1
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Wilson KR, Prophet AM. Chemical Kinetics in Microdroplets. Annu Rev Phys Chem 2024; 75:185-208. [PMID: 38382571 DOI: 10.1146/annurev-physchem-052623-120718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Micrometer-sized compartments play significant roles in driving heterogeneous transformations within atmospheric and biochemical systems as well as providing vehicles for drug delivery and novel reaction environments for the synthesis of industrial chemicals. Many reports now indicate that reaction kinetics are accelerated under microconfinement, for example, in sprays, thin films, droplets, aerosols, and emulsions. These observations are dramatic, posing a challenge to our understanding of chemical reaction mechanisms with potentially significant practical consequences for predicting the complex chemistry in natural systems. Here we introduce the idea of kinetic confinement, which is intended to provide a conceptual backdrop for understanding when and why microdroplet reaction kinetics differ from their macroscale analogs.
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Affiliation(s)
- Kevin R Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Alexander M Prophet
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
- Department of Chemistry, University of California, Berkeley, California, USA;
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2
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Zangi R. Breakdown of Langmuir Adsorption Isotherm in Small Closed Systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024. [PMID: 38315174 PMCID: PMC10883037 DOI: 10.1021/acs.langmuir.3c03894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
For more than a century, monolayer adsorptions in which adsorbate molecules and adsorbing sites behave ideally have been successfully described by Langmuir's adsorption isotherm. For example, the amount of adsorbed material, as a function of concentration of the material which is not adsorbed, obeys Langmuir's equation. In this paper, we argue that this relation is valid only for macroscopic systems. However, when particle numbers of adsorbate molecules and/or adsorbing sites are small, Langmuir's model fails to describe the chemical equilibrium of the system. This is because the kinetics of forming, or the probability of observing, occupied sites arises from two-body interactions, and as such, ought to include cross-correlations between particle numbers of the adsorbate and adsorbing sites. The effect of these correlations, as reflected by deviations in predicting composition when correlations are ignored, increases with decreasing particle numbers and becomes substantial when only few adsorbate molecules, or adsorbing sites, are present in the system. In addition, any change that augments the fraction of occupied sites at equilibrium (e.g., smaller volume, lower temperature, or stronger adsorption energy) further increases the discrepancy between observed properties of small systems and those predicted by Langmuir's theory. In contrast, for large systems, these cross-correlations become negligible, and therefore when expressing properties involving two-body processes, it is possible to consider independently the concentration of each component. By applying statistical mechanics concepts, we derive a general expression of the equilibrium constant for adsorption. It is also demonstrated that in ensembles in which total numbers of particles are fixed, the magnitudes of fluctuations in particle numbers alone can predict the average chemical composition of the system. Moreover, an alternative adsorption equation, predicting the average fraction of occupied sites from the value of the equilibrium constant, is proposed. All derived relations were tested against results obtained by Monte Carlo simulations.
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Affiliation(s)
- Ronen Zangi
- Donostia International Physics Center (DIPC), 20018 Donostia-San Sebastián, Spain
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
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3
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Lee C, Wallace DC, Burke PJ. Super-Resolution Imaging of Voltages in the Interior of Individual, Vital Mitochondria. ACS NANO 2024; 18:1345-1356. [PMID: 37289571 PMCID: PMC10795477 DOI: 10.1021/acsnano.3c02768] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
We present super-resolution microscopy of isolated functional mitochondria, enabling real-time studies of structure and function (voltages) in response to pharmacological manipulation. Changes in mitochondrial membrane potential as a function of time and position can be imaged in different metabolic states (not possible in whole cells), created by the addition of substrates and inhibitors of the electron transport chain, enabled by the isolation of vital mitochondria. By careful analysis of structure dyes and voltage dyes (lipophilic cations), we demonstrate that most of the fluorescent signal seen from voltage dyes is due to membrane bound dyes, and develop a model for the membrane potential dependence of the fluorescence contrast for the case of super-resolution imaging, and how it relates to membrane potential. This permits direct analysis of mitochondrial structure and function (voltage) of isolated, individual mitochondria as well as submitochondrial structures in the functional, intact state, a major advance in super-resolution studies of living organelles.
