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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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Žunar B, Ito T, Mosrin C, Sugahara Y, Bénédetti H, Guégan R, Vallée B. Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae. Biomater Res 2022; 26:85. [PMID: 36539854 PMCID: PMC9769040 DOI: 10.1186/s40824-022-00337-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive. METHODS We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging. RESULTS When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients. CONCLUSIONS F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.
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Affiliation(s)
- Bojan Žunar
- Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071, Orléans, Cedex 2, France
- Department of Chemistry and Biochemistry, Laboratory for Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000, Zagreb, Croatia
| | - Taiga Ito
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Christine Mosrin
- Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071, Orléans, Cedex 2, France
| | - Yoshiyuki Sugahara
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071, Orléans, Cedex 2, France
| | - Régis Guégan
- Global Center for Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo, 169-8555, Japan
- Institut des Sciences de la Terre d'Orléans (ISTO), UMR 7327, CNRS-Université d'Orléans, 1A Rue de la Férollerie, 45071, Orléans, Cedex 2, France
| | - Béatrice Vallée
- Centre de Biophysique Moléculaire (CBM), CNRS, UPR 4301, University of Orléans and INSERM, 45071, Orléans, Cedex 2, France.
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Holland LA, He Y, Guerrette JR, Crihfield CL, Bwanali L. Simple, rapid, and reproducible capillary gel electrophoresis separation and laser-induced fluorescence detection of DNA topoisomers with unmodified fused silica separation capillaries. Anal Bioanal Chem 2021; 414:713-720. [PMID: 34693472 DOI: 10.1007/s00216-021-03714-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
The topology of DNA is a critical quality attribute for plasmid-based pharmaceuticals, making quantification of trace levels of plasmid topoisomers an important analytical priority. An automated and cost-effective method based on capillary gel electrophoresis laser-induced fluorescence detection is described. The method outlined in this report is significant because it is easily implemented by any laboratory for which routine analyses of plasmid topology are critical for the development of new plasmid-based therapies as well as for quality control of gene therapies utilizing supercoiled DNA. Detection of topoisomers was achieved by incorporating ethidium bromide in the separation medium. The detector response was improved by 3 orders of magnitude by utilizing a 605-nm optical filter with a 15-nm bandwidth. Separations of linear, open circle, supercoiled, and multimer DNA plasmids ranging from 4.2 to 10.5 kbp were accomplished in under 6 min using an unmodified fused silica capillary (50-μm internal diameter). The background electrolyte was comprised of 0.5% gel, which was hydroxypropylmethyl cellulose, 1 mM ethylenediaminetetraacetic acid, and 50 mM N-(2-acetamido)-2-aminoethanesulfonic acid (pH of 6.25). The separations, which balanced the bulk electroosmotic flow, the electrophoretic mobility of the DNA, and gel sieving were dependent upon the pH of the electrolyte and the gel concentration. Reproducibility was dependent upon the procedure used to prepare the gel as well as other factors including the ethidium bromide concentration and capillary conditioning. A single unmodified capillary operated for more than 150 runs had an across-day migration time precision of 1% relative standard deviation and percent area precision of 10% relative standard deviation.
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Affiliation(s)
- Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
| | - Yan He
- Analytical Research and Development, 875 Chesterfield Parkway, PfizerChesterfield, MO, 63017, USA
| | - Jessica R Guerrette
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Cassandra L Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.,Biohybrid Solutions, LLC, 320 William Pitt Way, Pittsburgh, PA, 15238, USA
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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Peli Thanthri SH, Ward CL, Cornejo MA, Linz TH. Simultaneous Preconcentration and Separation of Native Protein Variants Using Thermal Gel Electrophoresis. Anal Chem 2020; 92:6741-6747. [PMID: 32249567 DOI: 10.1021/acs.analchem.0c00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Proteins must maintain proper folding conformations and express the correct post-translational modifications (PTMs) to exhibit appropriate biological activity. However, assessing protein folding and PTMs is difficult because routine polyacrylamide gel electrophoresis (PAGE) methods lack the separation resolution necessary to identify variants of a single protein. Additionally, standard PAGE denatures proteins prior to analysis precluding determinations of folding states or PTMs. To overcome these limitations, a microfluidic thermal gel electrophoresis platform was developed to provide high-sensitivity, high-resolution analyses of native protein variants. A thermally reversible gel was utilized as a separation matrix while in its solid state (30 °C). This thermal gel provided sufficient separation resolution to identify three variants of a fluorescently labeled model protein. To increase detection sensitivity, analyte preconcentration was conducted in parallel with the separation. Continuous analyte enrichment afforded detection limits of 500 fg of protein (250 pM) while simultaneous baseline separation resolution was achieved between variants. The effects of temperature on thermal gel electrophoresis were also characterized. The unique temperature-dependent outcomes illustrated how method performance can be tuned through a thermal dimension. Ultimately, the high detection sensitivity and separation resolution provided by thermal gel electrophoresis enabled rapid screening of native protein variants.
