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Casto-Boggess LD, Holland LA. Fluorescent parallel electrophoresis assay of enzyme inhibition. Anal Chim Acta 2024; 1296:342268. [PMID: 38401944 PMCID: PMC10911858 DOI: 10.1016/j.aca.2024.342268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND Enzyme inhibitors comprise the largest class of pharmaceutical compounds. The discovery and development of new enzyme inhibitor drug candidates depends on sensitive tools to quantify inhibition constants, Ki, for the most promising candidates. A high throughput, automated, and miniaturized approach to measure inhibition is reported. In this technique enzyme inhibition occurs within a 16 nL nanogel reaction zone that is integrated into a capillary. The reaction and electrophoresis separation are completed in under 10 min. The nanoliter enzyme reaction zones are easily positioned inside a standard separation capillary by pseudo-immobilizing enzymes within a thermally reversible nanogel. RESULTS This report optimizes and validates a capillary nanogel electrophoresis reaction and separation with a multi-capillary array instrument. Inhibitor constants are determined for the neuraminidase enzyme to quantify the effect of the transition state analog, 2,3-dehydro-2-deoxy-N-acetylneuraminic acid (DANA), as well as the inhibitor Siastatin B. With the multi-capillary array assay replicate Ki values are determined to be 5.7 ± 0.1 μM (n = 3) and 9.2 ± 0.2 μM (n = 3) for DANA and Siastatin B, respectively. The enzyme reaction in each separation capillary converts the substrate to a product in real time. The nanogel is used under suppressed electroosmotic flow, sustains enzyme function, and is easily filled and replaced by changing the capillary temperature. Using laser-induced fluorescence allows the determination to be achieved with substrate concentrations well below the Michaelis-Menten constant, making the method independent of the substrate concentration and therefore a more easily implemented assay. SIGNIFICANCE A lower measurement cost is realized when the reaction volume is miniaturized because the amounts of enzyme, substrate and inhibitor are reduced. Fast enzyme reactions are possible because of the small reaction volume. With a multi-capillary array, the inhibition assay is achieved in a fraction of the time required for traditional methods. The separation-based assay can even be applied to labeled substrates not cleaned up following the labeling reaction.
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Affiliation(s)
- Laura D Casto-Boggess
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA.
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2
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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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3
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Peli Thanthri SH, Linz TH. Controlling the separation of native proteins with temperature in thermal gel transient isotachophoresis. Anal Bioanal Chem 2023; 415:4163-4172. [PMID: 36151350 PMCID: PMC10033466 DOI: 10.1007/s00216-022-04331-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
Abstract
Polyacrylamide gel electrophoresis (PAGE) is a ubiquitous technique used in biochemical research laboratories to characterize protein samples. Despite its popularity, PAGE is relatively slow and provides limited separation resolution, especially for native proteins. This report describes the development of a microfluidic thermal gel transient isotachophoresis (TG-tITP) method to rapidly separate native proteins with high resolution. Thermal gels were employed as a separations matrix because of their unique ability to change viscosity in response to temperature. Proteins were added into thermal gel and loaded into a microfluidic device. Electrolyte optimization was conducted to achieve robust tITP to isotachophoretically preconcentrate proteins and then electrophoretically separate them. Electropherograms were collected through both time and distance to enable both small and large proteins to be measured within a single analysis. The effects of temperature were evaluated and found to exhibit a pronounced effect on the separation. Temperature gradients were then employed to alter thermal gel viscosity over time to maximize separation resolution between proteins. The results herein demonstrate how gradient TG-tITP achieves rapid, high-performance separations of native proteins. This analysis provided a wide mass range (6-464 kDa) with two-fold higher resolution than native PAGE while requiring 15,000-fold less protein loading and providing five-fold faster analysis times.
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Affiliation(s)
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Ave, Detroit, MI, 48202, USA.