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Affiliation(s)
- ChiaHung Lee
- Department
of Electrical Engineering and Computer Science, Department of Biomedical
Engineering, University of California, Irvine, California 92697, United States
| | - Douglas C. Wallace
- Center
for Mitochondrial and Epigenomic Medicine, Children’s Hospital
of Philadelphia and Department of Pediatrics, Division of Human Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Peter J. Burke
- Department
of Electrical Engineering and Computer Science, Department of Biomedical
Engineering, University of California, Irvine, California 92697, United States
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4
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Iijima K, Kaji N, Tokeshi M, Baba Y. Micro- and nanochamber array system for single enzyme assays. Sci Rep 2023; 13:13322. [PMID: 37587179 PMCID: PMC10432523 DOI: 10.1038/s41598-023-40544-4] [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: 02/22/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023] Open
Abstract
Arrays of small reaction containers, ranging from 624 femtoliters (10-15 L) to 270 attoliters (10-18 L), for capturing a single enzyme molecule and measuring the activity were developed along with a new reversible sealing system based on a pneumatic valve actuator made of polydimethylsiloxane (PDMS). The valve was actuated by PBS solution, effectively preventing evaporation of the solution from the micro- and nanochambers and allowing the assay to be performed over a long period of time. The hydrolysis rates of β-D-galactosidase (β-gal), kcat, were decreased according to the decrease of the chamber size, and the overall tendency seems to be symmetrically related to the specific surface area of the chambers even under the prevented condition of non-specific adsorption. The spatial localization of the protons in the chambers, which might could affect the dissociation state of the proteins, was also investigated to explain the decrease in the hydrolysis rate. The developed chamber system developed here may be useful for artificially reproducing the confined intracellular environment and molecular crowding conditions.
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Affiliation(s)
- Kazuki Iijima
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Noritada Kaji
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Manabu Tokeshi
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University, Kita-13, Nishi-8, Kita-Ku, Sapporo, 060-8628, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
- Institute for Quantum Life Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, 263-8555, Japan
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shih-Chuan 1st Rd., Kaohsiung, 807, Taiwan, ROC
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5
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Krasecki V, Sharma A, Cavell AC, Forman C, Guo SY, Jensen ET, Smith MA, Czerwinski R, Friederich P, Hickman RJ, Gianneschi N, Aspuru-Guzik A, Cronin L, Goldsmith RH. The Role of Experimental Noise in a Hybrid Classical-Molecular Computer to Solve Combinatorial Optimization Problems. ACS CENTRAL SCIENCE 2023; 9:1453-1465. [PMID: 37521801 PMCID: PMC10375572 DOI: 10.1021/acscentsci.3c00515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Indexed: 08/01/2023]
Abstract
Chemical and molecular-based computers may be promising alternatives to modern silicon-based computers. In particular, hybrid systems, where tasks are split between a chemical medium and traditional silicon components, may provide access and demonstration of chemical advantages such as scalability, low power dissipation, and genuine randomness. This work describes the development of a hybrid classical-molecular computer (HCMC) featuring an electrochemical reaction on top of an array of discrete electrodes with a fluorescent readout. The chemical medium, optical readout, and electrode interface combined with a classical computer generate a feedback loop to solve several canonical optimization problems in computer science such as number partitioning and prime factorization. Importantly, the HCMC makes constructive use of experimental noise in the optical readout, a milestone for molecular systems, to solve these optimization problems, as opposed to in silico random number generation. Specifically, we show calculations stranded in local minima can consistently converge on a global minimum in the presence of experimental noise. Scalability of the hybrid computer is demonstrated by expanding the number of variables from 4 to 7, increasing the number of possible solutions by 1 order of magnitude. This work provides a stepping stone to fully molecular approaches to solving complex computational problems using chemistry.
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Affiliation(s)
- Veronica
K. Krasecki
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Abhishek Sharma
- Department
of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Andrew C. Cavell
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christopher Forman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Si Yue Guo
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Evan Thomas Jensen
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Mackinsey A. Smith
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Rachel Czerwinski
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Pascal Friederich
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Riley J. Hickman
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Nathan Gianneschi
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Alán Aspuru-Guzik
- Department
of Chemistry, University of Toronto, Toronto, Ontario MS5 3H6, Canada
| | - Leroy Cronin
- Department
of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Randall H. Goldsmith
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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6
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Cha M, Jeong SH, Jung J, Baeg Y, Park S, Bae S, Lim CS, Park JH, Lee J, Gho YS, Oh SW, Shon MJ. Quantitative imaging of vesicle-protein interactions reveals close cooperation among proteins. J Extracell Vesicles 2023; 12:e12322. [PMID: 37186457 PMCID: PMC10130417 DOI: 10.1002/jev2.12322] [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: 10/12/2022] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Membrane-bound vesicles such as extracellular vesicles (EVs) can function as biochemical effectors on target cells. Docking of the vesicles onto recipient plasma membranes depends on their interaction with cell-surface proteins, but a generalizable technique that can quantitatively observe these vesicle-protein interactions (VPIs) is lacking. Here, we describe a fluorescence microscopy that measures VPIs between single vesicles and cell-surface proteins, either in a surface-tethered or in a membrane-embedded state. By employing cell-derived vesicles (CDVs) and intercellular adhesion molecule-1 (ICAM-1) as a model system, we found that integrin-driven VPIs exhibit distinct modes of affinity depending on vesicle origin. Controlling the surface density of proteins also revealed a strong support from a tetraspanin protein CD9, with a critical dependence on molecular proximity. An adsorption model accounting for multiple protein molecules was developed and captured the features of density-dependent cooperativity. We expect that VPI imaging will be a useful tool to dissect the molecular mechanisms of vesicle adhesion and uptake, and to guide the development of therapeutic vesicles.
