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Schwenzer AK, Kruse L, Jooß K, Neusüß C. Capillary electrophoresis-mass spectrometry for protein analyses under native conditions: Current progress and perspectives. Proteomics 2024; 24:e2300135. [PMID: 37312401 DOI: 10.1002/pmic.202300135] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/15/2023]
Abstract
Native mass spectrometry is a rapidly emerging technique for fast and sensitive structural analysis of protein constructs, maintaining the protein higher order structure. The coupling with electromigration separation techniques under native conditions enables the characterization of proteoforms and highly complex protein mixtures. In this review, we present an overview of current native CE-MS technology. First, the status of native separation conditions is described for capillary zone electrophoresis (CZE), affinity capillary electrophoresis (ACE), and capillary isoelectric focusing (CIEF), as well as their chip-based formats, including essential parameters such as electrolyte composition and capillary coatings. Further, conditions required for native ESI-MS of (large) protein constructs, including instrumental parameters of QTOF and Orbitrap systems, as well as requirements for native CE-MS interfacing are presented. On this basis, methods and applications of the different modes of native CE-MS are summarized and discussed in the context of biological, medical, and biopharmaceutical questions. Finally, key achievements are highlighted and concluded, while remaining challenges are pointed out.
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Affiliation(s)
| | - Lena Kruse
- Department of Chemistry, Aalen University, Aalen, Germany
| | - Kevin Jooß
- Department of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois, USA
- Division of Bioanalytical Chemistry, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Centre for Analytical Sciences Amsterdam (CASA), Amsterdam, The Netherlands
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2
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Benham CJ. DNA superhelicity. Nucleic Acids Res 2024; 52:22-48. [PMID: 37994702 PMCID: PMC10783518 DOI: 10.1093/nar/gkad1092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Closing each strand of a DNA duplex upon itself fixes its linking number L. This topological condition couples together the secondary and tertiary structures of the resulting ccDNA topoisomer, a constraint that is not present in otherwise identical nicked or linear DNAs. Fixing L has a range of structural, energetic and functional consequences. Here we consider how L having different integer values (that is, different superhelicities) affects ccDNA molecules. The approaches used are primarily theoretical, and are developed from a historical perspective. In brief, processes that either relax or increase superhelicity, or repartition what is there, may either release or require free energy. The energies involved can be substantial, sufficient to influence many events, directly or indirectly. Here two examples are developed. The changes of unconstrained superhelicity that occur during nucleosome attachment and release are examined. And a simple theoretical model of superhelically driven DNA structural transitions is described that calculates equilibrium distributions for populations of identical topoisomers. This model is used to examine how these distributions change with superhelicity and other factors, and applied to analyze several situations of biological interest.
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Affiliation(s)
- Craig J Benham
- UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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3
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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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4
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Leslie SR. Biophysical Reviews ‘Meet the Editors Series’ — a profile of Sabrina Leslie. Biophys Rev 2022; 14:417-421. [PMID: 35437452 PMCID: PMC9007050 DOI: 10.1007/s12551-022-00948-4] [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] [Accepted: 03/21/2022] [Indexed: 01/22/2023] Open
Abstract
It is my pleasure to introduce myself to the readers of Biophysical Reviews as part of the ‘Meet the Editors Series’.
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Affiliation(s)
- Sabrina R. Leslie
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
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5
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Shaheen C, Hastie C, Metera K, Scott S, Zhang Z, Chen S, Gu G, Weber L, Munsky B, Kouzine F, Levens D, Benham C, Leslie S. Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation. Nucleic Acids Res 2022; 50:2754-2764. [PMID: 35188541 PMCID: PMC8934633 DOI: 10.1093/nar/gkac101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/28/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.
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Affiliation(s)
- Cynthia Shaheen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Cameron Hastie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
| | - Kimberly Metera
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Shane Scott
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Institute of Materials Science, Kiel University, 24142 Kiel, Germany
| | - Zhi Zhang
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Sitong Chen
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Gracia Gu
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
| | - Lisa Weber
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian Munsky
- Department of Chemical and Biological Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Fedor Kouzine
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - David Levens
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Craig Benham
- Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Sabrina Leslie
- Department of Physics, McGill University, Montreal, QC H3A 2T8, Canada
- Michael Smith Laboratories, University of British Columbia, BC V6T 1Z4, Canada
- Department of Physics and Astronomy, University of British Columbia, BC V6T 1Z1, Canada
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Arsenie LV, Semsarilar M, Brendel JC, Lacroix-Desmazes P, Ladmiral V, Catrouillet S. Supramolecular co-assembly of water-soluble nucleobase-containing copolymers: bioinspired synthetic platforms towards new biomimetic materials. Polym Chem 2022. [DOI: 10.1039/d2py00872f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study presents the development of new co-assembled copolymers architectures at physiological pH (pH=7.4) formed via H-bonds between complementary nucleobase-containing copolymers. Well-defined hydrophilic copolymers were synthesised by RAFT polymerisation: statistical...