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Affiliation(s)
- Shakila H Peli Thanthri
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| | - Cassandra L Ward
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| | - Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
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5
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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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Talarico AM, Szerb EI, Ghedini M, Rossi CO. The potential of the F127-water soft system towards selective solubilisation of iridium(III) octahedral complexes. SOFT MATTER 2014; 10:6783-6790. [PMID: 25074753 DOI: 10.1039/c4sm01077a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In order to obtain new functional soft systems for use as templating agents for the construction of functional mesostructured materials, the dynamic ordered soft systems formed by a hydrophilic ionic iridium(III) complex (IrPa) embedded into two different concentration F127-water mixtures have been investigated. To this aim, combined spectral and time-resolved photophysical techniques and rheological methods have been employed. The position of the chromophore inside the micellar, cubic and hexagonal phases of the F127 polymeric neutral surfactant in water was effectively determined. The hydrophilic character of the iridium(III) complex chosen allowed preferential functionalization of the F127 corona in the micellar and cubic phases.
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Affiliation(s)
- Anna Maria Talarico
- LASCAMM CR-INSTM Unità della Calabria, Dipartimento di Chimica e Tecnologie Chimiche - CTC, Università della Calabria, Via P. Bucci Cubo 14C, Arcavacata (CS), 87036, Italy.
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Kohut A, Voronov A, Voronov S. Micellization and Adsolubilization of Amphilic Invertible Polyesters. CHEMISTRY & CHEMICAL TECHNOLOGY 2014. [DOI: 10.23939/chcht08.01.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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9
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Ye F, Yaghmur A, Jensen H, Larsen SW, Larsen C, Østergaard J. Real-time UV imaging of drug diffusion and release from Pluronic F127 hydrogels. Eur J Pharm Sci 2011; 43:236-43. [DOI: 10.1016/j.ejps.2011.04.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/08/2011] [Accepted: 04/20/2011] [Indexed: 11/15/2022]
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10
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Sieburg L, Kohut A, Kislenko V, Voronov A. Amphiphilic invertible polymers for adsolubilization on hydrophilic and hydrophobized silica nanoparticles. J Colloid Interface Sci 2010; 351:116-21. [DOI: 10.1016/j.jcis.2010.07.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Revised: 07/23/2010] [Accepted: 07/24/2010] [Indexed: 10/19/2022]
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11
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Simhadri JJ, Stretz HA, Oyanader M, Arce PE. Role of Nanocomposite Hydrogel Morphology in the Electrophoretic Separation of Biomolecules: A Review. Ind Eng Chem Res 2010. [DOI: 10.1021/ie1003762] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jyothirmai J. Simhadri
- Department of Chemical Engineering, Tennessee Technological University (TTU), Cookeville, Tennessee 38505, and Department of Chemical Engineering, Universidad Catolica del Norte, Antofagasta, Chile
| | - Holly A. Stretz
- Department of Chemical Engineering, Tennessee Technological University (TTU), Cookeville, Tennessee 38505, and Department of Chemical Engineering, Universidad Catolica del Norte, Antofagasta, Chile
| | - Mario Oyanader
- Department of Chemical Engineering, Tennessee Technological University (TTU), Cookeville, Tennessee 38505, and Department of Chemical Engineering, Universidad Catolica del Norte, Antofagasta, Chile
| | - Pedro E. Arce
- Department of Chemical Engineering, Tennessee Technological University (TTU), Cookeville, Tennessee 38505, and Department of Chemical Engineering, Universidad Catolica del Norte, Antofagasta, Chile
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12
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You S, Van Winkle DH. Single Molecule Observation of DNA Electrophoresis in Pluronic F127. J Phys Chem B 2010; 114:4171-7. [DOI: 10.1021/jp911183m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seungyong You
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
| | - David H. Van Winkle
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
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13
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Kaji N, Okamoto Y, Tokeshi M, Baba Y. Nanopillar, nanoball, and nanofibers for highly efficient analysis of biomolecules. Chem Soc Rev 2010; 39:948-56. [DOI: 10.1039/b900410f] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Ke F, Mo X, Yang R, Wang Y, Liang D. Polymer mixtures with enhanced compatibility and extremely low viscosity used as DNA separation media. Electrophoresis 2010; 31:520-7. [DOI: 10.1002/elps.200900440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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A block copolymer covalent coating acting as surfactants in separation of 2-[hydroxy(4-nitrophenyl)methyl]-cyclopent-2-enone and 4-nitrobenzaldehyde by capillary electrophoresis. Talanta 2009; 80:770-6. [DOI: 10.1016/j.talanta.2009.07.056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/24/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
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16
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Qiao J, Qi L, Ma H. Open tubular CEC with novel block copolymer coatings for separation of aromatic amines. J Sep Sci 2009; 32:3936-44. [DOI: 10.1002/jssc.200900527] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Schoch RB, Ronaghi M, Santiago JG. Rapid and selective extraction, isolation, preconcentration, and quantitation of small RNAs from cell lysate using on-chip isotachophoresis. LAB ON A CHIP 2009; 9:2145-2152. [PMID: 19606290 DOI: 10.1039/b903542g] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a technique which enables the separation of small RNAs-such as microRNAs (miRNAs), short interfering RNAs (siRNAs), and Piwi-interacting RNAs (piRNAs)-from >or=66 nucleotide RNAs and other biomolecules contained in a cell lysate. In particular, the method achieves separation of small RNAs from precursor miRNAs (pre-miRNAs) in less than 3 min. We use on-chip isotachophoresis (ITP) for the simultaneous extraction, isolation, preconcentration and quantitation of small RNAs (approximately 22 nucleotides) and employ the high-efficiency sieving matrix Pluronic F-127; a thermo-responsive triblock copolymer which allows convenient microchannel loading at low temperature. We present the isolation of small RNAs from the lysate of 293A human kidney cells, and quantitate the number of short RNA molecules per cell to be 2.9x10(7). We estimate this quantity is an aggregate of roughly 500 types of short RNA molecules per 293A cell. Currently, the minimal cell number for small RNA extraction and detection with our method is approximately 900 (from a 5 microL sample volume), and we believe that small RNA analysis from tens of cells is realizable. Techniques for rapid and sensitive extraction and isolation of small RNAs from cell lysate are much-needed to further uncover their full range and functionality, including RNA interference studies.
