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Chen H, Yan G, Wen MH, Brooks KN, Zhang Y, Huang PS, Chen TY. Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:331-344. [PMID: 38817319 PMCID: PMC11134610 DOI: 10.1021/cbmi.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Kameron N. Brooks
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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2
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Gao S, Deng J, Su Z, Liu M, Tang S, Hu T, Qi E, Fu C, Pan GY. Turning Polysaccharides into Injectable and Rapid Self-Healing Antibacterial Hydrogels for Antibacterial Treatment and Bacterial-Infected Wound Healing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9082-9096. [PMID: 38619979 DOI: 10.1021/acs.langmuir.4c00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Great efforts have been devoted to the development of novel and multifunctional wound dressing materials to meet the different needs of wound healing. Herein, we covalently grafted quaternary ammonium groups (QAGs) containing 12-carbon straight-chain alkanes to the dextran polymer skeleton. We then oxidized the resulting product into oxidized quaternized dextran (OQD). The obtained OQD polymer is rich in antibacterial QAGs and aldehyde groups. It can react with glycol chitosan (GC) via the Schiff-base reaction to form a multifunctional GC@OQD hydrogel with good self-healing behavior, hemostasis, injectability, inherent superior antibacterial activity, biocompatibility, and excellent promotion of healing of methicillin-resistant Staphylococcus aureus (MRSA)-infected wounds. The biosafe and nontoxic GC@OQD hydrogel with a three-dimensional porous network structure possesses an excellent swelling rate and water retention capacity. It can be used for hemostasis and treating irregular wounds. The designed GC@OQD hydrogel with inherent antibacterial activity possesses good antibacterial efficacy on both S. aureus (Gram-positive bacteria) and Escherichia coli (Gram-negative bacteria), as well as MRSA bacteria, with antibacterial activity greater than 99%. It can be used for the treatment of wounds infected by MRSA and significantly promotes the healing of wounds. Thus, the multifunctional antibacterial GC@OQD hydrogel has the potential to be applied in clinical practice as a wound dressing.
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Affiliation(s)
- Shiqi Gao
- School of Pharmacy, Guilin Medical University, Guilin 541100, P. R. China
| | - Jianbin Deng
- School of Pharmacy, Guilin Medical University, Guilin 541100, P. R. China
| | - Zhicheng Su
- School of Pharmacy, Guilin Medical University, Guilin 541100, P. R. China
| | - Mengqi Liu
- School of Pharmacy, Guilin Medical University, Guilin 541100, P. R. China
| | - Songyun Tang
- School of Pharmacy, Guilin Medical University, Guilin 541100, P. R. China
| | - Tingting Hu
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541100, P. R. China
| | - Enfeng Qi
- School of Mathematics and Statistics, Guangxi Normal University, Guilin 541000, P. R. China
| | - Can Fu
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541100, P. R. China
- Key Laboratory of Medical Biotechnology and Translational Medicine (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541100, P. R. China
| | - Guang-Yu Pan
- College of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin 541100, P. R. China
- Key Laboratory of Biochemistry and Molecular Biology (Guilin Medical University), Education Department of Guangxi Zhuang Autonomous Region, Guilin 541100, China
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3
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Ma H, Chen L, Lv J, Yan X, Li Y, Xu G. The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology. Chem Commun (Camb) 2023; 59:10330-10342. [PMID: 37615403 DOI: 10.1039/d3cc02597g] [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: 08/25/2023]
Abstract
DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.