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Affiliation(s)
- Minkwon Cha
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- POSTECH Biotech CenterPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Sang Hyeok Jeong
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jaehun Jung
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Yoonjin Baeg
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Sung‐Soo Park
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Seoyoon Bae
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Chan Seok Lim
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jun Hyuk Park
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Jie‐Oh Lee
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- Institute of Membrane ProteinsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Yong Song Gho
- Department of Life SciencesPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
| | - Seung Wook Oh
- Biodrone Research InstituteMDimune Inc.SeoulRepublic of Korea
| | - Min Ju Shon
- Department of PhysicsPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and Technology (POSTECH)PohangRepublic of Korea
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7
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Confinement anisotropy drives polar organization of two DNA molecules interacting in a nanoscale cavity. Nat Commun 2022; 13:4358. [PMID: 35902565 PMCID: PMC9334635 DOI: 10.1038/s41467-022-31398-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/15/2022] [Indexed: 11/08/2022] Open
Abstract
There is growing appreciation for the role phase transition based phenomena play in biological systems. In particular, self-avoiding polymer chains are predicted to undergo a unique confinement dependent demixing transition as the anisotropy of the confined space is increased. This phenomenon may be relevant for understanding how interactions between multiple dsDNA molecules can induce self-organized structure in prokaryotes. While recent in vivo experiments and Monte Carlo simulations have delivered essential insights into this phenomenon and its relation to bacteria, there are fundamental questions remaining concerning how segregated polymer states arise, the role of confinement anisotropy and the nature of the dynamics in the segregated states. To address these questions, we introduce an artificial nanofluidic model to quantify the interactions of multiple dsDNA molecules in cavities with controlled anisotropy. We find that two dsDNA molecules of equal size confined in an elliptical cavity will spontaneously demix and orient along the cavity poles as cavity eccentricity is increased; the two chains will then swap pole positions with a frequency that decreases with increasing cavity eccentricity. In addition, we explore a system consisting of a large dsDNA molecule and a plasmid molecule. We find that the plasmid is excluded from the larger molecule and will exhibit a preference for the ellipse poles, giving rise to a non-uniform spatial distribution in the cavity that may help explain the non-uniform plasmid distribution observed during in vivo imaging of high-copy number plasmids in bacteria.
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8
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Yaginuma H, Ohtake K, Akamatsu T, Noji H, Tabata KV. A microreactor sealing method using adhesive tape for digital bioassays. LAB ON A CHIP 2022; 22:2001-2010. [PMID: 35481587 DOI: 10.1039/d2lc00065b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Digital assays using microreactors fabricated on solid substrates are useful for carrying out sensitive assays of infectious diseases and other biological tests. However, sealing of the microchambers using fluid oil is difficult for non-experts, and thus hinders the widespread use of digital microreactor assays. Here, we propose the physical isolation of tiny reactors with adhesive tape (PITAT) using simple, commercially available pressure-sensitive adhesive (PSA) tape as a separator of the microreactors. We confirmed that PSA tape can effectively seal the microreactors and prevent molecules from diffusing out. By testing several types of adhesive tape, we found that rubber-based adhesives are the most suitable for this purpose. In addition, we demonstrated that single-molecule enzyme assays can be successfully performed inside microreactors sealed with PSA tape. The results obtained using PITAT are quantitatively comparable to conventional oil sealing, although it is quick and cost-effective. Finally, we demonstrated that single-particle virus counting of the influenza virus can be achieved using PITAT. Collectively, our results suggest that PITAT may be suitable for use in the design of sensitive tests for infectious diseases at the point of care, where no sophisticated equipment or machines are available.
