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Rinkovec T, Kalebic D, Dehaen W, Whitelam S, Harvey JN, De Feyter S. On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface. Chem Sci 2024; 15:6076-6087. [PMID: 38665531 PMCID: PMC11041291 DOI: 10.1039/d4sc00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.
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Affiliation(s)
- Tamara Rinkovec
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Demian Kalebic
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Wim Dehaen
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Steven De Feyter
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
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2
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Hashidzume A, Itami T, Kamon Y, Harada A. A Simplified Model for Multivalent Interaction Competing with a Low Molecular Weight Competitor. CHEM LETT 2020. [DOI: 10.1246/cl.200501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Akihito Hashidzume
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Itami
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuri Kamon
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akira Harada
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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3
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Erban A, Martinez-Seidel F, Rajarathinam Y, Dethloff F, Orf I, Fehrle I, Alpers J, Beine-Golovchuk O, Kopka J. Multiplexed Profiling and Data Processing Methods to Identify Temperature-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry. Methods Mol Biol 2020; 2156:203-239. [PMID: 32607984 DOI: 10.1007/978-1-0716-0660-5_15] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This book chapter describes the analytical procedures required for the profiling of a metabolite fraction enriched for primary metabolites. The profiling is based on routine gas chromatography coupled to mass spectrometry (GC-MS). The generic profiling method is adapted to plant material, specifically to the analysis of plant material that was exposed to temperature stress. The method can be combined with stable isotope labeling and tracing experiments and is equally applicable to preparations of plant material and microbial photosynthetic organisms. The described methods are modular and can be multiplexed, that is, the same sample or a paired identical backup sample can be analyzed sequentially by more than one of the described procedures. The modules include rapid sampling and metabolic inactivation protocols for samples in a wide weight range, sample extraction procedures, chemical derivatization steps that are required to make the metabolite fraction amenable to gas chromatographic analysis, routine GC-MS methods, and procedures of data processing and data mining. A basic and extendable set of standardizations for metabolite recovery and retention index alignment of the resulting GC-MS chromatograms is included. The methods have two applications: (1) The rapid screening for changes of relative metabolite pools sizes under temperature stress and (2) the verification by exact quantification using GC-MS protocols that are extended by internal and external standardization.
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Affiliation(s)
- Alexander Erban
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Federico Martinez-Seidel
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yogeswari Rajarathinam
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Frederik Dethloff
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Proteomics and Biomarkers, Max Planck Institute of Psychiatry, München, Germany
| | - Isabel Orf
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Owlstone Medical Ltd, Cambridge, UK
| | - Ines Fehrle
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Jessica Alpers
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Olga Beine-Golovchuk
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Nuclear Pore Complex and Ribosome Assembly, Biochemie-Zentrum, Universität Heidelberg, Heidelberg, Germany
| | - Joachim Kopka
- Applied Metabolome Analysis Research Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
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PET imaging of occult tumours by temporal integration of tumour-acidosis signals from pH-sensitive 64Cu-labelled polymers. Nat Biomed Eng 2019; 4:314-324. [PMID: 31235828 PMCID: PMC6928453 DOI: 10.1038/s41551-019-0416-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 05/13/2019] [Indexed: 11/08/2022]
Abstract
Owing to the diversity of cancer types and the spatiotemporal heterogeneity of tumour signals, high-resolution imaging of occult malignancy is challenging. 18F-fluorodeoxyglucose positron emission tomography allows for near-universal cancer detection, yet in many clinical scenarios it is hampered by false positives. Here, we report a method for the amplification of imaging contrast in tumours via the temporal integration of the imaging signals triggered by tumour acidosis. This method exploits the catastrophic disassembly, at the acidic pH of the tumour milieu, of pH-sensitive positron-emitting neutral copolymer micelles into polycationic polymers, which are then internalized and retained by the cancer cells. Positron emission tomography imaging of the 64Cu-labelled polymers detected small occult tumours (10-20 mm3) in the brain, head, neck and breast of mice at much higher contrast than 18F-fluorodeoxyglucose, 11C-methionine and pH-insensitive 64Cu-labelled nanoparticles. We also show that the pH-sensitive probes reduce false positive detection rates in a mouse model of non-cancerous lipopolysaccharide-induced inflammation. This macromolecular strategy for integrating tumour acidosis should enable improved cancer detection, surveillance and staging.