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Affiliation(s)
- Hongmin Ma
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Long Chen
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Jingnan Lv
- The Second Affiliated People's Hospital of Soochow University, Suzhou 215008, China
| | - Xiaoyu Yan
- Guang'an Vocational & Technical College, Sichuan 638000, China
| | - Yonghao Li
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Guoxin Xu
- Department of Clinical Laboratory, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
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4
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Tan X, Hou S, Niver A, Zhang C, Johnson A, Welsher KD. Active-Feedback 3D Single-Molecule Tracking Using a Fast-Responding Galvo Scanning Mirror. J Phys Chem A 2023; 127:6320-6328. [PMID: 37477600 PMCID: PMC11025461 DOI: 10.1021/acs.jpca.3c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Real-time three-dimensional single-particle tracking (RT-3D-SPT) allows continuous detection of individual freely diffusing objects with high spatiotemporal precision by applying closed-loop active feedback in an optical microscope. However, the current tracking speed in RT-3D-SPT is primarily limited by the response time of the control actuators, impeding long-term observation of fast diffusive objects such as single molecules. Here, we present an RT-3D-SPT system with improved tracking performance by replacing the XY piezoelectric stage with a galvo scanning mirror with an approximately 5 times faster response rate (∼5 kHz). Based on the previously developed 3D single-molecule active real-time tracking (3D-SMART), this new implementation with a fast-responding galvo mirror eliminates the mechanical movement of the sample and allows a more rapid response to particle motion. The improved tracking performance of the galvo mirror-based implementation is verified through simulation and proof-of-principle experiments. Fluorescent nanoparticles and ∼1 kB double-stranded DNA molecules were tracked via both the original piezoelectric stage and new galvo mirror implementations. With the new galvo-based implementation, notable increases in tracking duration, localization precision, and the degree to which the objects are locked to the center of the detection volume were observed. These results suggest that faster control response elements can expand RT-3D-SPT to a broader range of chemical and biological systems.
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Affiliation(s)
- Xiaochen Tan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Shangguo Hou
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Anastasia Niver
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Chen Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Alexis Johnson
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Kevin D Welsher
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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5
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Nguyen TD, Chen YI, Chen LH, Yeh HC. Recent Advances in Single-Molecule Tracking and Imaging Techniques. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:253-284. [PMID: 37314878 DOI: 10.1146/annurev-anchem-091922-073057] [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: 06/16/2023]
Abstract
Since the early 1990s, single-molecule detection in solution at room temperature has enabled direct observation of single biomolecules at work in real time and under physiological conditions, providing insights into complex biological systems that the traditional ensemble methods cannot offer. In particular, recent advances in single-molecule tracking techniques allow researchers to follow individual biomolecules in their native environments for a timescale of seconds to minutes, revealing not only the distinct pathways these biomolecules take for downstream signaling but also their roles in supporting life. In this review, we discuss various single-molecule tracking and imaging techniques developed to date, with an emphasis on advanced three-dimensional (3D) tracking systems that not only achieve ultrahigh spatiotemporal resolution but also provide sufficient working depths suitable for tracking single molecules in 3D tissue models. We then summarize the observables that can be extracted from the trajectory data. Methods to perform single-molecule clustering analysis and future directions are also discussed.
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Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Limin H Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA;
- Texas Materials Institute, University of Texas at Austin, Austin, Texas, USA
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6
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Yan X, Yue T, Winkler DA, Yin Y, Zhu H, Jiang G, Yan B. Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation. Chem Rev 2023. [PMID: 37262026 DOI: 10.1021/acs.chemrev.3c00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.
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Affiliation(s)
- Xiliang Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Tongtao Yue
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Institute of Coastal Environmental Pollution Control, Ocean University of China, Qingdao 266100, China
| | - David A Winkler
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- School of Pharmacy, University of Nottingham, Nottingham NG7 2QL, U.K
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hao Zhu
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bing Yan
- Institute of Environmental Research at the Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
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7
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Mieskes F, Ploetz E, Wehnekamp F, Rat V, Lamb DC. Multicolor 3D Orbital Tracking. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2204726. [PMID: 36709484 DOI: 10.1002/smll.202204726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Feedback-based single-particle tracking (SPT) is a powerful technique for investigating particle behavior with very high spatiotemporal resolution. The ability to follow different species and their interactions independently adds a new dimension to the information available from SPT. However, only a few approaches have been expanded to multiple colors and no method is currently available that can follow two differently labeled biomolecules in 4 dimensions independently. In this proof-of-concept paper, the new modalities available when performing 3D orbital tracking with a second detection channel are demonstrated. First, dual-color tracking experiments are described studying independently diffusing particles of different types. For interacting particles where their motion is correlated, a second modality is implemented where a particle is tracked in one channel and the position of the second fluorescence species is monitored in the other channel. As a third modality, 3D orbital tracking is performed in one channel while monitoring its spectral signature in a second channel. This last modality is used to successfully readout accurate Förster Resonance Energy Transfer (FRET) values over time while tracking a mobile particle.
