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Zhou K, Zhou J, Cao S, Zheng Y, Zhang XY, Chen C, Zhang XE, Men D. Bifunctional Protein TC1 Mediated One-Pot Strategy for Robust Immobilization of DNA with High Accessibility. SMALL METHODS 2024:e2400049. [PMID: 38804235 DOI: 10.1002/smtd.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/24/2024] [Indexed: 05/29/2024]
Abstract
Immobilizing DNA with high accessibility at the interface is attractive but challenging. Current methods often involve multiple chemical reactions and derivatives. In this study, an endonuclease, TC1, is introduced to develop a robust strategy for immobilizing DNA with enhanced accessibility. TC1 enables direct immobilization of DNA onto a solid support through self-catalytic DNA covalent coupling and robust solid adsorption capabilities. This method demonstrates high accessibility to target molecules, supported by the improved sensitivity of DNA hybridization and aptamer-target recognition assays. TC1-mediated DNA immobilization is a one-pot reaction that does not require chemical derivatives, making it promising for the development of high-performance DNA materials and technologies.
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Affiliation(s)
- Kun Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Juan Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Shanshan Cao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Ying Zheng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Xin-Yu Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Chen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen university of Advanced Technology, Shenzhen, 518055, P. R. China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- Guangzhou National Laboratory, Guangzhou, 510005, P. R. China
- State Key Laboratory of Respiratory Disease, Guangzhou institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510182, China
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2
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Sytu MRC, Cho DH, Hahm JI. Self-Assembled Block Copolymers as a Facile Pathway to Create Functional Nanobiosensor and Nanobiomaterial Surfaces. Polymers (Basel) 2024; 16:1267. [PMID: 38732737 PMCID: PMC11085100 DOI: 10.3390/polym16091267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Block copolymer (BCP) surfaces permit an exquisite level of nanoscale control in biomolecular assemblies solely based on self-assembly. Owing to this, BCP-based biomolecular assembly represents a much-needed, new paradigm for creating nanobiosensors and nanobiomaterials without the need for costly and time-consuming fabrication steps. Research endeavors in the BCP nanobiotechnology field have led to stimulating results that can promote our current understanding of biomolecular interactions at a solid interface to the never-explored size regimes comparable to individual biomolecules. Encouraging research outcomes have also been reported for the stability and activity of biomolecules bound on BCP thin film surfaces. A wide range of single and multicomponent biomolecules and BCP systems has been assessed to substantiate the potential utility in practical applications as next-generation nanobiosensors, nanobiodevices, and biomaterials. To this end, this Review highlights pioneering research efforts made in the BCP nanobiotechnology area. The discussions will be focused on those works particularly pertaining to nanoscale surface assembly of functional biomolecules, biomolecular interaction properties unique to nanoscale polymer interfaces, functionality of nanoscale surface-bound biomolecules, and specific examples in biosensing. Systems involving the incorporation of biomolecules as one of the blocks in BCPs, i.e., DNA-BCP hybrids, protein-BCP conjugates, and isolated BCP micelles of bioligand carriers used in drug delivery, are outside of the scope of this Review. Looking ahead, there awaits plenty of exciting research opportunities to advance the research field of BCP nanobiotechnology by capitalizing on the fundamental groundwork laid so far for the biomolecular interactions on BCP surfaces. In order to better guide the path forward, key fundamental questions yet to be addressed by the field are identified. In addition, future research directions of BCP nanobiotechnology are contemplated in the concluding section of this Review.
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Affiliation(s)
- Marion Ryan C. Sytu
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
| | - David H. Cho
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA;
| | - Jong-in Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, DC 20057, USA
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3
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Lei X, Ye W, Safdarin F, Baghaei S. Microfluidics devices for sports: A review on technology for biomedical application used in fields such as biomedicine, drug encapsulation, preparation of nanoparticles, cell targeting, analysis, diagnosis, and cell culture. Tissue Cell 2024; 87:102339. [PMID: 38432127 DOI: 10.1016/j.tice.2024.102339] [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: 11/28/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
Microfluidics is an interdisciplinary field that combines knowledge from various disciplines, including biology, chemistry, sports medicine, fluid dynamics, kinetic biomechanics, and microelectronics, to manipulate and control fluids and particles in micron-scale channels and chambers. These channels and chambers can be fabricated using different materials and methods to achieve various geometries and shapes. Microfluidics has numerous biomedical applications, such as drug encapsulation, nanoparticle preparation, cell targeting, analysis, diagnosis, and treatment of sports injuries in both professional and non-professional athletes. It can also be used in other fields, such as biological analysis, chemical synthesis, optics, and acceleration in the treatment of critical sports injuries. The objective of this review is to provide a comprehensive overview of microfluidic technology, including its fabrication methods, current platform materials, and its applications in sports medicine. Biocompatible, biodegradable, and semi-crystalline polymers with unique mechanical and thermal properties are one of the promising materials in microfluidic technology. Despite the numerous advantages of microfluidic technology, further research and development are necessary. Although the technology offers benefits such as ease of operation and cost efficiency, it is still in its early stages. In conclusion, this review emphasizes the potential of microfluidic technology and highlights the need for continued research to fully exploit its potential in the biomedical field and sport applications.
