types of live breast cancer cells and a structure-switching event of a macromolecule. The data matrices for each system were processed using Partial Least Squares (PLS) discriminant analysis. In all of the systems, the sensor array was able to identify each object or event as separate clusters with 95% confidence and without any overlap. Out of 15 unknown entities with unknown protein concentrations tested, 14 of them were predicted successfully with correct concentration. 8 breast cancer cell samples out of 9 unknown entities from three cell types were predicted correctly. During the assembly of each nanoprobe, the intrinsic non-covalent interactions between unmodified 2D nanoparticles and ssDNAs were exploited. The unmodified 2D materials offer remarkable simplicity in the layout and the use of ssDNAs as probes provides limitless possibilities because the natural interaction of a ssDNA and 2D surface can be fine-tuned with the nucleobase composition, oligonucleotide length and type of 2D nanomaterial. Therefore, the approach described here can be advanced and fine-tuned indefinitely for meeting a particular sensing criterion. Though we have only studied three distinct elements, this approach is universal enough to be applied to a wide-range of systems.
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Affiliation(s)
- Mustafa Salih Hizir
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Neil M Robertson
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mustafa Balcioglu
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Esma Alp
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Muhit Rana
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
| | - Mehmet V Yigit
- Department of Chemistry , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA . ; Tel: +1-518-442-3002
- The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , USA
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DNA adsorbed on graphene and graphene oxide: Fundamental interactions, desorption and applications. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Tello A, Cao R, Marchant MJ, Gomez H. Conformational Changes of Enzymes and Aptamers Immobilized on Electrodes. Bioconjug Chem 2016; 27:2581-2591. [PMID: 27748603 DOI: 10.1021/acs.bioconjchem.6b00553] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Conformation constitutes a vital property of biomolecules, especially in the cases of enzymes and aptamers, and is essential in defining their molecular recognition ability. When biomolecules are immobilized on electrode surfaces, it is very important to have a control on all the possible conformational changes that may occur, either upon the recognition of their targets or by undesired alterations. Both enzymes and aptamers immobilized on electrodes are susceptible to conformational changes as a response to the nature of the charge of the surface and of the surrounding environment (pH, temperature, ionic strength, etc.). The main goal of this review is to analyze how the conformational changes of enzymes and aptamers immobilized on electrode surfaces have been treated in reports on biosensors and biofuel cells. This topic was selected due to insufficient information found on the actual conformational changes involved in the function of these bioelectrochemical devices despite its importance.
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Affiliation(s)
- Alejandra Tello
- Universidad Andres Bello , Bionanotechnology and Microbiology Lab, Center for Bioinformatics and Integrative Biology (CBIB), Facultad de Ciencias Biológicas, República 239, Santiago, Chile
| | - Roberto Cao
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - María José Marchant
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
| | - Humberto Gomez
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso , Avenida Universidad 330, Curauma, Valparaíso, Chile
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Vangaveti S, Ranganathan SV, Chen AA. Advances in RNA molecular dynamics: a simulator's guide to RNA force fields. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1396] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/17/2016] [Accepted: 08/25/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Sweta Vangaveti
- The RNA Institute; University at Albany State University of New York; Albany NY USA
| | | | - Alan A. Chen
- The RNA Institute; University at Albany State University of New York; Albany NY USA
- Department of Chemistry; University at Albany State University of New York; Albany NY USA
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