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Affiliation(s)
- Frank Mieskes
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Evelyn Ploetz
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Fabian Wehnekamp
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Virgile Rat
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
| | - Don C Lamb
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, Butenandtstraße 11, 81377, Munich, Germany
- Nanosystems Initiative Munich (NIM), Ludwig-Maximilians-Universität München, Schellingstraße 4, 80799, Munich, Germany
- Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, Munich, Germany
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8
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Real-time single-molecule 3D tracking in E. coli based on cross-entropy minimization. Nat Commun 2023; 14:1336. [PMID: 36906676 PMCID: PMC10008558 DOI: 10.1038/s41467-023-36879-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 02/17/2023] [Indexed: 03/13/2023] Open
Abstract
Reaching sub-millisecond 3D tracking of individual molecules in living cells would enable direct measurements of diffusion-limited macromolecular interactions under physiological conditions. Here, we present a 3D tracking principle that approaches the relevant regime. The method is based on the true excitation point spread function and cross-entropy minimization for position localization of moving fluorescent reporters. Tests on beads moving on a stage reaches 67 nm lateral and 109 nm axial precision with a time resolution of 0.84 ms at a photon count rate of 60 kHz; the measurements agree with the theoretical and simulated predictions. Our implementation also features a method for microsecond 3D PSF positioning and an estimator for diffusion analysis of tracking data. Finally, we successfully apply these methods to track the Trigger Factor protein in living bacterial cells. Overall, our results show that while it is possible to reach sub-millisecond live-cell single-molecule tracking, it is still hard to resolve state transitions based on diffusivity at this time scale.
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9
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Patterson K, Romero-Reyes MA, Heemstra JM. Fluorescence Quenching of Xanthene Dyes during Amide Bond Formation Using DMTMM. ACS OMEGA 2022; 7:33046-33053. [PMID: 36157719 PMCID: PMC9494652 DOI: 10.1021/acsomega.2c03085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Fluorophore bioconjugation to proteins, nucleic acids, and other important molecules can provide a powerful approach to sensing, imaging, and quantifying chemical and biological processes. One of the most prevalent methods for fluorophore attachment is through the formation of amide bonds, which are often facilitated by coupling agents to activate carboxylic acid moieties for subsequent nucleophilic attack by amines. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methyl-morpholinium chloride (DMTMM) is among the most popular of these coupling agents for bioconjugation due to its ability to facilitate amide bond formation in water. After observing quenching of 5-fluoresceinamine (5-FAM)-conjugated oligonucleotides in the presence of DMTMM, we sought to evaluate the magnitude and scope of this challenge by surveying the effect of DMTMM on a range of fluorescent dyes. A higher quenching effect was consistently observed for xanthene dyes compared to that for cyanine dyes. Further analysis of the impact of DMTMM on FAM shows that quenching occurs independently of whether the dye is free in solution or attached to an oligonucleotide or antibody. Furthermore, we found that FAM-conjugated DNA was unable to recover its fluorescence after the removal of DMTMM, and UV-vis and NMR analyses suggest the formation of new products, such as an adduct formed between FAM and the dimethoxytriazine of DMTMM. As such, DMTMM at high concentrations is not recommended for coupling reactions where targets are fluorescently labeled. This research serves as a word of caution to those utilizing xanthene-containing fluorophores in bioconjugation reactions involving DMTMM.
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Affiliation(s)
- Kristen
N. Patterson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Misael A. Romero-Reyes
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Hanover College, Hanover, Indiana 47243, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University in St.