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Affiliation(s)
- Reto B Schoch
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
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18
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Stellwagen NC, Stellwagen E. Effect of the matrix on DNA electrophoretic mobility. J Chromatogr A 2009; 1216:1917-29. [PMID: 19100556 PMCID: PMC2643323 DOI: 10.1016/j.chroma.2008.11.090] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/24/2008] [Accepted: 11/27/2008] [Indexed: 11/18/2022]
Abstract
DNA electrophoretic mobilities are highly dependent on the nature of the matrix in which the separation takes place. This review describes the effect of the matrix on DNA separations in agarose gels, polyacrylamide gels and solutions containing entangled linear polymers, correlating the electrophoretic mobilities with information obtained from other types of studies. DNA mobilities in various sieving media are determined by the interplay of three factors: the relative size of the DNA molecule with respect to the effective pore size of the matrix, the effect of the electric field on the matrix, and specific interactions of DNA with the matrix during electrophoresis.
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Affiliation(s)
- Nancy C Stellwagen
- Department of Biochemistry, University of Iowa, 4403 Bowen Science Building, Iowa City, IA 52242, USA.
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19
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Wan F, Zhang J, Lau A, Tan S, Burger C, Chu B. Nanostructured copolymer gels for dsDNA separation by CE. Electrophoresis 2009; 29:4704-13. [PMID: 19053068 DOI: 10.1002/elps.200800267] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Pluronics are triblock copolymers of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) that are able to form many different ordered nanostructures at appropriate polymer concentrations and temperatures in selective solvents. These nanostructured "gels" showed desirable criteria when used as DNA separation media, especially in microchip electrophoresis, including dynamic coating and viscosity switching. A ternary system of F127 (E99P69E99)/TBE buffer/1-butanol was selected as a model system to test the sieving performance of different nanostructures in separating dsDNA by CE. The nanostructures and their lattice constants were determined by small-angle X-ray scattering. Viscosity measurements showed the sol-gel transition phenomena. In addition to the cubic structure, successful electrophoretic separation of dsDNA in 2-D hexagonally packed cylinders was achieved. Results showed that without further optimization, PhiX174 DNA-Hae III digest was well separated within 15 min in a 7-cm separation channel, by using F127/TBE/1-butanol gel with a 2-D hexagonal structure. A mechanism for DNA separations by those gels with both hydrophilic and hydrophobic domains is discussed.
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Affiliation(s)
- Fen Wan
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
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Kuroda D, Zhang Y, Wang J, Kaji N, Tokeshi M, Baba Y. A viscosity-tunable polymer for DNA separation by microchip electrophoresis. Anal Bioanal Chem 2008; 391:2543-9. [DOI: 10.1007/s00216-008-2196-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 05/12/2008] [Accepted: 05/20/2008] [Indexed: 10/21/2022]
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21
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Abstract
A nanostructured copolymer matrix has successfully separated oligonucleotides with high resolution by CE using a very short separation channel which simulates the real microchip condition for the first time. The triblock copolymer, E(45)B(14)E(45) (B20-5000) with E, B, and subscript denoting oxyethylene, oxybutylene, and segment length, respectively, has a unique temperature-dependent viscosity-adjustable property and a dynamic coating ability in 1xTBE buffer (89 mM Tris, 89 mM boric acid, 2 mM EDTA in Milli-Q water). The B-block is hydrophilic at low temperatures, e.g., 4 degrees C, and the polymer solution has a very low viscosity of about 100 cP in a 32.5% w/v solution. At room temperatures, the B-block becomes hydrophobic due to a breakdown of hydrogen bonds between B-blocks and water, and the polymer matrix forms a body-centered cubic structure at high concentrations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated with one-base resolution in a 1.5 cm long separation channel by E(45)B(14)E(45) in its gel-like state.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Stony Brook University, NY 11794-3400, USA
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22
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Harada A, Kataoka K. Supramolecular assemblies of block copolymers in aqueous media as nanocontainers relevant to biological applications. Prog Polym Sci 2006. [DOI: 10.1016/j.progpolymsci.2006.09.004] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Miksík I, Sedláková P, Mikulíková K, Eckhardt A. Capillary electromigration methods for the study of collagen. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 841:3-13. [PMID: 16546457 DOI: 10.1016/j.jchromb.2006.02.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 02/01/2006] [Accepted: 02/08/2006] [Indexed: 11/15/2022]
Abstract
This review paper gives an overview of capillary electromigration methods used in the analysis of collagen. Analyses of the parent chains as well as of the bromcyane and collagenase fragments of collagens are presented. Methods include capillary zone electrophoresis, capillary gel electrophoresis, micellar electrokinetic chromatography as well as combinations of HPLC and capillary electrophoresis, and capillary electrophoresis with mass spectrometry.