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Holland LA, Casto-Boggess LD. Gels in Microscale Electrophoresis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:161-179. [PMID: 37314879 DOI: 10.1146/annurev-anchem-091522-080207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gel matrices are fundamental to electrophoresis analyses of biopolymers in microscale channels. Both capillary gel and microchannel gel electrophoresis systems have produced fundamental advances in the scientific community. These analytical techniques remain as foundational tools in bioanalytical chemistry and are indispensable in the field of biotherapeutics. This review summarizes the current state of gels in microscale channels and provides a brief description of electrophoretic transport in gels. In addition to the discussion of traditional polymers, several nontraditional gels are introduced. Advances in gel matrices highlighted include selective polymers modified to contain added functionality as well as thermally responsive gels formed through self-assembly. This review discusses cutting-edge applications to challenging areas of discovery in DNA, RNA, protein, and glycan analyses. Finally, emerging techniques that result in multifunctional assays for real-time biochemical processing in capillary and three-dimensional channels are identified.
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Affiliation(s)
- Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA;
| | - Laura D Casto-Boggess
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA;
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5
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Cornejo MA, Linz TH. Multiplexed miRNA Quantitation Using Injectionless Microfluidic Thermal Gel Electrophoresis. Anal Chem 2022; 94:5674-5681. [PMID: 35349277 DOI: 10.1021/acs.analchem.2c00356] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
MicroRNAs (miRNAs) are a class of biomolecules that have high clinical and pharmaceutical significance because of their ability to regulate protein expression. Better methods are needed to quantify target miRNAs, but their similar sequence lengths and low concentrations in biomedical samples impede analysis. This report aimed to develop a simple, rapid method to directly quantify multiple miRNAs using microfluidic thermal gel electrophoresis (TGE). Fluorescent probes were designed complementarily in sequence to four target miRNAs that also contained variable DNA overhangs to alter their electrophoretic mobilities. Samples and probes were directly added into thermal gel and loaded throughout a microchannel. Applying voltage resulted in an inline preconcentration and separation of the miRNAs that did not require a sample injection nor user intervention to switch between modes. Baseline resolution was achieved between four double-stranded miRNA-probe hybrids and four excess single-stranded probes. Analytical performance was then improved by designing an innovative microfluidic device with a tapered channel geometry. This device exhibited superior detection limits and separation resolution compared to standard channel devices without increasing the complexity of microfabrication or device operation. A proof-of-concept demonstration was then performed, showing that target miRNAs could be detected from cell extracts. These results demonstrate that TGE provides a simple, inexpensive means of conducting multiplexed miRNA measurements, with the potential for automation to facilitate future clinical and pharmaceutical analyses.
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Affiliation(s)
- Mario A Cornejo
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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Abstract
A hydrogel is a solid form of polymer network absorbed in a substantial amount of aqueous solution. In electrophoresis, hydrogels play versatile roles including as support media, sieving matrixes, affinity scaffolds, and compositions of molecularly imprinting polymers. Recently, the study of hydrogels has been advancing with unprecedented speed, and the application of hydrogels in separation science has brought new opportunities and possible breakthroughs. A good understanding about the roles and effects of the material is essential for hydrogel applications. This review summarizes the hydrogels that has been described in various modes of electrophoretic separations, including isoelectric focusing gel electrophoresis (IEFGE), isotachophoresis (ITP), gel electrophoresis and affinity gel electrophoresis (AGE). As microchip electrophoresis (ME) is one of the future trends in electrophoresis, thought provoking studies related to hydrogels in ME are also introduced. Novel hydrogels and methods that improve separation performance, facilitate the experimental operation process, allow for rapid analysis, and promote the integration to microfluidic devices are highlighted.