Louis, St. Louis, Missouri 63130, United States
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10
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van Heerden B, Vickers NA, Krüger TPJ, Andersson SB. Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107024. [PMID: 35758534 PMCID: PMC9308725 DOI: 10.1002/smll.202107024] [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: 11/14/2021] [Revised: 04/07/2022] [Indexed: 05/14/2023]
Abstract
Real-time feedback-driven single-particle tracking (RT-FD-SPT) is a class of techniques in the field of single-particle tracking that uses feedback control to keep a particle of interest in a detection volume. These methods provide high spatiotemporal resolution on particle dynamics and allow for concurrent spectroscopic measurements. This review article begins with a survey of existing techniques and of applications where RT-FD-SPT has played an important role. Each of the core components of RT-FD-SPT are systematically discussed in order to develop an understanding of the trade-offs that must be made in algorithm design and to create a clear picture of the important differences, advantages, and drawbacks of existing approaches. These components are feedback tracking and control, ranging from simple proportional-integral-derivative control to advanced nonlinear techniques, estimation to determine particle location from the measured data, including both online and offline algorithms, and techniques for calibrating and characterizing different RT-FD-SPT methods. Then a collection of metrics for RT-FD-SPT is introduced to help guide experimentalists in selecting a method for their particular application and to help reveal where there are gaps in the techniques that represent opportunities for further development. Finally, this review is concluded with a discussion on future perspectives in the field.
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Affiliation(s)
- Bertus van Heerden
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nicholas A Vickers
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
| | - Tjaart P J Krüger
- Department of Physics, University of Pretoria, Pretoria, 0002, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Sean B Andersson
- Department of Mechanical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Systems Engineering, Boston University, Boston, MA, 02215, USA
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11
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Zhang C, Li D, Zhang G, Wang X, Mao L, Gan Q, Ding T, Xu H. Switching plasmonic nanogaps between classical and quantum regimes with supramolecular interactions. SCIENCE ADVANCES 2022; 8:eabj9752. [PMID: 35119919 PMCID: PMC8816333 DOI: 10.1126/sciadv.abj9752] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In the realm of extreme nanophotonics, nanogap plasmons support reliable field enhancements up to 1000, which provide unique opportunities to access a single molecule for strong coupling and a single atom for quantum catalysis. The quantum plasmonics are intriguing but difficult to modulate largely because of the lack of proper spacers that can reversibly actuate the sub-1-nm gaps. Here, we demonstrate that supramolecular systems made of oligoamide sequences can reversibly switch the gap plasmons of Au nanoparticles on mirror between classical and quantum tunneling regimes via supramolecular interactions. The results reveal detailed plasmon shift near the quantum tunneling limit, which fits well with both classical- and quantum-corrected models. In the quantum tunneling regime, we demonstrate that plasmonic hot electron tunneling can further blue shift the quantum plasmons because of the increased conductance in the nanogaps, making it a promising prototype of optical tunable quantum plasmonic devices.
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Affiliation(s)
- Chi Zhang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Dongyao Li
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guangdi Zhang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xujie Wang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Li Mao
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Quan Gan
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
- Corresponding author. (T.D.); (Q.G.)
| | - Tao Ding
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
- Corresponding author. (T.D.); (Q.G.)
| | - Hongxing Xu
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
- School of Microelectronics, Wuhan University, Wuhan 430072, China
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12
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Chen X, Liu T, Qin X, Nguyen QQ, Lee SK, Lee C, Ren Y, Chu J, Zhu G, Yoon TY, Park CY, Park H. Simultaneous Real-Time Three-Dimensional Localization and FRET Measurement of Two Distinct Particles. NANO LETTERS 2021; 21:7479-7485. [PMID: 34491760 DOI: 10.1021/acs.nanolett.1c01328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many biological processes employ mechanisms involving the locations and interactions of multiple components. Given that most biological processes occur in three dimensions, the simultaneous measurement of three-dimensional locations and interactions is necessary. However, the simultaneous three-dimensional precise localization and measurement of interactions in real time remains challenging. Here, we report a new microscopy technique to localize two spectrally distinct particles in three dimensions with an accuracy (2.35σ) of tens of nanometers with an exposure time of 100 ms and to measure their real-time interactions using fluorescence resonance energy transfer (FRET) simultaneously. Using this microscope, we tracked two distinct vesicles containing t-SNAREs or v-SNARE in three dimensions and observed FRET simultaneously during single-vesicle fusion in real time, revealing the nanoscale motion and interactions of single vesicles in vesicle fusion. Thus, this study demonstrates that our microscope can provide detailed information about real-time three-dimensional nanoscale locations, motion, and interactions in biological processes.
