Reversible phospholipid nanogels for deoxyribonucleic acid fragment size determinations up to 1500 base pairs and integrated sample stacking

Electric Field-Driven On-Request Instant in Situ Formation/Removal of Solid Hydrogel within Microchannels for Efficient Electrophoretic Separation

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.

Orthogonal Tip-to-Tip Nanocapillary Alignment Allows for Easy Detection of Fluorescent Emitters in Femtomolar Concentrations

Here we present the realization of a novel fluorescence detection method based on the electromigration of fluorescent molecules within a nanocapillary combined with the laser excitation through a platinum (Pt)-coated nanocapillary. By using the Pt nanocapillary assisted focusing of a laser beam, we completely remove the background scattering on the tip of the electrophoretic nanocapillary. In this excitation geometry, we demonstrate a 1000-fold sensitivity enhancement (1.0 nM to 1.0 pM) compared to the detection in microcapillaries with epifluorescence illumination and fluorescence spectrophotometry. Due to a significant electroosmotic flow, we observe a decelerating migration of DNA molecules close to the tip of the electrophoretic nanocapillary. The reduced DNA translocation velocity causes a two-step stacking process of molecules in the tip of the nanocapillary and can be used as a way to locally concentrate molecules. The sensitivity of our method is further improved by a continuous electrokinetic injection of DNA molecules followed by sample zone stacking on the tip of the nanocapillary. Concentrations ranging from 0.1 pM to 1.0 fM can be directly observed on the orifice of the electrophoretic nanocapillary. This is a 1000-fold improvement compared to traditional capillary electrophoresis with laser-induced fluorescence.

Multivariate Analysis of Mixed Lipid Aggregate Phase Transitions Monitored Using Raman Spectroscopy

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.

Capillary electrophoresis with stationary nanogel zones of galactosidase and Erythrina cristagalli lectin for the determination of β(1-3)-linked galactose in glycans

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.

Microscale Measurements of Michaelis-Menten Constants of Neuraminidase with Nanogel Capillary Electrophoresis for the Determination of the Sialic Acid Linkage

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 (K_M) 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 K_M value of 3.3 ± 0.8 mM (V_max, 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 K_M of 2 ± 1 mM (V_max, 400 ± 100 μM/min) was obtained for the 6'-sialyllactose substrate. An alternative neuraminidase selective for 2-3 sialic acid linkages generated a K_M value of 3 ± 2 mM (V_max, 900 ± 300 μM/min) for 3'-sialyllactose. With a knowledge of V_max, 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.

Recent progress of sample stacking in capillary electrophoresis (2014-2016)

The term "sample stacking" comprises a relatively broad spectrum of techniques that already form an almost inherent part of the methodology of CZE. Their principles are different but the effect is the same: concentration of a diluted analyte into a narrow zone and considerable increase of the method sensitivity. This review brings a survey of papers on electrophoretic sample stacking published approximately since the second quarter of 2014 till the first quarter of 2016. It is organized according to the principles of the stacking methods and includes chapters aimed at the concentration adjustment principle (Kohlrausch stacking), techniques based on pH changes, micellar methods, and other stacking techniques. Not reviewed are papers on transient ITP that are covered by another review in this issue.

A Unique Set of the Burkholderia Collagen-Like Proteins Provides Insight into Pathogenesis, Genome Evolution and Niche Adaptation, and Infection Detection

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.

Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014)

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.