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Affiliation(s)
- Hideyuki Yaginuma
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kuniko Ohtake
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Takako Akamatsu
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Hiroyuki Noji
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kazuhito V Tabata
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
- Sothis Technologies, Tokyo, Japan
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9
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Jonchhe S, Pandey S, Beneze C, Emura T, Sugiyama H, Endo M, Mao H. Dissection of nanoconfinement and proximity effects on the binding events in DNA origami nanocavity. Nucleic Acids Res 2022; 50:697-703. [PMID: 35037040 PMCID: PMC8789071 DOI: 10.1093/nar/gkab1298] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/06/2021] [Accepted: 01/09/2022] [Indexed: 12/02/2022] Open
Abstract
Both ligand binding and nanocavity can increase the stability of a biomolecular structure. Using mechanical unfolding in optical tweezers, here we found that a DNA origami nanobowl drastically increased the stability of a human telomeric G-quadruplex bound with a pyridostatin (PDS) ligand. Such a stability change is equivalent to >4 orders of magnitude increase (upper limit) in binding affinity (Kd: 490 nM → 10 pM (lower limit)). Since confined space can assist the binding through a proximity effect between the ligand-receptor pair and a nanoconfinement effect that is mediated by water molecules, we named such a binding as mechanochemical binding. After minimizing the proximity effect by using PDS that can enter or leave the DNA nanobowl freely, we attributed the increased affinity to the nanoconfinement effect (22%) and the proximity effect (78%). This represents the first quantification to dissect the effects of proximity and nanoconfinement on binding events in nanocavities. We anticipate these DNA nanoassemblies can deliver both chemical (i.e. ligand) and mechanical (i.e. nanocavity) milieus to facilitate robust mechanochemical binding in various biological systems.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Christian Beneze
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.,Organization for Research and Development of Innovative Science and Technology, Kansai University, Suita, Osaka 564-8680, Japan
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
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10
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Silverstein TP. The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry. Front Mol Biosci 2021; 8:764099. [PMID: 34901158 PMCID: PMC8661011 DOI: 10.3389/fmolb.2021.764099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pK a and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H+. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.
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Affiliation(s)
- Todd P Silverstein
- Chemistry Department (emeritus), Willamette University, Salem, OR, United States
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11
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12
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Gao J, Su H, Wang W. A microwell array-based approach for studying single nanoparticle catalysis with high turnover frequency. J Chem Phys 2021; 155:071101. [PMID: 34418929 DOI: 10.1063/5.0058402] [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
Measuring the catalytical activities of single catalysts in the case of high turnover frequency (TOF, realistic conditions) is highly desirable to accurately evaluate the functional heterogeneities among individuals and to understand the catalytic mechanism. Herein, we report a microwell array-based method to in operando measure the photocatalytic kinetics of single CdS nanoparticles (NPs) with high TOF. This was realized by sealing individual CdS NPs into separated micrometer-sized polydimethylsiloxane wells, thus eliminating the diffusion of products among individuals in the case of high concentration of reactants. This method allowed us to monitor the activities of single catalysts with an average TOF up to 2.1 × 105 s-1. Interestingly, two types of catalytical behaviors were revealed during single CdS photocatalysis: a rapid decline in activity for most CdS NPs and an initial increase in activity followed by a decrease for a minor population of individuals. The developed method will facilitate the investigation of catalytic activities of single particles under realistic conditions and hold great potential in the fields of photo/electro-catalysts, enzymes, functional bacteria, and so on.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hua Su
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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13
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Hosseini II, Liu Z, Capaldi X, AbdelFatah T, Montermini L, Rak J, Reisner W, Mahshid S. Nanofluidics for Simultaneous Size and Charge Profiling of Extracellular Vesicles. NANO LETTERS 2021; 21:4895-4902. [PMID: 34061534 DOI: 10.1021/acs.nanolett.0c02558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived membrane structures that circulate in body fluids and show considerable potential for noninvasive diagnosis. EVs possess surface chemistries and encapsulated molecular cargo that reflect the physiological state of cells from which they originate, including the presence of disease. In order to fully harness the diagnostic potential of EVs, there is a critical need for technologies that can profile large EV populations without sacrificing single EV level detail by averaging over multiple EVs. Here we use a nanofluidic device with tunable confinement to trap EVs in a free-energy landscape that modulates vesicle dynamics in a manner dependent on EV size and charge. As proof-of-principle, we perform size and charge profiling of a population of EVs extracted from human glioblastoma astrocytoma (U373) and normal human astrocytoma (NHA) cell lines.
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Affiliation(s)
- Imman I Hosseini
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Tamer AbdelFatah
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
| | - Laura Montermini
- Research Institute of the McGill University Health Centre, 1001 Decarie Boul., Montreal, Quebec H4A 3J1, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, Research Institute of the McGill University Health Centre, 1001 Decarie Boul., Montreal, Quebec H4A 3J1, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Sara Mahshid
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
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14
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Wilson KR, Prophet AM, Rovelli G, Willis MD, Rapf RJ, Jacobs MI. A kinetic description of how interfaces accelerate reactions in micro-compartments. Chem Sci 2020; 11:8533-8545. [PMID: 34123113 PMCID: PMC8163377 DOI: 10.1039/d0sc03189e] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A kinetic expression is derived to explain how interfaces alter bulk chemical equilibria and accelerate reactions in micro-compartments. This description, aided by the development of a stochastic model, quantitatively predicts previous experimental observations of accelerated imine synthesis in micron-sized emulsions. The expression accounts for how reactant concentration and compartment size together lead to accelerated reaction rates under micro-confinement. These rates do not depend solely on concentration, but rather the fraction of total molecules in the compartment that are at the interface. Although there are ∼107 to 1013 solute molecules in a typical micro-compartment, a kind of "stochasticity" appears when compartment size and reagent concentration yield nearly equal numbers of bulk and interfacial molecules. Although this is distinct from the stochasticity produced by nano-confinement, these results show how interfaces can govern chemical transformations in larger atmospheric, geologic and biological compartments.
