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Yang ZY, Jiang WY, Ran SY. Reductant-dependent DNA-templated silver nanoparticle formation kinetics. Phys Chem Chem Phys 2023; 25:23197-23206. [PMID: 37605826 DOI: 10.1039/d3cp02623j] [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: 08/23/2023]
Abstract
DNA molecules have been demonstrated to be good templates for producing silver nanoparticles (AgNPs), with the advantages of well-controlled sizes, shapes, and properties. Revealing the formation kinetics of DNA-templated AgNPs is crucial for their efficient synthesis. Herein, using magnetic tweezers, we studied the reduction kinetics of the Ag+-DNA structure and the subsequent nucleation kinetics by adding NaBH4, L-ascorbic acid, and sodium citrate solutions. At [Ag+] = 0.01 mM, the addition of NaBH4 solution with the same concentration resulted in the restoration of DNA. In contrast, by increasing the [NaBH4]/[Ag+] ratio (r) to 10 and 100, the DNA extension initially decreased rapidly and then increased, indicating nucleation-dissolution kinetics. With AgNO3 solutions of higher concentrations (0.1 mM and 1 mM), direct particle nucleation and growth kinetics were observed by adding a tenfold (r = 10) or a hundredfold (r = 100) amount of NaBH4, which were evidenced by a significant reduction in DNA extension. The reductant dependence of the kinetics was further investigated. Addition of L-ascorbic acid to the DNA-Ag+ solution yielded an increase-decrease kinetics that was different from that caused by NaBH4, suggesting that nucleation was not initially favored due to the lack of sufficient Ag atoms; while sodium citrate showed a weak nucleation-promoting ability to form AgNPs. We discussed the findings within the framework of classical nucleation theory, in which the supersaturation of the Ag atom is strongly influenced by multiple factors (including the reducing ability of the reductant), resulting in different kinetics.
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Affiliation(s)
- Zi-Yang Yang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Wen-Yan Jiang
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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Alston JJ, Soranno A. Condensation Goes Viral: A Polymer Physics Perspective. J Mol Biol 2023; 435:167988. [PMID: 36709795 PMCID: PMC10368797 DOI: 10.1016/j.jmb.2023.167988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The past decade has seen a revolution in our understanding of how the cellular environment is organized, where an incredible body of work has provided new insights into the role played by membraneless organelles. These rapid advancements have been made possible by an increasing awareness of the peculiar physical properties that give rise to such bodies and the complex biology that enables their function. Viral infections are not extraneous to this. Indeed, in host cells, viruses can harness existing membraneless compartments or, even, induce the formation of new ones. By hijacking the cellular machinery, these intracellular bodies can assist in the replication, assembly, and packaging of the viral genome as well as in the escape of the cellular immune response. Here, we provide a perspective on the fundamental polymer physics concepts that may help connect and interpret the different observed phenomena, ranging from the condensation of viral genomes to the phase separation of multicomponent solutions. We complement the discussion of the physical basis with a description of biophysical methods that can provide quantitative insights for testing and developing theoretical and computational models.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA; Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA.
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Ru XM, Yang ZY, Ran SY. Lanthanide ions induce DNA compaction with ionic specificity. Int J Biol Macromol 2022; 210:292-299. [DOI: 10.1016/j.ijbiomac.2022.04.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/05/2022]
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Zhang R, Wang Y, Yang G. DNA–Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction. Polymers (Basel) 2022; 14:polym14071377. [PMID: 35406251 PMCID: PMC9002893 DOI: 10.3390/polym14071377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 12/25/2022] Open
Abstract
The interaction between DNA and proteins is fundamentally important not only for basic research in biology, but also for potential applications in nanotechnology. In the present study, the complexes formed by λ DNA and lysozyme in a dilute aqueous solution have been investigated using magnetic tweezers (MT), dynamic light scattering (DLS), and atomic force microscopy (AFM). We found that lysozyme induced DNA charge inversion by measuring its electrophoretic mobility by DLS. Lysozyme is very effective at neutralizing the positive charge of DNA, and its critical charge ration to induce charge inversion in solution is only 2.26. We infer that the high efficiency of charge neutralization is due to the highly positively charged (+8 e) and compact structure of lysozyme. When increasing the concentration of lysozymes from 6 ng·µL−1 to 70 ng·µL−1, DNA mobility (at fixed concentration of 2 ng·µL−1) increases from −2.8 to 1.5 (in unit of 10−4 cm2·V−1·S), implying that the effective charge of DNA switches its sign from negative to positive in the process. The corresponding condensing force increased from 0 pN to its maximal value of about 10.7 pN at concentrations of lysozyme at 25 ng·µL−1, then decreases gradually to 3.8 pN at 200 ng·µL−1. The maximal condensing force occurs at the complete DNA charge neutralization point. The corresponding morphology of DNA–lysozyme complex changes from loosely extensible chains to compact globule, and finally to less compact flower-like structure due to the change of attached lysozyme particles as observed by AFM.
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Affiliation(s)
| | - Yanwei Wang
- Correspondence: (Y.W.); (G.Y.); Tel.: +86-577-8668-9033 (G.Y.); Fax: +86-577-8668-9010 (G.Y.)
| | - Guangcan Yang
- Correspondence: (Y.W.); (G.Y.); Tel.: +86-577-8668-9033 (G.Y.); Fax: +86-577-8668-9010 (G.Y.)