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7
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Kamanzi A, Gu Y, Tahvildari R, Friedenberger Z, Zhu X, Berti R, Kurylowicz M, Witzigmann D, Kulkarni JA, Leung J, Andersson J, Dahlin A, Höök F, Sutton M, Cullis PR, Leslie S. Simultaneous, Single-Particle Measurements of Size and Loading Give Insights into the Structure of Drug-Delivery Nanoparticles. ACS NANO 2021; 15:19244-19255. [PMID: 34843205 DOI: 10.1021/acsnano.1c04862] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanoparticles are a promising solution for delivery of a wide range of medicines and vaccines. Optimizing their design depends on being able to resolve, understand, and predict biophysical and therapeutic properties, as a function of design parameters. While existing tools have made great progress, gaps in understanding remain because of the inability to make detailed measurements of multiple correlated properties. Typically, an average measurement is made across a heterogeneous population, obscuring potentially important information. In this work, we develop and apply a method for characterizing nanoparticles with single-particle resolution. We use convex lens-induced confinement (CLiC) microscopy to isolate and quantify the diffusive trajectories and fluorescent intensities of individual nanoparticles trapped in microwells for long times. First, we benchmark detailed measurements of fluorescent polystyrene nanoparticles against prior data to validate our approach. Second, we apply our method to investigate the size and loading properties of lipid nanoparticle (LNP) vehicles containing silencing RNA (siRNA), as a function of lipid formulation, solution pH, and drug-loading. By taking a comprehensive look at the correlation between the intensity and size measurements, we gain insights into LNP structure and how the siRNA is distributed in the LNP. Beyond introducing an analytic for size and loading, this work allows for future studies of dynamics with single-particle resolution, such as LNP fusion and drug-release kinetics. The prime contribution of this work is to better understand the connections between microscopic and macroscopic properties of drug-delivery vehicles, enabling and accelerating their discovery and development.
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Affiliation(s)
- Albert Kamanzi
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
- Department of Physics Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, Canada V6T 1Z1
- Michael Smith Laboratories and Department of Physics, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, Canada V6T 1Z4
| | - Yifei Gu
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
| | - Radin Tahvildari
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
| | - Zachary Friedenberger
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
| | - Xingqi Zhu
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
| | - Romain Berti
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
- Michael Smith Laboratories and Department of Physics, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, Canada V6T 1Z4
- ScopeSys Inc., 33 Rue Prince, Montreal, Quebec, Canada H3C 2M7
| | - Marty Kurylowicz
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
- ScopeSys Inc., 33 Rue Prince, Montreal, Quebec, Canada H3C 2M7
| | - Dominik Witzigmann
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jayesh A Kulkarni
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jerry Leung
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - John Andersson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Andreas Dahlin
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Mark Sutton
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
| | - Pieter R Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Sabrina Leslie
- Department of Physics, McGill University, 3600 University, Montreal Quebec, Canada H3A2T8
- Department of Physics Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia, Canada V6T 1Z1
- Michael Smith Laboratories and Department of Physics, University of British Columbia, 2329 West Mall, Vancouver, British Columbia, Canada V6T 1Z4
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Toderich KN, Mamadrahimov AA, Khaitov BB, Karimov AA, Soliev AA, Nanduri KR, Shuyskaya EV. Differential Impact of Salinity Stress on Seeds Minerals, Storage Proteins, Fatty Acids, and Squalene Composition of New Quinoa Genotype, Grown in Hyper-Arid Desert Environments. FRONTIERS IN PLANT SCIENCE 2020; 11:607102. [PMID: 33365043 PMCID: PMC7750330 DOI: 10.3389/fpls.2020.607102] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/09/2020] [Indexed: 05/13/2023]
Abstract