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Affiliation(s)
- Kevin R Wilson
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Alexander M Prophet
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA .,Department of Chemistry, University of California Berkeley CA 94720 USA
| | - Grazia Rovelli
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Megan D Willis
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Rebecca J Rapf
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley CA 94720 USA
| | - Michael I Jacobs
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
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15
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Goch W, Bal W. Stochastic or Not? Method To Predict and Quantify the Stochastic Effects on the Association Reaction Equilibria in Nanoscopic Systems. J Phys Chem A 2020; 124:1421-1428. [PMID: 31999920 DOI: 10.1021/acs.jpca.9b09441] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stochastic nature of chemical reaction and impact of the stochasticity on their evolution is soundly documented. Both theoretical predictions and emerging experimental evidence indicate the influence of stochastic effects on the equilibrium state of association reaction. In this work simple mathematical formulas are introduced to estimate these effects. First, the dependence of the ratio of observed reactants (apparent association constant, equivalent of macroscopic association constant in stochastic analysis) on the volume and the number of molecules of reagents is discussed and the limiting factors of this effect are shown. Next, the apparent association constant is approximated for nanoscale systems by closed-form formulas derived for this purpose. Finally, an estimation for the macroscopic constant value from the apparent one is provided and validated on the published experimental data. This work was inspired by chemical reactions occurring in biological compartments, but the results can be used for all systems belonging to the stochastic regime of chemical reactions.
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Affiliation(s)
- Wojciech Goch
- Department of Physical Chemistry, Faculty of Pharmacy , The Medical University of Warsaw , 02-097 Warsaw , Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Pawinskiego 5a , 02-106 Warsaw , Poland
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16
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Bespalova MI, Mahanta S, Krishnan M. Single-molecule trapping and measurement in solution. Curr Opin Chem Biol 2019; 51:113-121. [DOI: 10.1016/j.cbpa.2019.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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17
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Scott S, Xu ZM, Kouzine F, Berard DJ, Shaheen C, Gravel B, Saunders L, Hofkirchner A, Leroux C, Laurin J, Levens D, Benham CJ, Leslie SR. Visualizing structure-mediated interactions in supercoiled DNA molecules. Nucleic Acids Res 2019; 46:4622-4631. [PMID: 29684182 PMCID: PMC5961182 DOI: 10.1093/nar/gky266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/03/2018] [Indexed: 01/23/2023] Open
Abstract
We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies on containing the DNA molecules within an enclosed array of glass nanopits using the Convex Lens-induced Confinement (CLiC) imaging method. This method traps molecules within the focal plane while excluding signal from out-of-focus probes. Simultaneously, the molecules can freely diffuse within the nanopits, allowing for accurate measurements of exchange rates, unlike other methods which could introduce an artifactual bias in measurements of binding kinetics. We demonstrate that the plasmid’s structure influences the binding of the fluorescent probes to the unwinding site through the presence, or lack, of other secondary structures. With this method, we observe an increase in the binding rate of the fluorescent probe to the unwinding site with increasing temperature and negative supercoiling. This increase in binding is consistent with the results of our numerical simulations of the probability of site-unwinding. The temperature dependence of the binding rate has allowed us to distinguish the effects of competing higher order DNA structures, such as Z-DNA, in modulating local site-unwinding, and therefore binding.
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Affiliation(s)
- Shane Scott
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Zhi Ming Xu
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Daniel J Berard
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Cynthia Shaheen
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Barbara Gravel
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Laura Saunders
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | | | - Catherine Leroux
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - Jill Laurin
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Craig J Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina R Leslie
- Department of Physics, McGill University, Montreal, Quebec H3A 2T8, Canada
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18
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Downs AM, McCallum C, Pennathur S. Confinement effects on DNA hybridization in electrokinetic micro- and nanofluidic systems. Electrophoresis 2019; 40:792-798. [PMID: 30597594 DOI: 10.1002/elps.201800356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/29/2018] [Accepted: 12/02/2018] [Indexed: 11/09/2022]
Abstract
Spatial confinement, within cells or micro- and nanofabricated devices, impacts the conformation and binding kinetics of biomolecules. Understanding the role of spatial confinement on molecular behavior is important for comprehending diverse biological phenomena, as well as for designing biosensors. Specifically, the behavior of molecular binding under an applied electric field is of importance in the development of electrokinetic biosensors. Here, we investigate whether confinement of DNA oligomers in capillary electrophoresis impacts the binding kinetics of the DNA. To infer the role of confinement on hybridization dynamics, we perform capillary electrophoresis measurements on DNA oligomers within micro- and nanochannels, then apply first-order reaction dynamics theory to extract kinetic parameters from electropherogram data. We find that the apparent dissociation constants at the nanoscale (i.e., within a 100 nm channel) are lower than at the microscale (i.e., within a 1 μm channel), indicating stronger binding with increased confinement. This confirms, for the first time, that confinement-based enhancement of DNA hybridization persists under application of an electric field.
