Microchannel wall coatings for protein separations by capillary and chip electrophoresis

The necessity for microchannel wall coatings in capillary and chip-based electrophoretic analysis of biomolecules is well understood. The regulation or elimination of EOF and the prevention of analyte adsorption is essential for the rapid, efficient separation of proteins and DNA within microchannels. Microchannel wall coatings and other wall modifications are especially critical for protein separations, both in fused-silica capillaries, and in glass or polymeric microfluidic devices. In this review, we present a discussion of recent advances in microchannel wall coatings of three major classes--covalently linked polymeric coatings, physically adsorbed polymeric coatings, and small molecule additives. We also briefly review modifications useful for polymeric microfluidic devices. Within each category of wall coatings, we discuss those used to eliminate EOF, to tune EOF, to prevent analyte adsorption, or to perform multiple functions. The knowledgeable application of the most promising recent developments in this area will allow for the separation of complex protein mixtures and for the development of novel microchannel wall modifications.     

Critical factors for high-performance physically adsorbed (dynamic) polymeric wall coatings for capillary electrophoresis of DNA

Physically adsorbed (dynamic) polymeric wall coatings for microchannel electrophoresis have distinct advantages over covalently linked coatings. In order to determine the critical factors that control the formation of dynamic wall coatings, we have created a set of model polymers and copolymers based on N,N-dimethylacrylamide (DMA) and N,N-diethylacrylamide (DEA), and studied their adsorption behavior from aqueous solution as well as their performance for microchannel electrophoresis of DNA. This study is revealing in terms of the polymer properties that help create an "ideal" wall coating. Our measurements indicate that the chemical nature of the coating polymer strongly impacts its electroosmotic flow (EOF) suppression capabilities. Additionally, we find that a critical polymer chain length is required for polymers of this type to perform effectively as microchannel wall coatings. The effective mobilities of double-stranded (dsDNA) fragments within dynamically coated capillaries were determined in order to correlate polymer hydrophobicity with separation performance. Even for dsDNA, which is not expected to be a strongly adsorbing analyte, wall coating hydrophobicity has a deleterious influence on separation performance.     

End-labeled free-solution electrophoresis of DNA

DNA is a free-draining polymer. This subtle but "unfortunate" property of highly charged polyelectrolytes makes it impossible to separate nucleic acids by free-flow electrophoresis. This is why one must typically use a sieving matrix, such as a gel or an entangled polymer solution, in order to obtain some electrophoretic size separation. An alternative approach consists of breaking the charge to friction balance of free-draining DNA molecules. This can be achieved by labeling the DNA with a large, uncharged molecule (essentially a hydrodynamic parachute, which we also call a drag-tag) prior to electrophoresis; the resulting methodology is called end-labeled free-solution electrophoresis (ELFSE). In this article, we review the development of ELFSE over the last decade. In particular, we examine the theoretical concepts used to predict the ultimate performance of ELFSE for single-stranded (ssDNA) sequencing, the experimental results showing that ELFSE can indeed overcome the free-draining issue raised above, and the technological advances that are needed to speed the development of competitive ELFSE-based sequencing and separation technologies. Finally, we also review the reverse process, called free-solution conjugate electrophoresis (FSCE), wherein uncharged polymers of different sizes can be analyzed using a short DNA molecule as an electrophoretic engine.     

DNA sequencing and genotyping in miniaturized electrophoresis systems

Advances in microchannel electrophoretic separation systems for DNA analyses have had important impacts on biological and biomedical sciences, as exemplified by the successes of the Human Genome Project (HGP). As we enter a new era in genomic science, further technological innovations promise to provide other far-reaching benefits, many of which will require continual increases in sequencing and genotyping efficiency and throughput, as well as major decreases in the cost per analysis. Since the high-resolution size- and/or conformation-based electrophoretic separation of DNA is the most critical step in many genetic analyses, continual advances in the development of materials and methods for microchannel electrophoretic separations will be needed to meet the massive demand for high-quality, low-cost genomic data. In particular, the development (and commercialization) of miniaturized genotyping platforms is needed to support and enable the future breakthroughs of biomedical science. In this review, we briefly discuss the major sequencing and genotyping techniques in which high-throughput and high-resolution electrophoretic separations of DNA play a significant role. We review recent advances in the development of technology for capillary electrophoresis (CE), including capillary array electrophoresis (CAE) systems. Most of these CE/CAE innovations are equally applicable to implementation on microfabricated electrophoresis chips. Major effort is devoted to discussing various key elements needed for the development of integrated and practical microfluidic sequencing and genotyping platforms, including chip substrate selection, microchannel design and fabrication, microchannel surface modification, sample preparation, analyte detection, DNA sieving matrices, and device integration. Finally, we identify some of the remaining challenges, and some of the possible routes to further advances in high-throughput DNA sequencing and genotyping technologies.     