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Affiliation(s)
- Ivan Miksík
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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Sedlakova P, Svobodova J, Miksik I. Capillary electrophoresis of peptides and proteins with plug of Pluronic gel. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 839:112-7. [PMID: 16740420 DOI: 10.1016/j.jchromb.2006.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2006] [Revised: 05/04/2006] [Accepted: 05/08/2006] [Indexed: 10/24/2022]
Abstract
Electromigration capillary methods are promising techniques in proteomics and they are still under research. We used a partial filling approach, i.e. a combination of gel and non-gel separation mechanisms in a single dimension. We tried using an interesting gel, Pluronic F 127, which can be considered as a surfactant capable of self-association both with isotropic and anisotropic gels. The Pluronic was inserted inside the capillary as a plug at the start of the capillary, and it provided separation at the first time. Separation by this gel was achieved according to molecular weight and/or hydrophobicity. The applicability of this method was demonstrated in the separation of real samples-peptides arising from collagen after CNBr or collagenase cleavage and albumin after trypsin cleavage (peptide mapping). Some peptides and proteins were selectively retained by the Pluronic gel. These interactions with the gel did not depended on their molecular weight alone, but they probably depend on a combination of both principles. It was confirmed that capillary electrophoresis with Pluronic plug can give us another new separation option, complementary to free solution capillary electrophoresis. The CE method presented here, consisting of a partial filling approach with combine gel and non-gel separation mechanisms seemed to be a promising method for the separation of complex mixtures of peptides.
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Affiliation(s)
- P Sedlakova
- Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic.
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25
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Zhang J, Gassmann M, He W, Wan F, Chu B. Reversible thermo-responsive sieving matrix for oligonucleotide separation. LAB ON A CHIP 2006; 6:526-33. [PMID: 16572215 DOI: 10.1039/b515557f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A reversible thermo-responsive gel system, consisting of Pluronic copolymer mixture of F87 and F127, has been used to successfully carry out the separation of oligonucleotides, for the first time, by microchip-based capillary electrophoresis. Pluronic triblock copolymers F87 (E(61)P(40)E(61)) and F127 (E(99)P(69)E(99)), with E, P, and subscript denoting oxyethylene, oxypropylene, and segment length respectively, have a unique temperature dependent viscosity-adjustable property and a dynamic coating ability in aqueous solution, including 1 x TBE buffer. The mixture solution has a reversible thermo-responsive property and its sol-gel transition temperature can be adjusted ranging from about 17 degrees C to 38 degrees C by varying the relative weight ratio of F87 and F127 at an optimized concentration of approximately 30% (w/v) for oligonucleotide separations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated in a 1.5 cm long separation channel by the mixture solution in its gel-like state. A 30% (w/v) with a F87/F127 weight ratio of 1 ratio 2 which has a "sol-gel" transition point of about 26 degrees C shows the best sieving ability. The sieving ability of the mixture solution was further confirmed in an Agilent Bioanalyzer 2100 system. Fast separation of oligonucleotides has been achieved within 40 s with one base resolution.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
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26
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Zhang J, Liang D, He W, Wan F, Ying Q, Chu B. Fast separation of single-stranded oligonucleotides by capillary electrophoresis using OliGreen as fluorescence inducing agent. Electrophoresis 2006; 26:4449-55. [PMID: 16315172 DOI: 10.1002/elps.200500099] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fast separation of oligonucleotide (oligos) sizing marker by CE using OliGreen and including effects due to the concentration of separation medium and urea denaturant is presented. OliGreen dye is found to be more sensitive than ethidium bromide (by a factor of about 6 based on S/N considerations) for the oligos' separations. Higher concentration of F127 in 1xTris-boricacid-EDTA (TBE) up to 30% w/v leads to better resolution of oligos separations. The addition of urea into the separation medium decreases the sensitivity. With an optimized running condition, the oligos sizing marker could be successfully separated with 1-base resolution within 1.3 min by using 30% w/v F127/1xTBE solution as the separation medium at an applied electric field of 800 V/cm in a 3 cm long capillary, the fastest capillary gel electrophoresis separation with high resolution reported to date for oligos in the similar size range.
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Affiliation(s)
- Jun Zhang
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
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27
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Khalil E, Schaefer U, Sallam A. Release characteristics of diclofenac diethylamine from emulgels containing Pluronic F127. J Drug Deliv Sci Technol 2006. [DOI: 10.1016/s1773-2247(06)50069-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Miksík I, Sedláková P, Mikulíková K, Eckhardt A, Cserhati T, Horváth T. Matrices for capillary gel electrophoresis—a brief overview of uncommon gels. Biomed Chromatogr 2006; 20:458-65. [PMID: 16779791 DOI: 10.1002/bmc.640] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This article gives an overview of uncommon replaceable matrices (gels) for capillary gel electrophoresis. This electrophoretic technique is useful mainly for the separation and analysis of biopolymers-nucleic acids and their fragments, and proteins/peptides. Commonly used gels are not reviewed. Those mentioned and discussed here are gels containing saccharides, newly developed acrylamide-based gels and thermoadjustable viscosity polymers, namely triblock copolymers and grafted polyacrylamide.