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Affiliation(s)
- Alex M Downs
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Christopher McCallum
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Sumita Pennathur
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
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19
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Malbec R, Cacheux J, Cordelier P, Leichlé T, Joseph P, Bancaud A. Microfluidics for minute DNA sample analysis: open challenges for genetic testing of cell-free circulating DNA in blood plasma. MICRO AND NANO ENGINEERING 2018. [DOI: 10.1016/j.mne.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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20
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Capaldi X, Liu Z, Zhang Y, Zeng L, Reyes-Lamothe R, Reisner W. Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity. SOFT MATTER 2018; 14:8455-8465. [PMID: 30187055 DOI: 10.1039/c8sm01444b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.
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Affiliation(s)
- Xavier Capaldi
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Yuning Zhang
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Lili Zeng
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Rodrigo Reyes-Lamothe
- Department of Biology, McGill University, 33649 Sir William Osler, Montreal, Quebec H3G 0B1, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
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21
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Rubinovich L, Polak M. Remarkable NanoConfinement Effects on Equilibrated Reactions: Statistical-Mechanics Modeling Focused on Ir Dimerization Beneath Surface Sites in Pd–Ir Nanoparticles. Top Catal 2018. [DOI: 10.1007/s11244-018-0978-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Galvin CJ, Shirai K, Rahmani A, Masaya K, Shen AQ. Total Capture, Convection-Limited Nanofluidic Immunoassays Exhibiting Nanoconfinement Effects. Anal Chem 2018; 90:3211-3219. [PMID: 29446612 DOI: 10.1021/acs.analchem.7b04664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding nanoconfinement phenomena is necessary to develop nanofluidic technology platforms. One example of nanoconfinement phenomena is shifts in reaction equilibria toward reaction products in nanoconfined systems, which have been predicted theoretically and observed experimentally in DNA hybridization. Here we demonstrate a convection-limited nanofluidic immunoassay that achieves total capture of a target analyte and an apparent shift in the antibody-antigen reaction equilibrium due to nanoconfinement. The system exhibits wavefronts of the target analyte that propagate along the length of the nanochannel at a velocity much slower than that of the carrier fluid. We apply an analytical model describing the propagation of these wavefronts to determine the density of capture antibody binding sites in the enclosed nanochannel for a known concentration of the target analyte. We then use this binding site density to estimate the concentration of solutions with 5× and 10× less analyte. Our analysis suggests that nanoconfinement results in a preference toward binding of the target analyte with the surface-grafted capture antibody, as evidenced by an apparent reduction in the equilibrium dissociation constant. Our findings motivate the advancement of new biomedical and chemical synthesis technologies by leveraging nanoconfinement effects, and demonstrate a useful platform for studying the effect of nanoconfinement on chemical systems.
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Affiliation(s)
- Casey J Galvin
- Micro/Bio/Nanofluidics Unit , Okinawa Institute of Science and Technology Graduate School , 1919-1 Tancha , Onna-son , Okinawa 904-0495 , Japan
| | - Kentaro Shirai
- Sysmex Corporation , 4-4-2 Takatsukadai , Kobe-shi , Hyogo 651-2271 , Japan
| | - Ali Rahmani
- Micro/Bio/Nanofluidics Unit , Okinawa Institute of Science and Technology Graduate School , 1919-1 Tancha , Onna-son , Okinawa 904-0495 , Japan
| | - Kakuta Masaya
- Sysmex Corporation , 4-4-2 Takatsukadai , Kobe-shi , Hyogo 651-2271 , Japan
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit , Okinawa Institute of Science and Technology Graduate School , 1919-1 Tancha , Onna-son , Okinawa 904-0495 , Japan
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23
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Maioli M, Varadi G, Kurdi R, Caglioti L, Pályi G. Limits of the Classical Concept of Concentration. J Phys Chem B 2016; 120:7438-45. [PMID: 27384879 DOI: 10.1021/acs.jpcb.6b02904] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Solutions of very low concentrations cannot be treated by the usual concept of concentration. Stochastic calculations are performed for the analysis of such solutions containing one or a few molecule(s). It is concluded that these systems escape the usual concentration parameters. Two "case histories" are also shown for demonstration of the practical consequences of the theoretical analysis.