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Yadav I, Al Sulaiman D, Soh BW, Doyle PS. Phase Transition of Catenated DNA Networks in Poly(ethylene glycol) Solutions. ACS Macro Lett 2021; 10:1429-1435. [PMID: 35549007 DOI: 10.1021/acsmacrolett.1c00463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Conformational phase transitions of macromolecules are an important class of problems in fundamental polymer physics. While the conformational phase transitions of linear DNA have been extensively studied, this feature of topologically complex DNA remains unexplored. We report herein the polymer-and-salt-induced (Ψ) phase transition of 2D catenated DNA networks, called kinetoplasts, using single-molecule fluorescence microscopy. We observe that kinetoplasts can undergo a reversible transition from the flat phase to the collapsed phase in the presence of NaCl as a function of the crowding agent poly(ethylene glycol). The nature of this phase transition is tunable through varying ionic strengths. For linear DNA, the coexistence of coil and globule phases was attributed to a first order phase transition associated with a double well potential in the transition regime. Kinetoplasts, however, navigate from the flat to the collapsed phase by passing through an intermediate regime, characterized by the coexistence of a multipopulation with varying shapes and sizes. Conformations of individual molecules in the multipopulation are long-lived, which suggests a rugged energy landscape.
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Affiliation(s)
- Indresh Yadav
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dana Al Sulaiman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Beatrice W. Soh
- Institute of Materials Research and Engineering, 2 Fusionopolis Way, Singapore 138634, Singapore
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard Medical School Initiative for RNA Medicine, Boston, Massachusetts 02215, United States
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Masella M, Crudu A, Léonforté F. Hybrid polarizable simulations of a conventional hydrophobic polyelectrolyte. Toward a theoretical tool for green science innovation. J Chem Phys 2021; 155:114903. [PMID: 34551548 DOI: 10.1063/5.0056508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid modeling approaches based on all-atom force fields to handle a solute and coarse-grained models to account for the solvent are promising numerical tools that can be used to understand the properties of large and multi-components solutions and thus to speed up the development of new industrial products that obey the standard of green and sustainable chemistry. Here, we discuss the ability of a full polarizable hybrid approach coupled to a standard molecular dynamics scheme to model the behavior in the aqueous phase and at infinite dilution conditions of a standard hydrophobic polyelectrolyte polymer whose charge is neutralized by explicit counterions. Beyond the standard picture of a polyelectrolyte behavior governed by an interplay between opposite intra-polyelectrolyte and inter-polyelectrolyte/counterion Coulombic effects, our simulations show the key role played by both intra-solute polarization effects and long range solute/solvent electrostatics to stabilize compact globular conformations of that polyelectrolyte. Our full polarizable hybrid modeling approach is thus a new theoretical tool well suited to be used in digital strategies for accelerating innovation for green science, for instance.
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Affiliation(s)
- Michel Masella
- Laboratoire de Biologie Structurale et Radiobiologie, Service de Bioénergétique, Biologie Structurale et Mécanismes, Institut Joliot, CEA Saclay, F-91191 Gif sur Yvette Cedex, France
| | - Alina Crudu
- L'Oréal Research and Innovation, Aulnay-Sous-Bois, France
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Liu YF, Ran SY. Divalent metal ions and intermolecular interactions facilitate DNA network formation. Colloids Surf B Biointerfaces 2020; 194:111117. [PMID: 32512310 DOI: 10.1016/j.colsurfb.2020.111117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn2+, Zn2+, Co2+, Ni2+, and Cd2+), except Mg2+ and Ca2+, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.
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Affiliation(s)
- Yin-Feng Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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Duan C, Li W, Wang R. Conformation of a single polyelectrolyte in poor solvents. J Chem Phys 2020; 153:064901. [DOI: 10.1063/5.0017371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Chao Duan
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, USA
- State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Computational Physical Sciences, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Weihua Li
- State Key Laboratory of Molecular Engineering of Polymers, Key Laboratory of Computational Physical Sciences, Department of Macromolecular Science, Fudan University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Lab, Berkeley, California 94720, USA
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Liu KT, Ran SY. Multistage dynamics of Hg 2+-DNA interactions: a single-molecule study. Phys Chem Chem Phys 2019; 21:2919-2928. [PMID: 30675618 DOI: 10.1039/c8cp07399f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The metal ion-DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T-Hg2+-T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanism has not been fully understood. In the present study, we used magnetic tweezers to explore the interactions between λ-DNA and two metal ions, Hg2+ and Cd2+, at the single-molecule level. Both metal ions caused considerable DNA conformational changes. The resulting DNA compaction dynamics were related to the ion concentration and the exerted force. The increase in the ion concentration promoted DNA compaction, whereas exerting greater forces inhibited this process. Application of a high force generated two-stage dynamics of the Hg2+-DNA interaction. However, at a sufficiently high Hg2+ concentration, a lower force led to a three-stage process. In contrast, the curves of the binding of Cd2+ ions to DNA had a stepwise pattern. Both the AFM scanning results and the single-molecule measurements confirmed that Hg2+ influences the DNA conformation in a more pronounced manner than Cd2+. The multistage Hg2+-DNA interaction was considered to be a result of the different binding mechanisms, including the mismatched base-pair formation. A model was then proposed to explain the peculiar dynamics.
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Affiliation(s)
- Kang-Tao Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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