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Affiliation(s)
- Xuehui Lei
- Graduate School of Wuhan Institute of Physical Education, Wuhan 430079, China
| | - Weiwu Ye
- National Traditional Sports College of Harbin Sports University, Harbin 150008, China.
| | - F Safdarin
- Mechanical Engineering Department, lslamic Azad University, Esfahan, Iran
| | - Sh Baghaei
- Mechanical Engineering Department, lslamic Azad University, Esfahan, Iran
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4
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TABATA M, MIYAHARA Y. Control of interface functions in solid-state biosensors for stable detection of molecular recognition. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:32-56. [PMID: 38199246 PMCID: PMC10864167 DOI: 10.2183/pjab.100.004] [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: 06/28/2023] [Accepted: 09/25/2023] [Indexed: 01/12/2024]
Abstract
Significant progress has been achieved in the field of solid-state biosensors over the past 50 years. Various sensing devices with high-density integration and flexible configuration, as well as new applications for clinical diagnosis and healthcare, have been developed using blood, serum, and other body fluids such as sweat, tears, and saliva. A high-density array of ion-sensitive field effect transistors was developed by exploiting the advantages of advanced semiconductor technologies and commercialized in combination with an enzymatic primer extension reaction as a DNA sequencer in 2011. Different types of materials such as inorganic materials, metals, polymers, and biomolecules are mixed together on the surface of the gate while maintaining their own functions; therefore, compatibility among different materials has to be optimized so that the best detection performance of solid-state biosensors, including stability and reliability, is achieved as designed. Solid-state biosensors are suitable for the rapid, cost-effective, and noninvasive identification of biomarkers at various timepoints over the course of a disease.
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Affiliation(s)
- Miyuki TABATA
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Yuji MIYAHARA
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
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5
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Zhou X, Zheng B. Surface modification for improving immunoassay sensitivity. LAB ON A CHIP 2023; 23:1151-1168. [PMID: 36636910 DOI: 10.1039/d2lc00811d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Immunoassays are widely performed in many fields such as biomarker discovery, proteomics, drug development, and clinical diagnosis. There is a growing need for high sensitivity of immunoassays to detect low abundance analytes. As a result, great effort has been made to improve the quality of surfaces, on which the immunoassay is performed. In this review article, we summarize the recent progress in surface modification strategies for improving the sensitivity of immunoassays. The surface modification strategies can be categorized into two groups: antifouling coatings to reduce background noise and nanostructured surfaces to amplify the signals. The first part of the review summarizes the common antifouling coating techniques to prevent nonspecific binding and reduce background noise. The techniques include hydrophilic polymer based self-assembled monomers, polymer brushes, and surface attached hydrogels, and omniphobicity based perfluorinated surfaces. In the second part, some common nanostructured surfaces to amplify the specific detection signals are introduced, including nanoparticle functionalized surfaces, two dimensional (2D) nanoarrays, and 2D nanomaterial coatings. The third part discusses the surface modification techniques for digital immunoassays. In the end, the challenges and the future perspectives of the surface modification techniques for immunoassays are presented.