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Affiliation(s)
- Marco Maioli
- Department of Mathematics, University of Modena and Reggio Emilia , Via Campi 213/B, I-41125 Modena, Italy
| | - Gyula Varadi
- Inpellis, Inc. , 100 Cummings Center, Suite 243C, Beverly, Massachusetts 01915-6133, United States
| | - Róbert Kurdi
- Institute of Environmental Engineering, University of Pannonia , Egyetem u. 10, H-8200 Veszprém, Hungary
| | - Luciano Caglioti
- Department of Chemistry and Technology of Biologically Active Compounds, University "La Sapienza"-Roma , P.le A. Moro 5, I-00185 Roma, Italy
| | - Gyula Pályi
- Department of Life Sciences, University of Modena and Reggio Emilia , Via Campi 103, I-41125 Modena, Italy
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24
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Banterle N, Lemke EA. Nanoscale devices for linkerless long-term single-molecule observation. Curr Opin Biotechnol 2016; 39:105-112. [PMID: 26990172 PMCID: PMC7611743 DOI: 10.1016/j.copbio.2016.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/11/2016] [Accepted: 02/15/2016] [Indexed: 01/07/2023]
Abstract
Total internal reflection fluorescence microscopy (TIRFM) can offer favorably high signal-to-noise observation of biological mechanisms. TIRFM can be used routinely to observe even single fluorescent molecules for a long duration (several seconds) at millisecond time resolution. However, to keep the investigated sample in the evanescent field, chemical surface immobilization techniques typically need to be implemented. In this review, we describe some of the recently developed novel nanodevices that overcome this limitation enabling long-term observation of free single molecules and outline their biological applications. The working concept of many devices is compatible with high-throughput strategies, which will further help to establish unbiased single molecule observation as a routine tool in biology to study the molecular underpinnings of even the most complex biological mechanisms.
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Affiliation(s)
- Niccolò Banterle
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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25
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Affiliation(s)
- Pradyumna S. Singh
- Intel
Labs, Intel Corporation, 2200 Mission College Boulevard, Santa Clara, California 95054, United States
| | - Serge G. Lemay
- MESA+
Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands
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26
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Abstract
As of 2015, it has been 26 years since the first optical detection and spectroscopy of single molecules in condensed matter. This area of science has expanded far beyond the early low temperature studies in crystals to include single molecules in cells, polymers, and in solution. The early steps relied upon high-resolution spectroscopy of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral fine structure arising directly from the position-dependent fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 1990s, a variety of fascinating physical effects were observed for individual molecules, including imaging of the light from single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency. In the room temperature regime, researchers showed that bursts of light from single molecules could be detected in solution, leading to imaging and microscopy by a variety of methods. Studies of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. All of these early steps provided important fundamentals underpinning the development of super-resolution microscopy based on single-molecule localization and active control of emitting concentration. Current thrust areas include extensions to three-dimensional imaging with high precision, orientational analysis of single molecules, and direct measurements of photodynamics and transport properties for single molecules trapped in solution by suppression of Brownian motion. Without question, a huge variety of studies of single molecules performed by many talented scientists all over the world have extended our knowledge of the nanoscale and many microscopic mechanisms previously hidden by ensemble averaging.
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Affiliation(s)
- W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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27
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Three-in-one enzyme assay based on single molecule detection in femtoliter arrays. Anal Bioanal Chem 2015; 407:7443-52. [DOI: 10.1007/s00216-015-8910-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/23/2015] [Accepted: 07/08/2015] [Indexed: 12/14/2022]
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28
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Kinz-Thompson CD, Gonzalez RL. smFRET studies of the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding. FEBS Lett 2014; 588:3526-38. [PMID: 25066296 PMCID: PMC4779314 DOI: 10.1016/j.febslet.2014.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
Abstract
The selectivity with which a biomolecule can bind its cognate ligand when confronted by the vast array of structurally similar, competing ligands that are present in the cell underlies the fidelity of some of the most fundamental processes in biology. Because they collectively comprise one of only a few methods that can sensitively detect the 'encounter' complexes and subsequent intermediate states that regulate the selectivity of ligand binding, single-molecule fluorescence, and particularly single-molecule fluorescence resonance energy transfer (smFRET), approaches have revolutionized studies of ligand-binding reactions. Here, we describe a widely used smFRET strategy that enables investigations of a large variety of ligand-binding reactions, and discuss two such reactions, aminoacyl-tRNA selection during translation elongation and splice site selection during spliceosome assembly, that highlight both the successes and challenges of smFRET studies of ligand-binding reactions. We conclude by reviewing a number of emerging experimental and computational approaches that are expanding the capabilities of smFRET approaches for studies of ligand-binding reactions and that promise to reveal the mechanisms that control the selectivity of ligand binding with unprecedented resolution.