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Affiliation(s)
- Ivan Miksík
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague.
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29
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Babu C V S, Song EJ, Babar SME, Wi MH, Yoo YS. Capillary electrophoresis at the omics level: Towards systems biology. Electrophoresis 2006; 27:97-110. [PMID: 16421959 DOI: 10.1002/elps.200500511] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Emerging systems biology aims at integrating the enormous amount of existing omics data in order to better understand their functional relationships at a whole systems level. These huge datasets can be obtained through advances in high-throughput, sensitive, precise, and accurate analytical instrumentation and technological innovation. Separation sciences play an important role in revealing biological processes at various omic levels. From the perspective of systems biology, CE is a strong candidate for high-throughput, sensitive data generation which is capable of tackling the challenges in acquiring qualitative and quantitative knowledge through a system-level study. This review focuses on the applicability of CE to systems-based analytical data at the genomic, transcriptomic, proteomic, and metabolomic levels.
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Affiliation(s)
- Suresh Babu C V
- Bioanalysis and Biotransformation Research Center, Korea Institute of Science and Technology, Cheongryang, Seoul, Korea
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30
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Shan W, He P, Hu N. Electrocatalytic reduction of nitric oxide and other substrates on hydrogel triblock copolymer Pluronic films containing hemoglobin or myoglobin based on protein direct electrochemistry. Electrochim Acta 2005. [DOI: 10.1016/j.electacta.2005.04.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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Pepić I, Jalsenjak N, Jalsenjak I. Micellar solutions of triblock copolymer surfactants with pilocarpine. Int J Pharm 2004; 272:57-64. [PMID: 15019069 DOI: 10.1016/j.ijpharm.2003.11.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 11/12/2003] [Accepted: 11/25/2003] [Indexed: 10/26/2022]
Abstract
Solutions of surface active triblock copolymer Pluronic F127 in the vicinity of the critical micellar concentration (cmc) were prepared with or without pilocarpine (either as the hydrochloride salt or the free base) in water and phosphate buffer. The characteristics parameters of the surface activity (cmc, Gamma and a) were determined for F127 solutions. Additionally, it was found that the pilocarpine solutions without F127 in water exhibits a certain surface activity. The solutions containing F127 (2 wt.%) well above the cmc and pilocarpine (2 wt.% for the salt, or equimolar 1.7 wt.% for the base) were further tested in vivo (miotic response) on rabbit eye. Though the entrapment efficiency of the drug in the micelles was rather low (maximal 1.9%) the pharmacokinetic parameters (duration of miotic response and the area under miotic curve) were improved when compared to the standard pilocarpine solutions. The best results were obtained for the micellar pilocarpine base solution which exhibits significant prolongation of miotic activity and an increase of AUC for 64%.
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Affiliation(s)
- I Pepić
- Department of Pharmaceutics, Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovac?ića 1, Zagreb 10000, Croatia
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32
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Ugaz VM, Elms RD, Lo RC, Shaikh FA, Burns MA. Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2004; 362:1105-29. [PMID: 15306487 DOI: 10.1098/rsta.2003.1365] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre sample volumes, and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.
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Affiliation(s)
- Victor M Ugaz
- Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA
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33
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Chapter 14 Chromatography of amino acids and peptides. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0301-4770(04)80027-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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34
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Riley SA, Giuliani JR, Augustine MP. Capture and manipulation of magnetically aligned Pf1 with an aqueous polymer gel. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 159:82-86. [PMID: 12468307 DOI: 10.1016/s1090-7807(02)00004-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The magnetic alignment of the Pseudomonas bacteriophage Pf1 is captured indefinitely in a gel of the aqueous triblock copolymer Pluronic F-127. In addition to preserving high-resolution liquids NMR spectra for dissolved solutes, the gel prevents the reorientation of the phage allowing mechanical manipulation of the angle between the axis of the phage alignment and the static magnetic field. The residual 2H quadrupolar couplings for several solutes dissolved in this material as a function of the angle Theta between the non-spinning sample tube and the static magnetic field are consistent with the value of P(2)(cosTheta)=(3cos(2)Theta-1)/2. The variable-angle correlation spectrum for these solutes is shown to separate residual quadrupolar effects from isotropic chemical shifts. Finally, the compatibility of Pluronic F-127 with NMR studies of aqueous biological macromolecules is demonstrated in a measurement of residual dipolar couplings in an 15N-labeled nucleic acid.
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Affiliation(s)
- Scott A Riley
- Department of Chemistry, One Shields Avenue, University of California, Davis, CA 95616, USA
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35
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Abstract
A review on copolymers used as DNA separation media in capillary electrophoresis is presented. Copolymers can combine the desirable properties of different monomers, yielding many attractive features, such as high sieving ability, low viscosity, self-assembly behavior and dynamic coating ability. Copolymers with different molecular architecture, including block copolymers, random copolymers, and graft copolymers, have been developed and tested as DNA separation media with unique and tailored properties that cannot be achieved easily by using only homopolymers.