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Affiliation(s)
- Chenchen Liu
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
| | - Takuya Kubo
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University
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Cornejo MA, Linz TH. Harnessing Joule heating in microfluidic thermal gel electrophoresis to create reversible barriers for cell enrichment. Electrophoresis 2021; 42:1238-1246. [PMID: 33570796 PMCID: PMC8178196 DOI: 10.1002/elps.202000379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 11/07/2022]
Abstract
Gel electrophoresis is a ubiquitous bioanalytical technique used to characterize the components of cell lysates. However, analyses of bulk lysates sacrifice detection sensitivity because intracellular biomolecules become diluted, and the liberation of proteases and nucleases can degrade target analytes. This report describes a method to enrich cells directly within a microfluidic gel as a first step toward online measurement of trace intracellular biomolecules with minimal dilution and degradation. Thermal gels were employed as the gel matrix because they can be reversibly converted between liquid and solid phases as a function of temperature. Rather than fabricate costly heating elements into devices to control temperature-and thus the phase of the gel-Joule heating was used instead. Adjoining regions of liquid-phase and solid-phase gel were formed within microfluidic channels by selectively inducing localized Joule heat. Cells migrated through the liquid gel but could not enter the solid gel-accumulating at the liquid-solid gel boundary-whereas small molecule contaminants passed through to waste. Barriers were then liquified on-demand by removing Joule heat to collect the purified, non-lysed cells for downstream analyses. Using voltage-controlled Joule heating to regulate the phase of thermal gels is an innovative approach to facilitate in-gel cell enrichment in low-cost microfluidic devices.
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Affiliation(s)
- Mario A Cornejo
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Thomas H Linz
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
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Affiliation(s)
- Cassandra L. Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lisa A. Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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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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Li H, Li F, Zhao L, Zhao L, Sun P, Wu J, Wang X, Pu Q. Electric Field-Driven On-Request Instant in Situ Formation/Removal of Solid Hydrogel within Microchannels for Efficient Electrophoretic Separation. ACS APPLIED MATERIALS & INTERFACES 2020; 12:8773-8779. [PMID: 31997635 DOI: 10.1021/acsami.9b22878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electrophoretic separation in short microchannels is a promising way for rapid analysis of biomolecules, but the pressurized laminar flow may compromise the separation efficiency. In this work, through an electric field, instant formation and removal of a solid chitosan/β-glycerol phosphate (CS/β-GP) hydrogel within microchannels of microchips were realized. In a typical cross-type microchip, the CS/β-GP hydrogel was precisely formed in the separation microchannel within 15 s of the application of a voltage of 2000 V. Highly efficient separation of peptides and proteins was achieved, and theoretical plate numbers of 0.6 to 1.5 × 106/m were attained for proteins in 120 s. The used hydrogel could be swiftly removed also with an electric field, and the whole procedure was achieved on a standard microchip electrophoresis device with no extra accessory or special operation required.
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Affiliation(s)
- Hongli Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Fengyun Li
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Lizhi Zhao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Lei Zhao
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Ping Sun
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Jing Wu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
| | - Xiayan Wang
- Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Chemical Engineering , Beijing University of Technology , Beijing 100124 , China
| | - Qiaosheng Pu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province, Department of Chemistry , Lanzhou University , Lanzhou , Gansu 730000 , China
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Neal SL. Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2018; 72:102-113. [PMID: 28805070 DOI: 10.1177/0003702817729347] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The phase behavior of aqueous 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC)/1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) mixtures between 8.0 ℃ and 41.0 ℃ were monitored using Raman spectroscopy. Temperature-dependent Raman matrices were assembled from series of spectra and subjected to multivariate analysis. The consensus of pseudo-rank estimation results is that seven to eight components account for the temperature-dependent changes observed in the spectra. The spectra and temperature response profiles of the mixture components were resolved by applying a variant of the non-negative matrix factorization (NMF) algorithm described by Lee and Seung (1999). The rotational ambiguity of the data matrix was reduced by augmenting the original temperature-dependent spectral matrix with its cumulative counterpart, i.e., the matrix formed by successive integration of the spectra across the temperature index (columns). Successive rounds of constrained NMF were used to isolate component spectra from a significant fluorescence background. Five major components exhibiting varying degrees of gel and liquid crystalline lipid character were resolved. Hydrogen-bonded water networks exhibiting varying degrees of organization are associated with the lipid components. Spectral parameters were computed to compare the chain conformation, packing, and hydration indicated by the resolved spectra. Based on spectral features and relative amounts of the components observed, four components reflect long chain lipid response. The fifth component could reflect the response of the short chain lipid, DHPC, but there were no definitive spectral features confirming this assignment. A minor component of uncertain assignment that exhibits a striking response to the DMPC pre-transition and chain melting transition also was recovered. While none of the spectra resolved exhibit features unequivocally attributable to a specific aggregate morphology or step in the gelation process, the results are consistent with the evolution of mixed phase bicelles (nanodisks) and small amounts of worm-like DMPC/DHPC aggregates, and perhaps DHPC micelles, at low temperature to suspensions of branched and entangled worm-like aggregates above the DMPC gel phase transition and perforated multi-lamellar aggregates at high temperature.