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Affiliation(s)
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, NY 10027, United States.
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29
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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30
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Berard DJ, Michaud F, Mahshid S, Ahamed MJ, McFaul CMJ, Leith JS, Bérubé P, Sladek R, Reisner W, Leslie SR. Convex lens-induced nanoscale templating. Proc Natl Acad Sci U S A 2014; 111:13295-300. [PMID: 25092333 PMCID: PMC4169971 DOI: 10.1073/pnas.1321089111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.
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Affiliation(s)
- Daniel J Berard
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - François Michaud
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sara Mahshid
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | | | | | - Jason S Leith
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Pierre Bérubé
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sabrina R Leslie
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
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31
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Enzyme molecules in solitary confinement. Molecules 2014; 19:14417-45. [PMID: 25221867 PMCID: PMC6271441 DOI: 10.3390/molecules190914417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 11/17/2022] Open
Abstract
Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.
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32
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Mathwig K, Aartsma TJ, Canters GW, Lemay SG. Nanoscale methods for single-molecule electrochemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:383-404. [PMID: 25000819 DOI: 10.1146/annurev-anchem-062012-092557] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.
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Affiliation(s)
- Klaus Mathwig
- MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, the Netherlands; ,
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Rubinovich L, Polak M. The intrinsic role of nanoconfinement in chemical equilibrium: evidence from DNA hybridization. NANO LETTERS 2013; 13:2247-2251. [PMID: 23600497 DOI: 10.1021/nl4008198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Recently we predicted that when a reaction involving a small number of molecules occurs in a nanometric-scale domain entirely segregated from the surrounding media, the nanoconfinement can shift the position of equilibrium toward products via reactant-product reduced mixing. In this Letter, we demonstrate how most-recently reported single-molecule fluorescence measurements of partial hybridization of ssDNA confined within nanofabricated chambers provide the first experimental confirmation of this entropic nanoconfinement effect. Thus, focusing separately on each occupancy-specific equilibrium constant, quantitatively reveals extra stabilization of the product upon decreasing the chamber occupancy or size. Namely, the DNA hybridization under nanoconfined conditions is significantly favored over the identical reaction occurring in bulk media with the same reactant concentrations. This effect, now directly verified for DNA, can be relevant to actual biological processes, as well as to diverse reactions occurring within molecular capsules, nanotubes, and other functional nanospaces.
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Affiliation(s)
- Leonid Rubinovich
- The Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Dynamics and prototropic reactivity of electronically excited states in simple surfactant aggregates. Curr Opin Colloid Interface Sci 2013. [DOI: 10.1016/j.cocis.2012.12.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chen A, Vu T, Stybayeva G, Pan T, Revzin A. Reconfigurable microfluidics combined with antibody microarrays for enhanced detection of T-cell secreted cytokines. BIOMICROFLUIDICS 2013; 7:24105. [PMID: 24404010 PMCID: PMC3612111 DOI: 10.1063/1.4795423] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/01/2013] [Indexed: 05/10/2023]
Abstract
Cytokines are small proteins secreted by leukocytes in blood in response to infections, thus offering valuable diagnostic information. Given that the same cytokines may be produced by different leukocyte subsets in blood, it is beneficial to connect production of cytokines to specific cell types. In this paper, we describe integration of antibody (Ab) microarrays into a microfluidic device to enable enhanced cytokine detection. The Ab arrays contain spots specific to cell-surface antigens as well as anti-cytokine detection spots. Infusion of blood into a microfluidic device results in the capture of specific leukocytes (CD4 T-cells) and is followed by detection of secreted cytokines on the neighboring Ab spots using sandwich immunoassay. The enhancement of cytokine signal comes from leveraging the concept of reconfigurable microfluidics. A three layer polydimethylsiloxane microfluidic device is fabricated so as to contain six microchambers (1 mm × 1 mm × 30 μm) in the ceiling of the device. Once the T-cell capture is complete, the device is reconfigured by withdrawing liquid from the channel, causing the chambers to collapse onto Ab arrays and enclose cell/anti-cytokine spots within a 30 nl volume. In a set of proof-of-concept experiments, we demonstrate that ∼90% pure CD4 T-cells can be captured inside the device and that signals for three important T-cell secreted cytokines, tissue necrosis factor-alpha, interferon-gamma, and interleukin-2, may be enhanced by 2 to 3 folds through the use of reconfigurable microfluidics.
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Affiliation(s)
- Arnold Chen
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - Tam Vu
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - Gulnaz Stybayeva
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - Tingrui Pan
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis, California 95616, USA
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