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Affiliation(s)
- Benjamin Chu
- Chemistry Department, State University of New York at Stony Brook, 11794-3400, USA.
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36
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Végvári A, Hjertén S. Stable homogeneous gel for molecular-sieving of DNA fragments in capillary electrophoresis. J Chromatogr A 2002; 960:221-7. [PMID: 12150560 DOI: 10.1016/s0021-9673(01)01436-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A polyacrylamide gel crosslinked with allyl-beta-cyclodextrin can be used repeatedly for several weeks for the separation of DNA fragments, since bubbles are not generated during a run. Allyl-beta-cyclodextrin can easily be synthesized in one step from allylglycidylether and beta-cyclodextrin. The plate numbers for DNA fragments, up to about 1500 bp, are high: for the separation of pBR322/HaeIII fragments they were in the range 450,000-1,600,000 m(-1). The resolution was almost independent of the concentration of the crosslinker (allyl-beta-cyclodextrin)--in sharp contrast to gels crosslinked with N,N'-methylenebisacrylamide.
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Affiliation(s)
- Akos Végvári
- Department of Biochemistry, Biomedical Center, Uppsala University, Sweden
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37
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Epperson JD, Dodge J, Rill RL, Greenbaum NL. Analysis of oligonucleotides and unincorporated nucleotides from in vitro transcription by capillary electrophoresis in Pluronic F127 gels. Electrophoresis 2001; 22:771-8. [PMID: 11296933 DOI: 10.1002/1522-2683(200102)22:4<771::aid-elps771>3.0.co;2-#] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Small functional RNAs required for structure studies are often prepared by in vitro transcription. Capillary electrophoresis in liquid crystalline gels of Pluronic F127 was used to analyze unfractionated in vitro transcription reactions and anion-exchange high-performance liquid chromatography (HPLC) fractions from transcription reactions. Guanosine monophosphate (GMP), the four nucleoside triphosphates (NTPs), abortive transcripts, and transcripts with lengths near the desired product length were simultaneously resolved and quantified in a single run. Oligonucleotides up to at least 35 nucleotides were resolved to baseline within 10 min using a moderate field (185 V/cm) and short effective capillary length (7.6 cm) for electrophoresis in 20% Pluronic F127 at pH 8.3 in Tris-borate-EDTA (TBE) buffer (30 degrees C). Nucleotide migration times were 4-5 min, in the order UTP+CTP (unresolved) <ATP<GTP<GMP. A single capillary filling was reused for 40-50 runs with little decrease in performance, and for up to 100 runs with performance acceptable for many applications. Higher electric fields appeared to affect the gel structure and necessitated more frequent capillary refilling. Capillary gel electrophoresis (CGE) of HPLC fractions in Pluronic gels facilitates rapid recovery of RNA products and the large remaining amounts of valuable, isotopically labeled NTPs. In addition, comparison of electrophoretic patterns under denaturing and nondenaturing conditions yields insights into potential conformational heterogeneity of the folded nucleic acid states. CGE in Pluronic gels provides a rapid, highly discriminating means for analyzing in vitro transcription reactions.
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Affiliation(s)
- J D Epperson
- Department of Chemistry and Institute of Molecular Biophysics, The Florida State University, Tallahassee 32306-4390, USA
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38
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Krishnan M, Namasivayam V, Lin R, Pal R, Burns MA. Microfabricated reaction and separation systems. Curr Opin Biotechnol 2001; 12:92-8. [PMID: 11167080 DOI: 10.1016/s0958-1669(00)00166-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Over the past year there have been a number of recent advances in the fields of miniaturized reaction and separation systems, including the construction of fully integrated 'lab-on-a-chip' systems. Microreactors, which initially targeted DNA-based reactions such as the polymerase chain reaction, are now used in several other chemical and biochemical assays. Miniaturized separation columns are currently employed for analyzing a wide variety of samples including DNA, RNA, proteins and cells. Although significant advances have been made at the component level, the realization of an integrated analysis system still remains at the early stages of development.
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Affiliation(s)
- M Krishnan
- Department of Chemical Engineering, University of Michigan, 2300 Hayward, 3022 HH Dow, Ann Arbor, MI 48109-2136, USA.
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39
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Liu T, Liang D, Song L, Nace VM, Chu B. Spatial open-network formed by mixed triblock copolymers as a new medium for double-stranded DNA separation by capillary electrophoresis. Electrophoresis 2001; 22:449-58. [PMID: 11258754 DOI: 10.1002/1522-2683(200102)22:3<449::aid-elps449>3.0.co;2-t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mixture of two polyoxybutylene-polyoxyethylene-polyoxybutylene (BEB) triblock copolymers (B6E46B6 and B10E271B10, respectively) was used as a new separation medium for separating double-stranded DNA (dsDNA) fragments by capillary electrophoresis (CE). The two block copolymer mixtures were designed to form mixed flower-like micelles in dilute solution and a homogeneous gel-like open-network with hydrophobic clusters as cross-linking points at higher polymer concentrations. Being a polyoxyalkylene block copolymer gel, the separation medium has some special advantages, including the temperature-dependent sol-gel transition that makes sample injection easy, and the self-coating of the inner capillary wall that makes experimental procedures simple and reproducible. Furthermore, it can shorten the elution time and further improve the separation resolution, especially for small dsDNA fragments, when compared with EPE-type separation media, e.g., F127 (E99P69E99, with P being polyoxypropylene) block copolymer gels formed by the closed packing of spherical micelles. Single base pair resolution can be achieved by using the new separation medium for dsDNA fragments up to over 100 base pairs.