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Affiliation(s)
- Sharon L Neal
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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12
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Li T, Wu Z, Qin W. Integration of capillary electrophoresis with gold nanoparticle-based colorimetry. Anal Chim Acta 2017; 995:114-121. [DOI: 10.1016/j.aca.2017.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 12/18/2022]
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13
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Application of nanocomposite polymer hydrogels for ultra-sensitive fluorescence detection of proteins in gel electrophoresis. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Holland LA, Gattu S, Crihfield CL, Bwanali L. Capillary electrophoresis with stationary nanogel zones of galactosidase and Erythrina cristagalli lectin for the determination of β(1-3)-linked galactose in glycans. J Chromatogr A 2017. [PMID: 28647147 DOI: 10.1016/j.chroma.2017.06.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A thermally responsive nanogel is used to create stationary zones of enzyme and lectin in a separation capillary. Once patterned in the capillary, analyte is driven through the zone, where it is converted to a specific product if an enzyme is used or captured if a lectin is used. These stationary zones are easily expelled after the analysis and then re-patterned in the capillary. The nanogel is compatible with enzymes and lectins and improves the stability of galactosidase, enabling more cost-effective use of biological reagents that provide insight into glycan structure. A feature of using stationary zones is that the reaction time can be controlled by the length of the zone, the applied field controlling the analyte mobility, or the use of electrophoretic mixing by switching the polarity of the applied voltage while the analyte is located in the zone. The temperature, applied voltage, and length of the stationary zone, which are factors that enhance the performance of the enzyme, are characterized. The combined use of enzymes and lectins in capillary electrophoresis is a new strategy to advance rapid and automated analyses of glycans using nanoliter volumes of enzymes and lectins. The applicability of this use of stationary zones of enzyme and lectin in capillary electrophoresis is demonstrated with the identification of β(1-3)-linked galactose in N-glycan.
