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Zhang CY, Zhang NH. Temperature-dependent ejection evolution arising from active and passive effects in DNA viruses. Biophys J 2024:S0006-3495(24)00514-9. [PMID: 39091028 DOI: 10.1016/j.bpj.2024.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/25/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Recent experiments have demonstrated that the ejection velocity of different species of DNA viruses is temperature dependent, potentially influencing the cellular infection mechanisms of these viruses. However, due to the challenge in quantifying the multiscale characteristics of DNA virus systems, there is currently a lack of systematic theoretical research on the temperature-dependent evolution of ejection dynamics. This work presents a multiscale model to quantitatively explore the temperature-dependent mechanical properties during the virus ejection process, and unveil the underlying mechanisms. Two different assumptions of DNA structures, featuring two or single domains, are used for the early and later stages of ejection, respectively. Temperature is introduced as an influencing variable into the mesoscopic energy model by considering the temperature dependence of Debye length, DNA persistence length, molecular kinetic energy, and other parameters. The results indicate that temperature variations alter the energy landscape associated with DNA structure, leading to the changes in the energy minimum and corresponding DNA structure remaining in the capsid. These changes affect both the active ejection force and passive friction during the DNA ejection, ultimately leading to a significant increase in ejection velocity at higher temperatures. Furthermore, our model supports the previous hypothesis that temperature-induced changes in the size of viral portal pore could dramatically enhance DNA ejection velocity.
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Affiliation(s)
- Cheng-Yin Zhang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, School of Mechanics and Engineering Science, Shanghai University, Shanghai, China; Department of Engineering Mechanics, Faculty of Civil Engineering and Mechanics, Kunming University of Science and Technology, Kunming, China
| | - Neng-Hui Zhang
- Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, School of Mechanics and Engineering Science, Shanghai University, Shanghai, China.
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Zhang H, Yang S, Zeng J, Li X, Chuai R. A Genosensor Based on the Modification of a Microcantilever: A Review. MICROMACHINES 2023; 14:427. [PMID: 36838127 PMCID: PMC9959632 DOI: 10.3390/mi14020427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
When the free end of a microcantilever is modified by a genetic probe, this sensor can be used for a wider range of applications, such as for chemical analysis, biological testing, pharmaceutical screening, and environmental monitoring. In this paper, to clarify the preparation and detection process of a microcantilever sensor with genetic probe modification, the core procedures, such as probe immobilization, complementary hybridization, and signal extraction and processing, are combined and compared. Then, to reveal the microcantilever's detection mechanism and analysis, the influencing factors of testing results, the theoretical research, including the deflection principle, the establishment and verification of a detection model, as well as environmental influencing factors are summarized. Next, to demonstrate the application results of the genetic-probe-modified sensors, based on the classification of detection targets, the application status of other substances except nucleic acid, virus, bacteria and cells is not introduced. Finally, by enumerating the application results of a genetic-probe-modified microcantilever combined with a microfluidic chip, the future development direction of this technology is surveyed. It is hoped that this review will contribute to the future design of a genetic-probe-modified microcantilever, with further exploration of the sensitive mechanism, optimization of the design and processing methods, expansion of the application fields, and promotion of practical application.
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Affiliation(s)
- He Zhang
- Correspondence: ; Tel.: +86-024-2549-6401
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Rao D, Yan T, Qiao Z, Wang Y, Peng Y, Tu H, Wu S, Zhang Q. Relay-type sensing mode: A strategy to push the limit on nanomechanical sensor sensitivity based on the magneto lever. NANO RESEARCH 2022; 16:3231-3239. [PMID: 36405983 PMCID: PMC9661467 DOI: 10.1007/s12274-022-5049-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/04/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Ultrasensitive molecular detection and quantization are crucial for many applications including clinical diagnostics, functional proteomics, and drug discovery; however, conventional biochemical sensors cannot satisfy the stringent requirements, and this has resulted in a long-standing dilemma regarding sensitivity improvement. To this end, we have developed an ultrasensitive relay-type nanomechanical sensor based on a magneto lever. By establishing the link between very weak molecular interaction and five orders of magnitude larger magnetic force, analytes at ultratrace level can produce a clearly observable mechanical response. Initially, proof-of-concept studies showed an improved detection limit up to five orders of magnitude when employing the magneto lever, as compared with direct detection using probe alone. In this study, we subsequently demonstrated that the relay-type sensing mode was universal in application ranging from micromolecule to macromolecule detection, which can be easily extended to detect enzymes, DNA, proteins, cells, viruses, bacteria, chemicals, etc. Importantly, we found that, sensitivity was no longer subject to probe affinity when the magneto lever was sufficiently high, theoretically, even reaching single-molecule resolution. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (experimental section) is available in the online version of this article at 10.1007/s12274-022-5049-0.