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Affiliation(s)
- Xiaohu Zhou
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Bo Zheng
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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6
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Ma X, Zhou W, Li H, Zhang B, Miao P. MnO 2@Au nanostructures supported colorimetric biosensing with duplex-specific nuclease-assisted DNA structural transition. Mater Today Bio 2023; 19:100571. [PMID: 36816603 PMCID: PMC9932214 DOI: 10.1016/j.mtbio.2023.100571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Manganese dioxide (MnO2) nanosheets are regarded as a new class of two-dimensional nanomaterials with several attractive properties with enormous progress in biomedical fields. Gold nanoparticles (AuNPs) are also important biocompatible nanomaterials with unusual optical properties. Hetero-nanostructure of MnO2 and AuNPs with the medium of DNA is an interesting topic. In this work, the protection of the hetero-nanostructure from salt-induced aggregation is systematically investigated including the effects of sequence length, reagents concentrations, incubation time and temperature. The MnO2@Au nanostructures are thus applied for the analysis of miRNA. Duplex-specific nuclease (DSN) catalyzed digestion, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are utilized for signal amplification. By finally analyzing the optical responses of the nanocomponents, highly sensitive analysis of target miRNA can be achieved. Excellent analytical performances are attributed to the unique features of MnO2@Au nanostructures and signal amplification designs. They are promising basis for the construction of novel biosensors for clinical applications.
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Affiliation(s)
- Xiaoyi Ma
- University of Science and Technology of China, Hefei 230026, China,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Wuping Zhou
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Haiwen Li
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Bo Zhang
- Department of Radiology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China,Corresponding author.
| | - Peng Miao
- University of Science and Technology of China, Hefei 230026, China,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China,Jinan Guokeyigong Science and Technology Development Co., Ltd., Jinan 250103, China,Corresponding author. University of Science and Technology of China, Hefei 230026, China.
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7
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Chen G, Yang L, Liu G, Zhu Y, Yang F, Dong X, Xu F, Zhu F, Cao C, Zhong D, Li S, Zhang H, Li B. Research progress in protein microarrays: Focussing on cancer research. Proteomics Clin Appl 2023; 17:e2200036. [PMID: 36316278 DOI: 10.1002/prca.202200036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/10/2022] [Accepted: 09/27/2022] [Indexed: 01/22/2023]
Abstract
Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.
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Affiliation(s)
- Guang Chen
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Lina Yang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Guoxiang Liu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Yunfan Zhu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Fanghao Yang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Xiaolei Dong
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Fenghua Xu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Feng Zhu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Can Cao
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Di Zhong
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Shuang Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Huhu Zhang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Bing Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China.,Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, China
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8
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Snyder M, Iraola-Guzmán S, Saus E, Gabaldón T. Discovery and Validation of Clinically Relevant Long Non-Coding RNAs in Colorectal Cancer. Cancers (Basel) 2022; 14:cancers14163866. [PMID: 36010859 PMCID: PMC9405614 DOI: 10.3390/cancers14163866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Recent efforts in biomedical research have focused on the identification of molecular biomarkers to improve the diagnosis, prognosis and eventually treatment of the most common human diseases worldwide, including cancer. In this context, a large number of studies point to a pivotal role of long non-coding RNAs (lncRNAs) in the pathophysiology of carcinogenesis, suggesting diagnostic or therapeutic potential. However, for most of them, supporting evidence is scarce and often based on a single large-scale analysis. Here, focusing on colorectal cancer (CRC), we present an overview of the main approaches for discovering and validating lncRNA candidate molecules, and provide a curated list of the most promising lncRNAs associated with this malignancy. Abstract Colorectal cancer (CRC) is the third most prevalent cancer worldwide, with nearly two million newly diagnosed cases each year. The survival of patients with CRC greatly depends on the cancer stage at the time of diagnosis, with worse prognosis for more advanced cases. Consequently, considerable effort has been directed towards improving population screening programs for early diagnosis and identifying prognostic markers that can better inform treatment strategies. In recent years, long non-coding RNAs (lncRNAs) have been recognized as promising molecules, with diagnostic and prognostic potential in many cancers, including CRC. Although large-scale genome and transcriptome sequencing surveys have identified many lncRNAs that are altered in CRC, most of their roles in disease onset and progression remain poorly understood. Here, we critically review the variety of detection methods and types of supporting evidence for the involvement of lncRNAs in CRC. In addition, we provide a reference catalog that features the most clinically relevant lncRNAs in CRC. These lncRNAs were selected based on recent studies sorted by stringent criteria for both supporting experimental evidence and reproducibility.
