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Ward CL, Cornejo MA, Peli Thanthri SH, Linz TH. A review of electrophoretic separations in temperature-responsive Pluronic thermal gels. Anal Chim Acta 2023; 1276:341613. [PMID: 37573098 DOI: 10.1016/j.aca.2023.341613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 08/14/2023]
Abstract
Gel electrophoresis is a ubiquitous bioanalytical technique used in research laboratories to validate protein and nucleic acid samples. Polyacrylamide and agarose have been the gold standard gel materials for decades, but an alternative class of polymer has emerged with potentially superior performance. Pluronic thermal gels are water-soluble polymers that possess the unique ability to undergo a change in viscosity in response to changing temperature. Thermal gels can reversibly convert between low-viscosity liquids and high-viscosity solid gels using temperature as an adjustable parameter. The properties of thermal gels provide unmatched flexibility as a dynamic separations matrix to measure analytes ranging from small molecules to cells. This review article describes the physical and chemical properties of Pluronic thermal gels to provide a fundamental overview of polymer behavior. The performance of thermal gels is then reviewed to highlight their applications as a gel matrix for electrokinetic separations in capillary, microfluidic, and slab gel formats. The use of dynamic temperature-responsive gels in bioanalytical separations is an underexplored area of research but one that holds exciting potential to achieve performance unattainable with conventional static polymers.
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Affiliation(s)
- Cassandra L Ward
- Department of Chemistry, Wayne State University, Detroit, MI, USA; Lumigen Instrument Center, Wayne State University, Detroit, MI, USA.
| | - Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Thomas H Linz
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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2
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Balakrishnan D, Lamblin G, Thomann JS, van den Berg A, Olthuis W, Pascual-García C. Electrochemical Control of pH in Nanoliter Volumes. NANO LETTERS 2018; 18:2807-2815. [PMID: 29617568 DOI: 10.1021/acs.nanolett.7b05054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The electrochemical management of the proton concentration in miniaturized dimensions opens the way to control and parallelize multistep chemical reactions, but still it faces many challenges linked to the efficient proton generation and control of their diffusion. Here we present a device operated electrochemically that demonstrates the control of the pH in a cell of ∼140 nL. The device comprises a microfluidic reactor integrated with a pneumatic mechanism that allows the exchange of reagents and the isolation of protons to decrease the effect of their diffusion. We monitored the pH with a fluorescence marker and calculated the final value from the redox currents. We demonstrate a large pH amplitude control from neutral pH values beyond the fluorescence marker range at pH 5. On the basis of the calculations from the Faradaic currents, the minimum pH reached should undergo pH ∼ 0.9. The pH contrast between neutral and acid pH cells can be maintained during periods longer than 15 min with an appropriate design of a diffusion barrier.
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Affiliation(s)
- Divya Balakrishnan
- Luxembourg Institute of Science and Technology (LIST) , 41 Rue du Brill , L-4422 Belvaux , Luxembourg
- MESA+ Institute , University of Twente , Drienerlolaan 5 , 7522 NB Enschede , Netherlands
| | - Guillaume Lamblin
- Luxembourg Institute of Science and Technology (LIST) , 41 Rue du Brill , L-4422 Belvaux , Luxembourg
| | - Jean Sebastien Thomann
- Luxembourg Institute of Science and Technology (LIST) , 41 Rue du Brill , L-4422 Belvaux , Luxembourg
| | - Albert van den Berg
- MESA+ Institute , University of Twente , Drienerlolaan 5 , 7522 NB Enschede , Netherlands
| | - Wouter Olthuis
- MESA+ Institute , University of Twente , Drienerlolaan 5 , 7522 NB Enschede , Netherlands
| | - César Pascual-García
- Luxembourg Institute of Science and Technology (LIST) , 41 Rue du Brill , L-4422 Belvaux , Luxembourg
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3
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Tangen U, Minero GAS, Sharma A, Wagler PF, Cohen R, Raz O, Marx T, Ben-Yehezkel T, McCaskill JS. DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip. BIOMICROFLUIDICS 2015. [PMID: 26221198 PMCID: PMC4499045 DOI: 10.1063/1.4926616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.
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Affiliation(s)
- Uwe Tangen
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Gabriel Antonio S Minero
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Abhishek Sharma
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Patrick F Wagler
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Rafael Cohen
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Ofir Raz
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Tzipy Marx
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Tuval Ben-Yehezkel
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - John S McCaskill
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
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4
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Freage L, Trifonov A, Tel-Vered R, Golub E, Wang F, McCaskill JS, Willner I. Addressing, amplifying and switching DNAzyme functions by electrochemically-triggered release of metal ions. Chem Sci 2015; 6:3544-3549. [PMID: 29511515 PMCID: PMC5812549 DOI: 10.1039/c5sc00744e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 04/08/2015] [Indexed: 01/01/2023] Open
Abstract
The addressable potential-controlled release of metal ions into electrolyte solutions containing mixtures of nucleic acids leads to the metal ion-guided generation of different DNAzymes and to the activation of DNA cascades.