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Affiliation(s)
- T Liu
- Department of Chemistry, State University of New York at Stony Brook, 11794-3400, USA
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40
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Abstract
We review the wide range of polymeric materials that have been employed for DNA sequencing separations by capillary electrophoresis. Intensive research in the area has converged in showing that highly entangled solutions of hydrophilic, high molar mass polymers are required to achieve high DNA separation efficiency and long read length, system attributes that are particularly important for genomic sequencing. The extent of DNA-polymer interactions, as well as the robustness of the entangled polymer network, greatly influence the performance of a given polymer matrix for DNA separation. Further fundamental research in the field of polymer physics and chemistry is needed to elucidate the specific mechanisms by which DNA is separated in dynamic, uncross-linked polymer networks.
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Affiliation(s)
- M N Albarghouthi
- Department of Chemical Engineering, Northwestern University, Evanston, IL 60208, USA
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41
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Guillaume YC, Peyrin E, Thomassin M, Ravel A, Grosset C, Villet A, Robert JF, Guinchard C. Column efficiency and separation of DNA fragments using slalom chromatography: hydrodynamic study and fractal considerations. Anal Chem 2000; 72:4846-52. [PMID: 11055698 DOI: 10.1021/ac000281t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel equations (Guillaume Y. C.; et al. Anal. Chem. 2000, 72, 853) were developed to describe the large double-stranded DNA molecule retention in slalom chromatography (SC). These equations were applied for the first time to model both the "apparent selectivity" and the resolution between two eluted DNA fragments on a chromatogram. A study of the column efficiency corroborated the fact that slalom chromatography is not based on an adsorption or equilibrium phenomenon, but can be attributed to a hydrodynamic phenomenon. Using a combination of the dynamics of DNA fragment progression in the column and fractal considerations, it was shown that the apparent selectivity depends both on the DNA fragment sizes and mobile-phase flow rate and therefore a balance between two hydrodynamic regimes. A chromatographic response function was also used to obtain the most efficient separation conditions for a mixture of DNA fragments in a minimum analysis time. The chromatographic data confirmed that in SC the flow rate can increase or maintain the separation efficiency with an associated decrease in the analysis time. This constitutes an attractive outcome in relation to the classical chromatographic separation.
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Affiliation(s)
- Y C Guillaume
- Laboratoire de Chimie Organique, Faculté de Medecine Pharmacie, Besançon, France.
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42
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Kutter JP. Current developments in electrophoretic and chromatographic separation methods on microfabricated devices. Trends Analyt Chem 2000. [DOI: 10.1016/s0165-9936(00)00014-5] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Hadden DA, Rill RL, McFaddan L, Locke BR. Oligonucleotide and Water Self-Diffusion in Systems of Pluronic Triblock Copolymers and in Buffer Solutions by Pulsed Field Gradient Nuclear Magnetic Resonance. Macromolecules 2000. [DOI: 10.1021/ma9915071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Darren A. Hadden
- Department of Chemical Engineering, Florida State University and Florida A & M University, FAMU-FSU College of Engineering, and Department of Chemistry and Department of Biological Sciences, Florida State University, Tallahassee, Florida 32310-6046
| | - Randolph L. Rill
- Department of Chemical Engineering, Florida State University and Florida A & M University, FAMU-FSU College of Engineering, and Department of Chemistry and Department of Biological Sciences, Florida State University, Tallahassee, Florida 32310-6046
| | - Lori McFaddan
- Department of Chemical Engineering, Florida State University and Florida A & M University, FAMU-FSU College of Engineering, and Department of Chemistry and Department of Biological Sciences, Florida State University, Tallahassee, Florida 32310-6046
| | - Bruce R. Locke
- Department of Chemical Engineering, Florida State University and Florida A & M University, FAMU-FSU College of Engineering, and Department of Chemistry and Department of Biological Sciences, Florida State University, Tallahassee, Florida 32310-6046
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44
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Miksík I, Deyl Z, Kasicka V. Capillary electrophoretic separation of proteins and peptides using Pluronic liquid crystals and surface-modified capillaries. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2000; 741:37-42. [PMID: 10839130 DOI: 10.1016/s0378-4347(00)00063-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Separation of model mixtures of peptides/proteins carried out in a hydrophilically coated capillary in 10 mmol/l Tris and 75 mmol/l phosphate buffer containing 7.5% (w/w) Pluronic F127 copolymer (apparent pH 2.9) revealed that the separation is predominantly driven by the charge/mass ratio with little or no sieving effect. Using a coated capillary helped to remove current fluctuations that are observed in the fused-silica capillaries in the presence of the Pluronic copolymer. With peptides bearing distinct positive charge (polylysine of Mr around 3300) molecular sieving helps more detailed separation of individual species. Polyamino acids carrying negative charge can be brought to the detector window in the reversed polarity mode, however, no detailed separation of the individual species involved was observed under the conditions used. With a naturally occurring mixture of collagen fragments released by CNBr treatment of the protein the sequence of emerging peptides (positive polarity mode) with no relation to the rel. mol. mass could be revealed. It is concluded that separation of proteins/peptides in the presence of Pluronic in the background electrolyte occur on the charge/mass ratio basis with molecular sieving effects acting as a secondary partition mechanism.