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Affiliation(s)
- Depeng Rao
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Tianhao Yan
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Zihan Qiao
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Yu Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Yongpei Peng
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Han Tu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Shangquan Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Qingchuan Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
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Sato RH, Kosaka PM, Omori ÁT, Ferreira EA, Petri DFS, Malvar Ó, Domínguez CM, Pini V, Ahumada Ó, Tamayo J, Calleja M, Cunha RLOR, Fiorito PA. Development of a methodology for reversible chemical modification of silicon surfaces with application in nanomechanical biosensors. Biosens Bioelectron 2019; 137:287-293. [PMID: 31125818 DOI: 10.1016/j.bios.2019.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/09/2019] [Accepted: 04/14/2019] [Indexed: 10/26/2022]
Abstract
Hypervalent tellurium compounds have a particular reactivity towards thiol compounds which are related to their biological properties. In this work, this property was assembled to tellurium-functionalized surfaces. These compounds were used as linkers in the immobilization process of thiolated biomolecules (such as DNA) on microcantilever surfaces. The telluride derivatives acted as reversible binding agents due to their redox properties, providing the regeneration of microcantilever surfaces and allowing their reuse for further biomolecules immobilizations, recycling the functional surface. Initially, we started from the synthesis of 4-((3-((4-methoxyphenyl) tellanyl) phenyl) amino)-4-oxobutanoic acid, a new compound, which was immobilized on a silicon surface. In nanomechanical systems, the detection involved a hybridization study of thiolated DNA sequences. Fluorescence microscopy technique was used to confirm the immobilization and removal of the telluride-DNA system and provided revealing results about the potentiality of applying redox properties to chalcogen derivatives at surfaces.
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Affiliation(s)
- Roseli H Sato
- CCNH, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Avenida dos Estados, 5001, 09210-580, Santo André, São Paulo, Brazil
| | - Priscila M Kosaka
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Álvaro T Omori
- CCNH, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Avenida dos Estados, 5001, 09210-580, Santo André, São Paulo, Brazil
| | - Edgard A Ferreira
- Escola de Engenharia, Universidade Presbiteriana Mackenzie, 01302-907, São Paulo, SP, Brazil
| | - Denise F S Petri
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, P.O. Box 26077, São Paulo, SP, 05513-970, Brazil
| | - Óscar Malvar
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Carmen M Domínguez
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Valerio Pini
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Óscar Ahumada
- Mecwins S.A, Plaza de la Encina 10-11, Núcleo 5, 2 B, 28760, Tres Cantos, Madrid, Spain
| | - Javier Tamayo
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Montserrat Calleja
- Instituto Micro y Nanotecnología (IMN-CNM), CSIC, Isaac Newton 8 (PTM), Tres Cantos, Madrid, Spain
| | - Rodrigo L O R Cunha
- CCNH, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, UFABC, Avenida dos Estados, 5001, 09210-580, Santo André, São Paulo, Brazil
| | - Pablo A Fiorito
- Centro de Investigaciones y Transferencia Villa María (CIT VM - CONICET), Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Av. Arturo Jauretche 1555, Villa María, C.P, 5900, Córdoba, Argentina.
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Wu J, Zhang Y, Zhang N. Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E543. [PMID: 30987225 PMCID: PMC6523535 DOI: 10.3390/nano9040543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022]
Abstract
The condensation of DNA helices has been regularly found in cell nucleus, bacterial nucleoids, and viral capsids, and during its relevant biodetections the attractive interactions between DNA helices could not be neglected. In this letter, we theoretically characterize the elastic properties of double-stranded DNA (dsDNA) self-assembled 2D films and their multiscale correlations with the dynamic detection signals of DNA-microbeams. The comparison of attraction- and repulsion-dominated DNA films shows that the competition between attractive and repulsive micro-interactions endows dsDNA films in multivalent salt solutions with anomalous elastic properties such as tensile surface stresses and negative moduli; the occurrence of the tensile surface stress for the attraction-dominated DNA self-assembled film reveals the possible physical mechanism of the condensation found in organism. Furthermore, dynamic analyses of a hinged-hinged DNA-microbeam reveal non-monotonous frequency shifts due to attraction- or repulsion-dominated dsDNA adsorptions and dynamic instability occurrence during the detections of repulsion-dominated DNA films. This dynamic instability implies the existence of a sensitive interval of material parameters in which DNA adsorptions will induce a drastic natural frequency shift or a jump of vibration mode even with a tiny variation of the detection conditions. These new insights might provide us some potential guidance to achieve an ultra-highly sensitive biodetection method in the future.
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Affiliation(s)
- Junzheng Wu
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China.
| | - Ying Zhang
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China.
| | - Nenghui Zhang
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China.
- Department of Mechanics, College of Sciences, Shanghai University, Shanghai 200444, China.
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