The effects of climate change and soil salinization on dryland ecosystems are already widespread, and ensuring food security is a crucial challenge. In this article, we demonstrate changes in growth performance and seed quality of a new high-yielding quinoa genotype (Q5) exposed to sodium chloride (NaCl), sodium sulfate (Na2SO4), and mixed salts (NaCl + Na2SO4). Differential responses to salt stress in growth performance, seed yield, and seed quality were identified. High salinity (mixed Na2SO4 + NaCl) reduces plant height by ∼30%, shoot and root dry weights by ∼29%, head panicle length and panicle weight by 36-43%, and seed yield by 37%, compared with control conditions. However, the 1,000-seed weight changes insignificantly under salinity. High content of essential minerals, such as Fe, Zn, and Ca in quinoa Q5 seeds produced under salinity, gives the Q5 genotype a remarkable advantage for human consumption. Biomarkers detected in our studies show that the content of most essential amino acids is unchanged under salinity. The content of amino acids Pro, Gly, and Ile positively correlates with Na+ concentration in soil and seeds, whereas the content of squalene and most fatty acids negatively correlates. Variation in squalene content under increasing salinity is most likely due to toxic effects of sodium and chlorine ions as a result of the decrease in membrane permeability for ion movement as a protective reaction to an increase in the sodium ion concentration. Low squalene accumulation might also occur to redirect the NADPH cofactor to enhance the biosynthesis of proline in response to salinity, as both syntheses (squalene and proline) require NADPH. This evidence can potentially be used by the food and pharmaceutical industries in the development of new food and health products.
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Affiliation(s)
- Kristina N. Toderich
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- International Center for Biosaline Agriculture for Central Asia and Caucasus (ICBA-CAC), Tashkent, Uzbekistan
| | | | - Botir B. Khaitov
- International Center for Biosaline Agriculture for Central Asia and Caucasus (ICBA-CAC), Tashkent, Uzbekistan
| | - Aziz A. Karimov
- International Center for Biosaline Agriculture for Central Asia and Caucasus (ICBA-CAC), Tashkent, Uzbekistan
| | - Azamjon A. Soliev
- Institute of Bioorganic Chemistry Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Kameswara Rao Nanduri
- International Center for Biosaline Agriculture for Central Asia and Caucasus (ICBA-CAC), Tashkent, Uzbekistan
| | - Elena V. Shuyskaya
- K.A. Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Elena V. Shuyskaya,
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Leslie S, Berard D, Kamanzi A, Metera K, Scott S, Shaheen C, Shayegan M, Tahvildari R, Zhang Z. Single-molecule imaging of the biophysics of molecular interactions with precision and control, in cell-like conditions, and without tethers. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Thiombane NK, Coutin N, Berard D, Tahvildari R, Leslie S, Nislow C. Single-cell analysis for drug development using convex lens-induced confinement imaging. Biotechniques 2019; 67:210-217. [DOI: 10.2144/btn-2019-0067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
New technologies have powered rapid advances in cellular imaging, genomics and phenotypic analysis in life sciences. However, most of these methods operate at sample population levels and provide statistical averages of aggregated data that fail to capture single-cell heterogeneity, complicating drug discovery and development. Here we demonstrate a new single-cell approach based on convex lens-induced confinement (CLiC) microscopy. We validated CLiC on yeast cells, demonstrating subcellular localization with an enhanced signal-to-noise and fluorescent signal detection sensitivity compared with traditional imaging. In the live-cell CLiC assay, cellular proliferation times were consistent with flask culture. Using methotrexate, we provide drug response data showing a fivefold cell size increase following drug exposure. Taken together, CLiC enables high-quality imaging of single-cell drug response and proliferation for extended observation periods.
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Affiliation(s)
- Ndeye Khady Thiombane
- Pharmaceutical Sciences, 2405 Wesbrook Mall, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Nicolas Coutin
- Pharmaceutical Sciences, 2405 Wesbrook Mall, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
| | - Daniel Berard
- Department of Physics, 214 Rutherford Physics Building, McGill University, 3600 rue University, Montreal, QC, H3A 2T8, Canada
| | - Radin Tahvildari
- Department of Physics, 214 Rutherford Physics Building, McGill University, 3600 rue University, Montreal, QC, H3A 2T8, Canada
| | - Sabrina Leslie
- Department of Physics, 214 Rutherford Physics Building, McGill University, 3600 rue University, Montreal, QC, H3A 2T8, Canada
| | - Corey Nislow
- Pharmaceutical Sciences, 2405 Wesbrook Mall, University of British Columbia, Vancouver, BC, V6T1Z3, Canada
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