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Affiliation(s)
- Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
| | - Srikanth Gattu
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Cassandra L Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
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Gattu S, Crihfield CL, Holland LA. Microscale Measurements of Michaelis-Menten Constants of Neuraminidase with Nanogel Capillary Electrophoresis for the Determination of the Sialic Acid Linkage. Anal Chem 2016; 89:929-936. [PMID: 27936604 PMCID: PMC5214287 DOI: 10.1021/acs.analchem.6b04074] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Phospholipid nanogels enhance the stability and performance of the exoglycosidase enzyme neuraminidase and are used to create a fixed zone of enzyme within a capillary. With nanogels, there is no need to covalently immobilize the enzyme, as it is physically constrained. This enables rapid quantification of Michaelis-Menten constants (KM) for different substrates and ultimately provides a means to quantify the linkage (i.e., 2-3 versus 2-6) of sialic acids. The fixed zone of enzyme is inexpensive and easily positioned in the capillary to support electrophoresis mediated microanalysis using neuraminidase to analyze sialic acid linkages. To circumvent the limitations of diffusion during static incubation, the incubation period is reproducibly achieved by varying the number of forward and reverse passes the substrate makes through the stationary fixed zone using in-capillary electrophoretic mixing. A KM value of 3.3 ± 0.8 mM (Vmax, 2100 ± 200 μM/min) was obtained for 3'-sialyllactose labeled with 2-aminobenzoic acid using neuraminidase from Clostridium perfringens that cleaves sialic acid monomers with an α2-3,6,8,9 linkage, which is similar to values reported in the literature that required benchtop analyses. The enzyme cleaves the 2-3 linkage faster than the 2-6, and a KM of 2 ± 1 mM (Vmax, 400 ± 100 μM/min) was obtained for the 6'-sialyllactose substrate. An alternative neuraminidase selective for 2-3 sialic acid linkages generated a KM value of 3 ± 2 mM (Vmax, 900 ± 300 μM/min) for 3'-sialyllactose. With a knowledge of Vmax, the method was applied to a mixture of 2-3 and 2-6 sialyllactose as well as 2-3 and 2-6 sialylated triantennary glycan. Nanogel electrophoresis is an inexpensive, rapid, and simple alternative to current technologies used to distinguish the composition of 3' and 6' sialic acid linkages.
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Affiliation(s)
- Srikanth Gattu
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Cassandra L Crihfield
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University , Morgantown, West Virginia 26506, United States
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A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection. PLoS One 2015; 10:e0137578. [PMID: 26356298 PMCID: PMC4565658 DOI: 10.1371/journal.pone.0137578] [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: 05/11/2015] [Accepted: 08/18/2015] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei and Burkholderia mallei, classified as category B priority pathogens, are significant human and animal pathogens that are highly infectious and broad-spectrum antibiotic resistant. Currently, the pathogenicity mechanisms utilized by Burkholderia are not fully understood, and correct diagnosis of B. pseudomallei and B. mallei infection remains a challenge due to limited detection methods. Here, we provide a comprehensive analysis of a set of 13 novel Burkholderia collagen-like proteins (Bucl) that were identified among B. pseudomallei and B. mallei select agents. We infer that several Bucl proteins participate in pathogenesis based on their noncollagenous domains that are associated with the components of a type III secretion apparatus and membrane transport systems. Homology modeling of the outer membrane efflux domain of Bucl8 points to a role in multi-drug resistance. We determined that bucl genes are widespread in B. pseudomallei and B. mallei; Fischer’s exact test and Cramer’s V2 values indicate that the majority of bucl genes are highly associated with these pathogenic species versus nonpathogenic B. thailandensis. We designed a bucl-based quantitative PCR assay which was able to detect B. pseudomallei infection in a mouse with a detection limit of 50 CFU. Finally, chromosomal mapping and phylogenetic analysis of bucl loci revealed considerable genomic plasticity and adaptation of Burkholderia spp. to host and environmental niches. In this study, we identified a large set of phylogenetically unrelated bucl genes commonly found in Burkholderia select agents, encoding predicted pathogenicity factors, detection targets, and vaccine candidates.