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Zhao YK, Gao ZZ, Wang H, Zhang DW, Li ZT. Self-assembly of supramolecular polymers in water from tetracationic and tetraanionic monomers in water through cooperative electrostatic attraction and aromatic stacking. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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Annenkov VV, Krishnan UM, Pal'shin VA, Zelinskiy SN, Kandasamy G, Danilovtseva EN. Design of Oligonucleotide Carriers: Importance of Polyamine Chain Length. Polymers (Basel) 2018; 10:E1297. [PMID: 30961222 PMCID: PMC6401700 DOI: 10.3390/polym10121297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 01/05/2023] Open
Abstract
Amine containing polymers are extensively studied as special carriers for short-chain RNA (13⁻25 nucleotides), which are applied as gene silencing agents in gene therapy of various diseases including cancer. Elaboration of the oligonucleotide carriers requires knowledge about peculiarities of the oligonucleotide⁻polymeric amine interaction. The critical length of the interacting chains is an important parameter which allows us to design sophisticated constructions containing oligonucleotide binding segments, solubilizing, protective and aiming parts. We studied interactions of (TCAG)n, n = 1⁻6 DNA oligonucleotides with polyethylenimine and poly(N-(3-((3-(dimethylamino)propyl)(methyl)amino)propyl)-N-methylacrylamide). The critical length for oligonucleotides in interaction with polymeric amines is 8⁻12 units and complexation at these length can be accompanied by "all-or-nothing" effects. New dimethylacrylamide based polymers with grafted polyamine chains were obtained and studied in complexation with DNA and RNA oligonucleotides. The most effective interaction and transfection activity into A549 cancer cells and silencing efficiency against vascular endothelial growth factor (VEGF) was found for a sample with average number of nitrogens in polyamine chain equal to 27, i.e., for a sample in which all grafted chains are longer than the critical length for polymeric amine⁻oligonucleotide complexation.
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Affiliation(s)
- Vadim V Annenkov
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India.
| | - Viktor A Pal'shin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Stanislav N Zelinskiy
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
| | - Gayathri Kandasamy
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), School of Chemical and Biotechnology, SASTRA University, Thanjavur 613401, Tamil Nadu, India.
| | - Elena N Danilovtseva
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3, Ulan-Batorskaya St., P.O. Box 278, Irkutsk 664033, Russia.
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Abstract
Nanomedicine is a discipline that applies nanoscience and nanotechnology principles to the prevention, diagnosis, and treatment of human diseases. Self-assembly of molecular components is becoming a common strategy in the design and syntheses of nanomaterials for biomedical applications. In both natural and synthetic self-assembled nanostructures, molecular cooperativity is emerging as an important hallmark. In many cases, interplay of many types of noncovalent interactions leads to dynamic nanosystems with emergent properties where the whole is bigger than the sum of the parts. In this review, we provide a comprehensive analysis of the cooperativity principles in multiple self-assembled nanostructures. We discuss the molecular origin and quantitative modeling of cooperative behaviors. In selected systems, we describe the examples on how to leverage molecular cooperativity to design nanomedicine with improved diagnostic precision and therapeutic efficacy in medicine.