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Affiliation(s)
- Madison Snyder
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Susana Iraola-Guzmán
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Ester Saus
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), 08028 Barcelona, Spain
- Correspondence:
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Kumar R, Llewellyn S, Vasantham SK, Nie K, Sekula-Neuner S, Vijayaraghavan A, Hirtz M. Protein spot arrays on graphene oxide coatings for efficient single-cell capture. Sci Rep 2022; 12:3895. [PMID: 35273174 PMCID: PMC8913813 DOI: 10.1038/s41598-022-06225-4] [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: 11/18/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Biomedical applications such as cell screening or cell–cell interaction studies require placement and adhesion of cells on surfaces with controlled numbers and location. In particular, single-cell arraying and positioning has come into focus as a basis of such applications. An ideal substrate would combine biocompatibility with favorable attributes such as pattern stability and easy processing. Here, we present a simple yet effective approach to single-cell arraying based on a graphene oxide (GO) surface carrying protein (fibronectin) microarrays to define cell adhesion points. These capture NIH-3T3 cells, resulting in cell arrays, which are benchmarked against analogous arrays on silanized glass samples. We reveal significant improvement in cell-capture performance by the GO coating with regards to overall cell adhesion and single-cell feature occupancy. This overall improvement of cell-arraying combined with retained transparency of substrate for microscopy and good biocompatibility makes this graphene-based approach attractive for single-cell experiments.
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Affiliation(s)
- R Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - S Llewellyn
- Department of Materials, The University of Manchester, Manchester, UK.,Blond McIndoe Laboratories, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - S K Vasantham
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Kaiwen Nie
- Department of Materials, The University of Manchester, Manchester, UK
| | | | - A Vijayaraghavan
- Department of Materials, The University of Manchester, Manchester, UK.
| | - M Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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The Bioanalytical and Biomedical Applications of Polymer Modified Substrates. Polymers (Basel) 2022; 14:polym14040826. [PMID: 35215740 PMCID: PMC8878960 DOI: 10.3390/polym14040826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/11/2023] Open
Abstract
Polymers with different structures and morphology have been extensively used to construct functionalized surfaces for a wide range of applications because the physicochemical properties of polymers can be finely adjusted by their molecular weights, polydispersity and configurations, as well as the chemical structures and natures of monomers. In particular, the specific functions of polymers can be easily achieved at post-synthesis by the attachment of different kinds of active molecules such as recognition ligand, peptides, aptamers and antibodies. In this review, the recent advances in the bioanalytical and biomedical applications of polymer modified substrates were summarized with subsections on functionalization using branched polymers, polymer brushes and polymer hydrogels. The review focuses on their applications as biosensors with excellent analytical performance and/or as nonfouling surfaces with efficient antibacterial activity. Finally, we discuss the perspectives and future directions of polymer modified substrates in the development of biodevices for the diagnosis, treatment and prevention of diseases.
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11
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Cao J, Zhang R, Zhang Y, Wang Y. Combined screening analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. J Gastrointest Oncol 2022; 13:311-325. [PMID: 35284134 PMCID: PMC8899745 DOI: 10.21037/jgo-21-866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Methylation plays an important role in hepatocellular carcinoma (HCC) by altering the expression of key genes. The aim of this study was to screen the aberrantly methylated-differentially expressed genes (DEGs) in HCC and elucidate their underlying molecular mechanism. METHODS Gene expression microarrays (GSE101685) and gene methylation microarrays (GSE44909) were selected. DEGs and differentially methylated genes (DMGs) were screened. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the Database for Annotation, Visualization, and Integrated discovery (DAVID). The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to analyze the functional protein-protein interaction (PPI) network. Molecular Complex Detection (MCODE) analysis was performed using the Cytoscape software. Hub genes were verified in The Cancer Genome Atlas (TCGA) database. RESULTS A total of 80 hypomethylation-high expression genes (Hypo-HGs) were identified. Pathway enrichment analysis showed DNA replication, cell cycle, viral carcinogenesis, and the spliceosome. The top 5 hub genes were minichromosome maintenance complex component 3 (MCM3), checkpoint kinase 1 (CHEK1), kinesin family member 11 (KIF11), PDZ binding kinase (PBK), and Rac GTPase activating protein 1 (RACGAP1). In addition, 189 hypermethylation-low expression genes (Hyper-LGs) were identified. Pathway enrichment analysis indicated enrichment in metabolic pathways, drug metabolism-other enzymes, and chemical carcinogenesis. The top 5 hub genes were leukocyte immunoglobulin like receptor B2 (LILRB2), formyl peptide receptor 1 (FPR1), S100 calcium binding protein A9 (S100A9), S100 calcium binding protein A8 (S100A8), and myeloid cell nuclear differentiation antigen (MNDA). The methylation status and mRNA expression of MCM3, CHEK1, KIF11, PBK, and S100A9 were consistent in the TCGA database and significantly correlated with the prognosis of patients. CONCLUSIONS Combined screening of aberrantly methylated-DEGs based on bioinformatic analysis may provide new clues for elucidating the epigenetic mechanism in HCC. Hub genes, including MCM3, CHEK1, KIF11, PBK, and S100A9, may serve as biomarkers for the precise diagnosis of HCC.