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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Durney BC, Bachert BA, Sloane HS, Lukomski S, Landers JP, Holland LA. Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking. Anal Chim Acta 2015; 880:136-44. [PMID: 26092346 DOI: 10.1016/j.aca.2015.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/02/2015] [Accepted: 03/04/2015] [Indexed: 01/13/2023]
Abstract
Phospholipid additives are a cost-effective medium to separate deoxyribonucleic acid (DNA) fragments and possess a thermally-responsive viscosity. This provides a mechanism to easily create and replace a highly viscous nanogel in a narrow bore capillary with only a 10°C change in temperature. Preparations composed of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) self-assemble, forming structures such as nanodisks and wormlike micelles. Factors that influence the morphology of a particular DMPC-DHPC preparation include the concentration of lipid in solution, the temperature, and the ratio of DMPC and DHPC. It has previously been established that an aqueous solution containing 10% phospholipid with a ratio of [DMPC]/[DHPC]=2.5 separates DNA fragments with nearly single base resolution for DNA fragments up to 500 base pairs in length, but beyond this size the resolution decreases dramatically. A new DMPC-DHPC medium is developed to effectively separate and size DNA fragments up to 1500 base pairs by decreasing the total lipid concentration to 2.5%. A 2.5% phospholipid nanogel generates a resolution of 1% of the DNA fragment size up to 1500 base pairs. This increase in the upper size limit is accomplished using commercially available phospholipids at an even lower material cost than is achieved with the 10% preparation. The separation additive is used to evaluate size markers ranging between 200 and 1500 base pairs in order to distinguish invasive strains of Streptococcus pyogenes and Aspergillus species by harnessing differences in gene sequences of collagen-like proteins in these organisms. For the first time, a reversible stacking gel is integrated in a capillary sieving separation by utilizing the thermally-responsive viscosity of these self-assembled phospholipid preparations. A discontinuous matrix is created that is composed of a cartridge of highly viscous phospholipid assimilated into a separation matrix of low viscosity. DNA sample stacking is facilitated with longer injection times without sacrificing separation efficiency.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States
| | - Beth A Bachert
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, United States
| | - Hillary S Sloane
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Slawomir Lukomski
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Mechanical Engineering, University of Virginia, Charlottesville, VA 22904, United States; Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22904, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, United States.
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Chung M, Kim D, Herr AE. Polymer sieving matrices in microanalytical electrophoresis. Analyst 2014; 139:5635-54. [DOI: 10.1039/c4an01179a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Tuntevski K, Durney BC, Snyder AK, LaSala PR, Nayak AP, Green BJ, Beezhold DH, Rio RVM, Holland LA, Lukomski S. Aspergillus collagen-like genes (acl): identification, sequence polymorphism, and assessment for PCR-based pathogen detection. Appl Environ Microbiol 2013; 79:7882-95. [PMID: 24123732 PMCID: PMC3837832 DOI: 10.1128/aem.02835-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 10/02/2013] [Indexed: 12/16/2022] Open
Abstract
The genus Aspergillus is a burden to public health due to its ubiquitous presence in the environment, its production of allergens, and wide demographic susceptibility among cystic fibrosis, asthmatic, and immunosuppressed patients. Current methods of detection of Aspergillus colonization and infection rely on lengthy morphological characterization or nonstandardized serological assays that are restricted to identifying a fungal etiology. Collagen-like genes have been shown to exhibit species-specific conservation across the noncollagenous regions as well as strain-specific polymorphism in the collagen-like regions. Here we assess the conserved region of the Aspergillus collagen-like (acl) genes and explore the application of PCR amplicon size-based discrimination among the five most common etiologic species of the Aspergillus genus, including Aspergillus fumigatus, A. flavus, A. nidulans, A. niger, and A. terreus. Genetic polymorphism and phylogenetic analysis of the aclF1 gene were additionally examined among the available strains. Furthermore, the applicability of the PCR-based assay to identification of these five species in cultures derived from sputum and bronchoalveolar fluid from 19 clinical samples was explored. Application of capillary electrophoresis on nanogels was additionally demonstrated to improve the discrimination between Aspergillus species. Overall, this study demonstrated that Aspergillus acl genes could be used as PCR targets to discriminate between clinically relevant Aspergillus species. Future studies aim to utilize the detection of Aspergillus acl genes in PCR and microfluidic applications to determine the sensitivity and specificity for the identification of Aspergillus colonization and invasive aspergillosis in immunocompromised subjects.
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Affiliation(s)
| | | | | | - P. Rocco LaSala
- Department of Pathology, West Virginia University
- Clinical Laboratory, West Virginia University Healthcare, Morgantown, West Virginia, USA
| | - Ajay P. Nayak
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
| | - Brett J. Green
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
| | - Donald H. Beezhold
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Centers for Disease Control and Prevention, Morgantown, West Virginia, USA
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