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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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Yin B, Ho WKH, Zhang Q, Li C, Huang Y, Yan J, Yang H, Hao J, Wong SHD, Yang M. Magnetic-Responsive Surface-Enhanced Raman Scattering Platform with Tunable Hot Spot for Ultrasensitive Virus Nucleic Acid Detection. ACS APPLIED MATERIALS & INTERFACES 2022; 14:4714-4724. [PMID: 35081679 DOI: 10.1021/acsami.1c21173] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Surface-enhanced Raman scattering (SERS)-based biosensors are promising tools for virus nucleic acid detection. However, it remains challenging for SERS-based biosensors using a sandwiching strategy to detect long-chain nucleic acids such as nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because the extension of the coupling distance (CD) between the two tethered metallic nanostructures weakens electric field and SERS signals. Herein, we report a magnetic-responsive substrate consisting of heteoronanostructures that controls the CD for ultrasensitive and highly selective detection of the N gene of SARS-CoV-2. Significantly, our findings show that this platform reversibly shortens the CD and enhances SERS signals with a 10-fold increase in the detection limit from 1 fM to 100 aM, compared to those without magnetic modulation. The optical simulation that emulates the CD shortening process confirms the CD-dependent electric field strength and further supports the experimental results. Our study provides new insights into designing a stimuli-responsive SERS-based platform with tunable hot spots for long-chain nucleic acid detection.
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Affiliation(s)
- Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Willis Kwun Hei Ho
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Qin Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Chuanqi Li
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Yingying Huang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Jiaxiang Yan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Hongrong Yang
- Department of Bioengineering, College of Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jianhua Hao
- Department of Applied Physics, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong 999077, China
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Wang Z, Nie J, Shi S, Li G, Zheng P. Transforming de novo protein α 3D into a mechanically stable protein by zinc binding. Chem Commun (Camb) 2021; 57:11489-11492. [PMID: 34651619 DOI: 10.1039/d1cc04908a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
α3D is a de novo designed three-helix bundle protein. Like most naturally occurring helical proteins, it is mechanically labile with an unfolding force of <15 pN, revealed by atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). This protein has been further designed with a tri-cysteine metal-binding site, named α3DIV, which can bind heavy transition metals. Here, we demonstrate that incorporating such a metal-binding site can transform this mechanically labile protein into a stable one. We show that zinc binds to the tri-cysteine site and increases the unfolding force to ∼160 pN. This force is one order of magnitude higher than that of the apo-protein (<15 pN). Moreover, the unfolding mechanism of Zn-α3DIV indicates the correct zinc binding with the tri-cysteine site, forming three mechanostable Zn-thiolate bonds. Thus, α3DIV could be a potential α-helical structure-based building block for synthesizing biomaterials with tunable mechanical properties.
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Affiliation(s)
- Ziyi Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Shengcao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Guoqiang Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Centre (ChemBIC), Nanjing University, Nanjing, China.
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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Lee HD, Tivanski AV. Atomic Force Microscopy: An Emerging Tool in Measuring the Phase State and Surface Tension of Individual Aerosol Particles. Annu Rev Phys Chem 2021; 72:235-252. [PMID: 33428467 DOI: 10.1146/annurev-physchem-090419-110133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Atmospheric aerosols are suspended particulate matter of varying composition, size, and mixing state. Challenges remain in understanding the impact of aerosols on the climate, atmosphere, and human health. The effect of aerosols depends on their physicochemical properties, such as their hygroscopicity, phase state, and surface tension. These properties are dynamic with respect to the highly variable relative humidity and temperature of the atmosphere. Thus, experimental approaches that permit the measurement of these dynamic properties are required. Such measurements also need to be performed on individual, submicrometer-, and supermicrometer-sized aerosol particles, as individual atmospheric particles from the same source can exhibit great variability in their form and function. In this context, this review focuses on the recent emergence of atomic force microscopy as an experimental tool in physical, analytical, and atmospheric chemistry that enables such measurements. Remaining challenges are noted and suggestions for future studies are offered.
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Affiliation(s)
- Hansol D Lee
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA; ,
| | - Alexei V Tivanski
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA; ,
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Abstract
In the scanning probe microscope system, the weak signal detection of cantilever vibration is one of the important factors affecting the sensor sensitivity. In our current work, we present a novel design concept for an atomic force microscope (AFM) combined with optomechanics with an ultra-high quality factor and a low thermal noise. The detection system consists of a fixed mirror placed on the cantilever of the AFM and pump-probe beams that is equivalent to a Fabry-Perot cavity. We realize that the AFM combined with an optical cavity can achieve ultra-sensitive detection of force gradients of 10-12 N m-1 in the case of high-vacuum and low effective temperature of 1 mK, which may open up new avenues for super-high resolution imaging and super-high precision force spectroscopy.
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Affiliation(s)
- Fei He
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Jian Liu
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
| | - Ka-Di Zhu
- Key Laboratory of Artificial Structures and Quantum Control (Ministry of Education), School of Physics and Astronomy, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, People's Republic of China
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Srinivasan B. Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery*. ChemMedChem 2020; 16:899-918. [PMID: 33231926 DOI: 10.1002/cmdc.202000791] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/27/2022]
Abstract
Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential to sustain life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were mostly tested and implemented for cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more-complex systems (for instance, multiprotein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate, and the development of a new kind of kinetic analysis to study these systems is required. This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling Discovery Sciences, R&D, AstraZeneca, 310, Milton Rd, Milton CB4 0WG, Cambridge, UK
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