Thermoresponsive N,N-dialkylacrylamide copolymer blends as DNA sieving matrices with a thermally tunable mesh size

In an earlier study we showed that a blend of thermoresponsive and nonthermoresponsive hydroxyalkylcelluloses could be used to create a thermally tunable polymer network for double-stranded (ds) DNA separation. Here, we show the generality of this approach using a family of polymers suited to a wider range of DNA separations: a blended mixture of N,N-dialkylacrylamide copolymers with different thermoresponsive behaviors. A mixture of 47% w/w N,N-diethylacrylamide (DEA)/53% w/w N,N-dimethylacrylamide (DMA) (DEA47; thermoresponsive, transition temperature = 55 degrees C in water) and 30% w/w DEA/70% w/w DMA (DEA30; nonthermoresponsive, transition temperature > 85 degrees C in water) copolymers in the ratio of 1:5 w/w DEA47:DEA30 was used to separate a dsDNA restriction digest (PhiX174-HaeIII). We investigated the effects of changing mesh size on dsDNA separation, as controlled by temperature. We observed good DNA separation performance with the copolymer blend at temperatures ranging from 25 degrees C to 48 degrees C. The separation selectivity was evaluated quantitatively for certain DNA fragment pairs as a function of temperature. The results were compared with those obtained with a control matrix consisting only of the nonthermoresponsive DEA30. Different DNA fragment pairs of various sizes show distinct temperature-dependent selectivities. Over the same temperature range, no significant temperature dependence of selectivity is observed for these DNA fragment pairs in the nonthermoresponsive control matrix. Overall, the results show similar trends in the temperature dependency of separation selectivity to what was previously observed in hydroxyalkylcellulose blends, for the same DNA fragment pairs. Finally, we showed that a ramped temperature scheme enables improved separation in the blended copolymer matrix for both small and large DNA fragments, simultaneously in a single capillary electrophoresis (CE) run.     

Detection of Escherichia coli O157:H7 bacteria by a combination of immunofluorescent staining and capillary electrophoresis

As the number of incidents of bacterial infections continues to rise around the globe, simpler, faster, and more sensitive diagnostic techniques are required to improve the safety of the food supply and to screen for potential bacterial infections in humans. We present here direct and indirect approaches for the detection of bacteria, which are based upon a combination of immunofluorescent staining and capillary electrophoresis. In the direct approach, Escherichia coli O157:H7 bacteria stained with fluorescein-tagged specific antibodies are detected by CE, while in the indirect approach fluorescein-tagged specific antibodies to E. coli are first captured by E. coli O157:H7 bacteria and then released and detected by CE. We have identified suitable bacteria staining and CE protocols, which involved a 10 mM Tris-borate-EDTA (TBE) buffer, 0.25 micro g antibody/1 million bacteria, and capillaries dynamically coated with poly-N-hydroxyethylacrylamide (polyDuramide). We have also successfully detected the presence of E. coli O157:H7 in contaminated meat. The total time required for analysis was 6-8 h, which is less than that realized in most commercial assays presently available.     

Poly-N-hydroxyethylacrylamide as a novel, adsorbed coating for protein separation by capillary electrophoresis.

We present the polymer poly-N-hydroxyethylacrylamide (PHEA) (polyDuramide) as a novel, hydrophilic, adsorbed capillary coating for electrophoretic protein analysis. Preparation of the PHEA coating requires a simple and fast (30 min) protocol that can be easily automated in capillary electrophoresis instruments. Over the pH range of 3-8.4, the PHEA coating is shown to reduce electroosmotic flow (EOF) by about 2 orders of magnitude compared to the bare silica capillary. In a systematic comparative study, the adsorbed PHEA coating exhibited minimal interactions with both acidic and basic proteins, providing efficient protein separations with excellent reproducibility on par with a covalent polyacrylamide coating. Hydrophobic interactions between proteins and a relatively hydrophobic poly-N,N-dimethylacrylamide (PDMA) adsorbed coating, on the other hand, adversely affected separation reproducibility and efficiency. Under both acidic and basic buffer conditions, the adsorbed PHEA coating produced an EOF suppression performance comparable to that of covalent polyacrylamide coating and superior to that of adsorbed PDMA coating. The protein separation performance in PHEA-coated capillaries was retained for 275 consecutive protein separation runs at pH 8.4, and for more than 800 runs at pH 4.4. The unique and novel combination of hydrophilicity and adsorptive coating ability of PHEA makes it a suitable wall coating for automated microscale analysis of proteins by capillary array systems.     