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Affiliation(s)
- Jisen Cao
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Ruiqiang Zhang
- Department of Orthopedics, General Hospital of Tianjin Medical University, Tianjin, China
| | - Ye Zhang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
| | - Yijun Wang
- Department of Hepatobiliary Surgery, The Third Central Hospital of Tianjin, Tianjin, China
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Miftakhov RA, Lapa SA, Kuznetsova VE, Zolotov AM, Vasiliskov VA, Shershov VE, Surzhikov SA, Zasedatelev AS, Chudinov AV. Effect of Spacers on DNA Probe Properties in Hybridization Analysis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Mu J, Gao S, Yang J, Wu F, Zhou H. Fundamental and Clinical Applications of Materials Based on Cancer-Associated Fibroblasts in Cancers. Int J Mol Sci 2021; 22:11671. [PMID: 34769102 PMCID: PMC8583912 DOI: 10.3390/ijms222111671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer stromal cells play a role in promoting tumor relapse and therapeutic resistance. Therefore, the current treatment paradigms for cancers are usually insufficient to eradicate cancer cells, and anti-cancer therapeutic strategies targeting stromal cells have been developed. Cancer-associated fibroblasts (CAFs) are perpetually activated fibroblasts in the tumor stroma. CAFs are the most abundant and highly heterogeneous stromal cells, and they are critically involved in cancer occurrence and progression. These effects are due to their various roles in the remodeling of the extracellular matrix, maintenance of cancer stemness, modulation of tumor metabolism, and promotion of therapy resistance. Recently, biomaterials and nanomaterials based on CAFs have been increasingly developed to perform gene or protein expression analysis, three-dimensional (3D) co-cultivation, and targeted drug delivery in cancer treatment. In this review, we systematically summarize the current research to fully understand the relevant materials and their functional diversity in CAFs, and we highlight the potential clinical applications of CAFs-oriented biomaterials and nanomaterials in anti-cancer therapy.
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Affiliation(s)
- Jingtian Mu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Shengtao Gao
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu 610041, China;
| | - Jin Yang
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Fanglong Wu
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
| | - Hongmei Zhou
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, Frontier Innovation Center for Dental Medicine Plus, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China; (J.M.); (J.Y.)
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14
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Xu J, Yin Y, Lin Y, Tian M, Liu T, Li X, Chen S. Long non-coding RNAs: Emerging roles in periodontitis. J Periodontal Res 2021; 56:848-862. [PMID: 34296758 DOI: 10.1111/jre.12910] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023]
Abstract
Periodontitis is a major burden of public health, affecting 20%-50% of the global population. It is a complex inflammatory disease characterized by the destruction of supporting structures of the teeth, leading to tooth loss and the emergence or worsening of systematic diseases. Understanding the molecular mechanisms underlying the physiopathology of periodontitis is beneficial for targeted therapeutics. Long non-coding RNAs (lncRNAs), transcripts made up of more than 200 nucleotides, have emerged as novel regulators of many biological and pathological processes. Recently, an increasing number of dysregulated lncRNAs have been found to be implicated in periodontitis. In this review, an overview of lncRNAs, including their biogenesis, characteristics, function mechanisms and research approaches, is provided. And we summarize recent research reports on the emerging roles of lncRNAs in regulating proliferation, apoptosis, inflammatory responses, and osteogenesis of periodontal cells to elucidate lncRNAs related physiopathology of periodontitis. Furthermore, we have highlighted the underlying mechanisms of lncRNAs in periodontitis pathology by interacting with microRNAs. Finally, the potential clinical applications, current challenges, and prospects of lncRNAs as diagnostic and prognostic biomarkers and therapeutic targets for periodontitis disease are discussed.