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Affiliation(s)
- I Miksík
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague.
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45
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Miksik I, Deyl Z. Application of Pluronic copolymer liquid crystals for the capillary electrophoretic separation of collagen type I cyanogen bromide fragments. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2000; 739:109-16. [PMID: 10744319 DOI: 10.1016/s0378-4347(99)00555-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A capillary electrophoretic method exploiting the properties of Pluronic copolymer liquid crystals (F127) was developed for the separation of collagen cyanogen bromide (CNBr) fragments. The separations obtained were at least comparable (if not better) to those obtained by other methods applicable to this category of compounds. In the optimized version a bare silica capillary [47 cm (40 cm to the detector) x 75 microm I.D.] was used with 10 mM Tris and 75 mM phosphate buffer (pH 2.5) containing 7.5% Pluronic F127 copolymer. The separation mechanism which involves both the molecular sieving and surfactant properties of the Pluronic F127 gel phase is discussed.
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Affiliation(s)
- I Miksik
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague.
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46
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Deyl Z, Miksík I. Advanced separation methods for collagen parent alpha-chains, their polymers and fragments. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2000; 739:3-31. [PMID: 10744310 DOI: 10.1016/s0378-4347(99)00515-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Current techniques used for collagen alpha-chains and their CNBr fragments are reviewed. Ion exchange, gel permeation, reversed-phase and affinity chromatography are discussed mainly from the preparative aspects as these are both the techniques of choice to remove biological matrix contaminants always present in collagen preparations and techniques routinely used for preparative purposes. Among electromigration procedures gel electrophoresis is widely used both for intact collagen alpha-chains and their fragments. Recently this technique was applied also for miniaturised preparations. Immunoblotting techniques serve more specific detection of otherwise hard to distinguish different collagen polypeptide chains. Capillary electromigration techniques brought recently new aspects of understanding the behaviour of collagen proteins upon different separation modes and seem to represent a smart perspective for better quantitation of individual collagen species.
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Affiliation(s)
- Z Deyl
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague.
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Peyrin E, Guillaume YC, Villet A, Favier A. Mechanism of DNA hydrodynamic separation in chromatography. Anal Chem 2000; 72:853-7. [PMID: 10701273 DOI: 10.1021/ac990841s] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An alternative chromatographic procedure for the separation of large double-stranded DNA molecules was discovered recently and called "slalom chromatography". This fractionation is based on a new hydrodynamic process that is determined by the progression of the mobile-phase flow through the interstitial spaces created between the highly packed particles inside the column. Here, the separation is treated as the result of a slowing down of the large double-stranded DNA fragments in relation to their size with the flow direction changing around the particles. A model, based on the concept derived from the reorientation time of macromolecules, was adequate to describe the hydrodynamic phenomenon. This model constitutes an attractive tool to enhance the expansion of this chromatographic procedure and provide valuable information on the dynamic behavior of biological polymers.
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Affiliation(s)
- E Peyrin
- Laboratoire de Chimie Analytique, UFR de Pharmacie, La Tronche, France
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Abstract
The Ogston-Morris-Rodbard-Chrambach theory of gel electrophoresis is consistent with predictions from the volume averaging method with respect to the equivalence of the accessible volume fraction to the ratios of gel mobility to free solution mobility and the gel diffusion coefficient to free solution diffusion coefficient for the limiting case of small molecule electrophoresis with low electrical fields, low gel concentrations, and nonconductive gel fibers. When these conditions are not valid, more extensive calculations are required to determine the mobility and diffusion coefficient ratios as functions of the geometry and electrical field within the gel. The volume averaging theory shows that it is important to account for the electrical conductivity properties of the fibers that make up a gel electrophoresis medium, and this aspect is consistent with early theories of transport phenomena in gel electrophoresis.
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Affiliation(s)
- B R Locke
- Department of Chemical Engineering, FAMU-FSU College of Engineering, Tallahassee, FL 32310-6046, USA.
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Abstract
The current status of capillary electrophoresis (CE) in pharmaceutical analyses is reviewed with about 300 references, mainly from 1996 until 1999. This article covers the use of CE for assay and purity determination of the main component, analysis of natural medicines, antisense DNA, peptides, and proteins. Analysis of hydrophobic and/or electrically neutral drugs by electrokinetic chromatography, capillary electrochromatography and nonaqueous CE is critically evaluated. Detailed techniques for the separation of enantiomers are given in the text with some actual applications. Furthermore, this review includes sensitivity and regulatory aspects for the actual use of CE in new drug applications (NDA). The analytical validation required for CE in NDA is also treated.
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Affiliation(s)
- H Nishi
- Analytical Chemistry Department, Tanabe Seiyaku Co., Osaka, Japan.
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Rill RL, Liu Y, Ramey BA, Van Winkle DH, Locke BR. Capillary gel electrophoresis of nucleic acids in pluronic F127 copolymer liquid crystals. Chromatographia 1999. [DOI: 10.1007/bf02468978] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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