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Affiliation(s)
- Yang Li
- Department of Pharmacology, Simmons Comprehensive Cancer Center , UT Southwestern Medical Center , 5323 Harry Hines Boulevard , Dallas , Texas 75390 , United States
| | - Yiguang Wang
- Department of Pharmacology, Simmons Comprehensive Cancer Center , UT Southwestern Medical Center , 5323 Harry Hines Boulevard , Dallas , Texas 75390 , United States.,Beijing Key Laboratory of Molecular Pharmaceutics and State Key Laboratory of Natural and Biomimetic Drugs , Peking University , Beijing , 100191 , China
| | - Gang Huang
- Department of Pharmacology, Simmons Comprehensive Cancer Center , UT Southwestern Medical Center , 5323 Harry Hines Boulevard , Dallas , Texas 75390 , United States
| | - Jinming Gao
- Department of Pharmacology, Simmons Comprehensive Cancer Center , UT Southwestern Medical Center , 5323 Harry Hines Boulevard , Dallas , Texas 75390 , United States
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Campanella C, Lopez-Fontal E, Milanesi L, Tomas S. Modulation of the cooperativity in the assembly of multistranded supramolecular polymers. Phys Chem Chem Phys 2018; 19:9617-9624. [PMID: 28346555 DOI: 10.1039/c7cp01127j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It is highly desirable that supramolecular polymers self-assemble following small changes in the environment. The degree of responsiveness depends on the degree of cooperativity at play during the assembly. Understanding how to modulate and quantify cooperativity is therefore highly desirable for the study and design of responsive polymers. Here we show that the cooperative assembly of a porphyrin-based, double-stranded polymer is triggered by changes in building blocks and in salt concentration. We develop a model that accounts for this responsiveness by assuming the binding of the salt countercations to the double-stranded polymer. Using our assembly model we generate plots that show the increase in concentration of polymer versus the normalized concentration of monomer. These plots are ideally suited to appreciate changes in cooperativity, and show that, for our system, these changes are consistent with the increase in polymer length observed experimentally. Unexpectedly, we find that polymer stability increases when cooperativity decreases. We attribute this behaviour to the fact that increasing salt concentration stabilizes the overall polymer more than the nucleus. In other words, the cooperativity factor α, defined as the ratio between the growth constant Kg and the nucleation constant Kn decreases as the overall stability of the polymer increases. Using our model to simulate the data, we generate cooperativity plots to explore changes in cooperativity for multistranded polymers. We find that, for the same pairwise association constants, the cooperativity sharply increases with the number of strands in the polymer. We attribute this dependence to the fact that the larger the number of strands, the larger is the nucleus necessary to trigger polymer growth. We show therefore that the cooperativity factor α does not properly account for the cooperativity behaviour of multistranded polymers, or any supramolecular polymer with a nucleus composed of more than 2 building blocks, and propose the use of the corrected cooperativity factor αm. Finally, we show that multistranded polymers display highly cooperative polymerisation with pairwise association constants as low as 10 M-1 between the building blocks, which should simplify the design of responsive supramolecular polymers.
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Affiliation(s)
- Cristiana Campanella
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Elkin Lopez-Fontal
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London, Malet Street, London WC1E 7HX, UK.
| | - Lilia Milanesi
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - Salvador Tomas
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London, Malet Street, London WC1E 7HX, UK.
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9
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Lopez-Fontal E, Grochmal A, Foran T, Milanesi L, Tomas S. Ship in a bottle: confinement-promoted self-assembly. Chem Sci 2017; 9:1760-1768. [PMID: 29675219 PMCID: PMC5885595 DOI: 10.1039/c7sc04553k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/07/2017] [Indexed: 02/04/2023] Open
Abstract
Understanding self-assembly in confined spaces is essential to fully understand molecular processes in confined cell compartments and will offer clues on the behaviour of simple confined systems, such as protocells and lipid-vesicle based devices. Using a model system composed of lipid vesicles, a membrane impermeable receptor and a membrane-permeable ligand, we have studied in detail how compartmentalization modulates the interaction between the confined receptor and its ligand. We demonstrate that confinement of one of the building blocks stabilizes complex self-assembled structures to the extent that dilution leads, counterintuitively, to the formation of long range assemblies. The behaviour of the system can be explained by considering a confinement factor that is analogous, although not identical, to the effective molarity for intramolecular binding events. The confinement effect renders complex self-assembled species robust and persistent under conditions where they do not form in bulk solution. Moreover, we show that the formation of stable complex assemblies in systems compartmentalized by semi-permeable membranes does not require the prior confinement of all components, but only that of key membrane impermeable building blocks. To use a macroscopic analogy, lipid vesicles are like ship-in-a bottle constructs that are capable of directing the assembly of the confined ship following the confinement of a few key wooden planks. Therefore, we believe that the confinement effect described here would have played an important role in shaping the increase of chemical complexity within protocells during the first stages of abiogenesis. Additionally, we argue that this effect can be exploited to design increasingly efficient functional devices based on comparatively simple vesicles for applications in biosensing, nanoreactors and drug delivery vehicles.
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Affiliation(s)
- Elkin Lopez-Fontal
- Institute of Structural and Molecular Biology , Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
| | - Anna Grochmal
- Institute of Structural and Molecular Biology , Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
| | - Tom Foran
- Institute of Structural and Molecular Biology , Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
| | - Lilia Milanesi
- School of Biological and Chemical Sciences , Queen Mary , University of London , Mile End Road , London E1 4NS , UK
| | - Salvador Tomas
- Institute of Structural and Molecular Biology , Department of Biological Sciences , School of Science , Birkbeck University of London , Malet Street , London WC1E 7HX , UK .
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