The design of artificial cells, which mimic the functions of native cells, is an ongoing scientific goal. The development of stimuli-responsive chemical systems that stimulate cascaded catalytic transformations, trigger chemical networks, and control vectorial branched transformations and dose-controlled processes, are the minimum requirements for mimicking cell functions. We have studied the electrochemical programmed release of ions from electrodes, which trigger selective DNAzyme-driven chemical reactions, cascaded reactions that self-assemble catalytic DNAzyme polymers, and the ON–OFF switching and dose-controlled operation of catalytic reactions. The addressable and potential-controlled release of Pb2+ or Ag+ ions into an electrolyte that includes a mixture of nucleic acids, results in the metal ion-guided selection of nucleic acids yielding the formation of specific DNAzymes, which stimulate orthogonal reactions or activate DNAzyme cascades.
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Affiliation(s)
- Lina Freage
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Alexander Trifonov
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Ran Tel-Vered
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Eyal Golub
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - Fuan Wang
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
| | - John S McCaskill
- Biomolecular Information Processing (BioMIP) , Ruhr-Universität Bochum , Universitätsstr 150 , Bochum , 44801 , Germany
| | - Itamar Willner
- Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem , 91904 , Israel .
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Minero GAS, Wagler PF, Oughli AA, McCaskill JS. Electronic pH switching of DNA triplex reactions. RSC Adv 2015. [DOI: 10.1039/c5ra02628h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Remote electronic control of fast DNA processing reactions such as S–S-ligation is achievedviapH switching of triplex structures.
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Affiliation(s)
- Gabriel Antonio S. Minero
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Patrick F. Wagler
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - Alaa A. Oughli
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
| | - John S. McCaskill
- Faculty of Chemistry and Biochemistry
- Microsystems Chemistry and BioIT (BioMIP)
- Ruhr-University Bochum
- 44780 Bochum
- Germany
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Tangen U, Sharma A, Wagler P, McCaskill JS. On demand nanoliter-scale microfluidic droplet generation, injection, and mixing using a passive microfluidic device. BIOMICROFLUIDICS 2015; 9:014119. [PMID: 25759752 PMCID: PMC4327917 DOI: 10.1063/1.4907895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/29/2015] [Indexed: 05/10/2023]
Abstract
We here present and characterize a programmable nanoliter scale droplet-on-demand device that can be used separately or readily integrated into low cost single layer rapid prototyping microfluidic systems for a wide range of user applications. The passive microfluidic device allows external (off-the-shelf) electronically controlled pinch valves to program the delivery of nanoliter scale aqueous droplets from up to 9 different inputs to a central outlet channel. The inputs can be either continuous aqueous fluid streams or microliter scale aqueous plugs embedded in a carrier fluid, in which case the number of effective input solutions that can be employed in an experiment is no longer strongly constrained (100 s-1000 s). Both nanoliter droplet sequencing output and nanoliter-scale droplet mixing are reported with this device. Optimization of the geometry and pressure relationships in the device was achieved in several hardware iterations with the support of open source microfluidic simulation software and equivalent circuit models. The requisite modular control of pressure relationships within the device is accomplished using hydrodynamic barriers and matched resistance channels with three different channel heights, custom parallel reversible microfluidic I/O connections, low dead-volume pinch valves, and a simply adjustable array of external screw valves. Programmable sequences of droplet mixes or chains of droplets can be achieved with the device at low Hz frequencies, limited by device elasticity, and could be further enhanced by valve integration. The chip has already found use in the characterization of droplet bunching during export and the synthesis of a DNA library.
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Affiliation(s)
- Uwe Tangen
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Abhishek Sharma
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Patrick Wagler
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - John S McCaskill
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
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Fellermann H, Cardelli L. Programming chemistry in DNA-addressable bioreactors. J R Soc Interface 2014; 11:rsif.2013.0987. [PMID: 25121647 DOI: 10.1098/rsif.2013.0987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.
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Affiliation(s)
- Harold Fellermann
- School of Computing Science, Newcastle University, King's Gate, Newcastle upon Tyne NE1 7RU, UK Center for Fundamental Living Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Luca Cardelli
- Microsoft Research Cambridge, 21 Station Road, Cambridge CB1 2FB, UK
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The MATCHIT automaton: exploiting compartmentalization for the synthesis of branched polymers. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:467428. [PMID: 24489601 PMCID: PMC3893812 DOI: 10.1155/2013/467428] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/08/2013] [Indexed: 11/18/2022]
Abstract
We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.
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