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Affiliation(s)
- Jingchen Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuanyuan Yin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yao Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mi Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinyi Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Song Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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15
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Li S, Song G, Bai Y, Song N, Zhao J, Liu J, Hu C. Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases. Front Immunol 2021; 12:645632. [PMID: 34012435 PMCID: PMC8126629 DOI: 10.3389/fimmu.2021.645632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 01/18/2023] Open
Abstract
Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.
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Affiliation(s)
- Siting Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yina Bai
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Ning Song
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jian Liu
- Department of Rheumatology, Aerospace Center Hospital, Aerospace, Clinical Medical College, Peking University, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
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16
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Tabata M, Kataoka-Hamai C, Nogami K, Tsuya D, Goda T, Matsumoto A, Miyahara Y. Organic and inorganic mixed phase modification of a silver surface for functionalization with biomolecules and stabilization of electromotive force. RSC Adv 2021; 11:24958-24967. [PMID: 35481016 PMCID: PMC9036890 DOI: 10.1039/d1ra03449a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/12/2021] [Indexed: 02/06/2023] Open
Abstract
A solid-state potentiometric biosensor based on the organic and inorganic mixed phase modification of a silver surface is proposed. Stabilization of the electromotive force and functionalization with biomolecules on the sensing surface were simultaneously achieved using silver chloride chemically deposited with 1,3-diaminopropanetetraacetic acid ferric ammonium salt monohydrate and a self-assembled monolayer with oligonucleotide probes, respectively. The formation of silver chloride and adsorption of alkanethiol on the silver surface were confirmed with X-ray photoelectron spectroscopy. The resulting modified surface reduced the nonspecific binding of interfering biomolecules and achieved a high signal to noise ratio. The electromotive forces of the modified silver thin film electrodes were stable under constant chloride ion concentrations. Hybridization assays were performed to detect microRNA 146. The lower limit of detection was 0.1 pM because of the small standard deviation. The proposed biosensor could be useful as a disposable single-use sensor in medical fields such as liquid biopsies. The organic and inorganic mixed phase modification of a silver surface is proposed for solid-state potentiometric biosensors.![]()
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Affiliation(s)
- Miyuki Tabata
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
| | | | - Kozue Nogami
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
| | - Daiju Tsuya
- National Institute for Materials Science
- Ibaraki
- 305-0047 Japan
| | - Tatsuro Goda
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
| | | | - Yuji Miyahara
- Tokyo Medical and Dental University
- Tokyo 101-0062
- Japan
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17
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Polymer microarrays rapidly identify competitive adsorbents of virus-like particles. Biointerphases 2020; 15:061005. [PMID: 33203214 DOI: 10.1116/6.0000586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The emergence of SARS-CoV-2 highlights the global need for platform technologies to enable the rapid development of diagnostics, vaccines, treatments, and personal protective equipment (PPE). However, many current technologies require the detailed mechanistic knowledge of specific material-virion interactions before they can be employed, for example, to aid in the purification of vaccine components or in the design of a more effective PPE. Here, we show that an adaption of a polymer microarray method for screening bacterial-surface interactions allows for the screening of polymers for desirable material-virion interactions. Nonpathogenic virus-like particles including fluorophores are exposed to the arrays in an aqueous buffer as a simple model of virions carried to the surface in saliva/sputum. Competitive binding of Lassa and Rubella virus-like particles is measured to probe the relative binding properties of a selection of copolymers. This provides the first step in the development of a method for the discovery of novel materials with promise for viral binding, with the next being development of this method to assess absolute viral adsorption and assessment of the attenuation of the activity of live virus, which we propose would be part of a material scale up step carried out in high containment facilities, alongside the use of more complex media to represent biological fluids.
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18
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Xie Z, Gan T, Fang L, Zhou X. Recent progress in creating complex and multiplexed surface-grafted macromolecular architectures. SOFT MATTER 2020; 16:8736-8759. [PMID: 32969442 DOI: 10.1039/d0sm01043j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Surface-grafted macromolecules, including polymers, DNA, peptides, etc., are versatile modifications to tailor the interfacial functions in a wide range of fields. In this review, we aim to provide an overview of the most recent progress in engineering surface-grafted chains for the creation of complex and multiplexed surface architectures over micro- to macro-scopic areas. A brief introduction to surface grafting is given first. Then the fabrication of complex surface architectures is summarized with a focus on controlled chain conformations, grafting densities and three-dimensional structures. Furthermore, recent advances are highlighted for the generation of multiplexed arrays with designed chemical composition in both horizontal and vertical dimensions. The applications of such complicated macromolecular architectures are then briefly discussed. Finally, some perspective outlooks for future studies and challenges are suggested. We hope that this review will be helpful to those just entering this field and those in the field requiring quick access to useful reference information about the progress in the properties, processing, performance, and applications of functional surface-grafted architectures.