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Affiliation(s)
- Xingxiang Chen
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Quang Quan Nguyen
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Chanwoo Lee
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Yaguang Ren
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tae-Young Yoon
- School of Biological Sciences and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, South Korea
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, UNIST, 44919, Ulsan, Republic of Korea
| | - Hyokeun Park
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Zhang Z, Ma W, He K, Yuan B, Yang K. Ligand-decoration determines the translational and rotational dynamics of nanoparticles on a lipid bilayer membrane. Phys Chem Chem Phys 2021; 23:9158-9165. [PMID: 33885120 DOI: 10.1039/d1cp00643f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanoparticles (NPs) promise a huge potential for clinical diagnostic and therapeutic applications. However, nano-bio (e.g., the NP-cell membrane) interactions and underlying mechanisms are still largely elusive. In this study, two types of congeneric peptides, namely PGLa and magainin 2 (MAG2), with similar membrane activities were employed as model ligands for NP decoration, and the diffusion behaviours (including both translation and rotation) of the ligand-decorated NPs on a lipid bilayer membrane were studied via molecular dynamics simulations. It was found that, although both PGLa- and MAG2-coated NPs showed alternatively "hopping" and "jiggling" diffusions, the PGLa-coated ones had an enhanced circling at the hopping stage, while a much confined circling at the jiggling stage. In contrast, the MAG2-coated NPs demonstrated constant circling tendencies throughout the diffusion process. Such differences in the coupling between translational and rotational dynamics of these two types of NPs are ascribed to the different ligand-lipid interactions of PGLa and MAG2, in which the PGLa ligands prefer to vertically insert into the membrane, while MAG2 tends to lie flat on the membrane surface. Our results are helpful for the understanding the underlying associations between the NP motions and their interfacial membrane interactions, and shed light on the possibility of regulating NP behaviours on a cellular surface for better biomedical uses.
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Affiliation(s)
- Zhihong Zhang
- Center for Soft Condensed Matter Physics and Interdisciplinary Research & School of Physical Science and Technology, Soochow University, Suzhou, 215006, P. R. China.
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Recent developments in the characterization of nucleic acid hybridization kinetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2021; 19. [PMID: 34368519 DOI: 10.1016/j.cobme.2021.100305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hybridization of nucleic acids (NAs) is a fundamental molecular mechanism that drives many cellular processes and enables new biotechnologies as well as therapeutics. However, existing methods that measure hybridization kinetics of nucleic acids are either performed at the ensemble level or constrained to non-native physiological conditions. Recent advances in 3D single-molecule tracking techniques break these limitations by allowing multiple annealing and melting events to be observed on a single oligonucleotide freely diffusing inside a live mammalian cell. This review provides an overview of diverse approaches to measuring NA hybridization kinetics at the single-molecule level and in live cells, and concludes with a synopsis of unresolved challenges and opportunities in the live-cell hybridization kinetics measurements. Important discoveries made by NA kinetics measurements and biotechnologies that can be improved with a deeper understanding of hybridization kinetics are also described.
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15
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Xu M, Tang D. Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review. Anal Chim Acta 2021; 1171:338523. [PMID: 34112433 DOI: 10.1016/j.aca.2021.338523] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/08/2023]
Abstract
DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.
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Affiliation(s)
- Mingdi Xu
- College of Ecological Environment and Urban Construction, Fujian University of Technology, Fuzhou 350108, People's Republic of China; Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
| | - Dianping Tang
- Key Laboratory of Analytical Science for Food Safety and Biology (MOE & Fujian Province), Department of Chemistry, Fuzhou University, Fuzhou 350108, People's Republic of China.
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