New Sphingolipids and Other Constituents of Pancovia laurentii

Phytochemical investigation of the bark and leaves of Pancovia laurentii (Sapindaceae) resulted in the isolation of a new ceramide and a new cerebroside, named pancoviamide ( 1 ), and pancovioside ( 2 ) respectively, together with six known compounds: uracil, (R)‐N‐[(1S,2S,3R)‐2,3‐dihydroxy‐1‐(hydroxymethyl)heptadec‐5‐en‐1‐yl]‐2‐hydroxytetracosanamide, stigmasta‐7,22‐dien‐3‐ol, β‐stitosterol, β‐sitosterol 3‐O‐β‐D ‐glucopyranoside, and 2,3‐dihydroxypropyl pentadecanoate. The structures of 1 and 2 were determined by means of spectroscopic methods. Compounds 1 and 2 were tested in vitro for their antiprotozoal properties against several protozoa and for their cytotoxicity.     

Structure elucidation of new acacic acid‐type saponins from Albizia coriaria

Three new acacic acid derivatives, named coriariosides C, D, and E ( 1–3 ) were isolated from the roots of Albizia coriaria. Their structures were elucidated on the basis of extensive 1D‐ and 2D‐NMR studies and mass spectrometry as 3‐O‐[β‐D ‐xylopyranosyl‐(1 → 2)‐β‐D ‐fucopyranosyl‐(1 → 6)‐2‐(acetamido)‐2‐deoxy‐β‐D ‐glucopyranosyl]‐21‐O‐{(2E,6S)‐6‐O‐{4‐O‐[(2E,6S)‐2,6‐dimethyl‐ 6‐O‐(β‐D ‐quinovopyranosyl)octa‐2,7‐dienoyl]‐4‐O‐[(2E,6S)‐2,6‐dimethyl‐6‐O‐(β‐D ‐quinovopyranosyl)octa‐2,7‐dienoyl]‐β‐D ‐quinovopyranosyl}‐2,6‐dimethylocta‐2,7‐dienoyl}acacic acid 28‐O‐β‐D ‐xylopyranosyl‐(1 → 4)‐α‐L ‐rhamnopyranosyl‐(1 → 2)‐β‐D ‐glucopyranosyl ester ( 1 ), 3‐O‐{β‐D ‐fucopyranosyl‐(1 → 6)‐[β‐D ‐glucopyranosyl‐(1 → 2)]‐β‐D ‐glucopyranosyl}‐21‐O‐{(2E,6S)‐6‐O‐{4‐O‐[(2E,6S)‐2,6‐dimethyl‐6‐O‐(β‐D ‐quinovopyranosyl)octa‐2,7‐dienoyl]‐4‐O‐[(2E,6S)‐2,6‐dimethyl‐6‐O‐(β‐D ‐quinovopyranosyl)octa‐2,7‐dienoyl]‐β‐D ‐quinovopyranosyl}‐2,6‐dimethylocta‐2,7‐dienoyl}acacic acid 28‐O‐α‐L ‐rhamno pyranosyl‐(1 → 2)‐β‐D ‐glucopyranosyl ester ( 2 ), and 3‐O‐[β‐D ‐fucopyranosyl‐(1 → 6)‐β‐D ‐glucopyranosyl]‐21‐O‐{(2E,6S)‐6‐O‐{4‐O‐[(2E,6S)‐2,6‐dimethyl‐6‐O‐(β‐D ‐quinovopyranosyl)octa‐2,7‐dienoyl)‐β‐D ‐quinovopyranosyl]octa‐2,7‐dienoyl}acacic acid 28‐O‐β‐D ‐glucopyranosyl ester ( 3 ). Copyright © 2010 John Wiley & Sons, Ltd.