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Affiliation(s)
- Zhuang Xie
- School of Materials Science and Engineering, and Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-sen University, Xingangxi Road No. 135, Guangzhou, Guangdong Province 510275, P. R. China.
| | - Tiansheng Gan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Shenzhen, Guangdong Province 518055, P. R. China.
| | - Lvye Fang
- School of Materials Science and Engineering, and Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Sun Yat-sen University, Xingangxi Road No. 135, Guangzhou, Guangdong Province 510275, P. R. China.
| | - Xuechang Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Shenzhen, Guangdong Province 518055, P. R. China.
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19
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Lee EY, Kim Y, Koo B, Noh GS, Lee H, Shin Y. A novel nucleic acid amplification system based on nano-gap embedded active disk resonators. SENSORS AND ACTUATORS. B, CHEMICAL 2020. [PMID: 32501366 DOI: 10.1016/j.snb.2020.128358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Recent advances in nucleic acid based testing using bio-optical sensor approaches have been introduced but most are based on hybridization between the optical sensor and the bio-molecule and not on an amplification mechanism. Direct nucleic acid amplification on an optical sensor has several technical limitations, such as the sensitivity of the temperature sensor, instrument complexity, and high background signal. We here describe a novel nucleic acid amplification method based on a whispering gallery mode active resonator and discuss its potential molecular diagnostic application. By implanting nanoclusters as active compounds, this active resonator operates without tapered fiber coupling and emits a strong photoluminescence signal with low background in the wavelength of low absorption in an aqueous environment that is typical of biosensors. Our method also offers an extremely low detection threshold down to a single copy within 10 min due to the strong light-matter interaction in a nano-gap structure. We envision that this active resonator provides a high refractive index contrast for tight mode confinement with simple alignment as well as the possibility of reducing the device size so that a point-of-care system with low-cost, high-sensitivity and simplicity.
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Affiliation(s)
- Eun Yeong Lee
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bonhan Koo
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Geun Su Noh
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yong Shin
- Department of Convergence Medicine, Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
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20
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Chen M, Grazon C, Sensharma P, Nguyen TT, Feng Y, Chern M, Baer RC, Varongchayakul N, Cook K, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection. ACS APPLIED MATERIALS & INTERFACES 2020; 12:43513-43521. [PMID: 32893612 DOI: 10.1021/acsami.0c13489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immobilization of biosensors in or on a functional material is critical for subsequent device development and translation to wearable technology. Here, we present the development and assessment of an immobilized quantum dot-transcription factor-nucleic acid complex for progesterone detection as a first step toward such device integration. The sensor, composed of a polyhistidine-tagged transcription factor linked to a quantum dot and a fluorophore-modified cognate DNA, is embedded within a hydrogel as an immobilization matrix. The hydrogel is optically transparent, soft, and flexible as well as traps the quantum dot-transcription factor DNA assembly but allows free passage of the analyte, progesterone. Upon progesterone exposure, DNA dissociates from the quantum dot-transcription factor DNA assembly resulting in an attenuated ratiometric fluorescence output via Förster resonance energy transfer. The sensor performs in a dose-dependent manner with a limit of detection of 55 nM. Repeated analyte measurements are similarly successful. Our approach combines a systematically characterized hydrogel as an immobilization matrix and a transcription factor-DNA assembly as a recognition/transduction element, offering a promising framework for future biosensor devices.
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Affiliation(s)
- Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- CNRS, Bordeaux INP, LCPO, UMR 5629, Univ. Bordeaux, F-33600 Pessac, France
| | - Prerana Sensharma
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Thuy T Nguyen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yunpeng Feng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Margaret Chern
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - R C Baer
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Nitinun Varongchayakul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Katherine Cook
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | | | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mark W Grinstaff
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
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21
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Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods. MATERIALS 2020; 13:ma13132888. [PMID: 32605060 PMCID: PMC7372444 DOI: 10.3390/ma13132888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/20/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022]
Abstract
The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young’s moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.
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