Capillary gel electrophoresis for rapid, high resolution DNA sequencing.

Capillary gel electrophoresis has been demonstrated for the separation and detection of DNA sequencing samples. Enzymatic dideoxy nucleotide chain termination was employed, using fluorescently tagged oligonucleotide primers and laser based on-column detection (limit of detection is 6,000 molecules per peak). Capillary gel separations were shown to be three times faster, with better resolution (2.4 x), and higher separation efficiency (5.4 x) than a conventional automated slab gel DNA sequencing instrument. Agreement of measured values for velocity, resolution and separation efficiency with theory, predicts further improvements will result from increased electric field strengths (higher voltages and shorter capillaries). Advantages of capillary gel electrophoresis for automatic DNA sequencing instruments and for genomic sequencing are discussed.     

Producing Improved Glass Knives for Ultra-Microtomy; A Glass Breaker Featuring a Linear Fulcrum and a Device for Controlling Fracturing Velocity

Innovations include: (1) interchangeable round linear fulcra of different diameters, (2) compressible materials covering pressure sites, and (3) a screw-compression mechanism for initiating breaks and controlling fracturing velocity. The instrument consists of a cross-shaped pressure plate hinged to a rectangular metal base bearing the pressure-applying mechanism opposite the hinge. A longitudinal slot in the pressure plate parallels the long axis of the fulcrum and permits positioning of prescored glass pieces or permits scoring of an engaged glass piece by guiding a scorer inserted through the slot. Knives with straight, flawless edges have been obtained from different types of glass (up to 7/16 inch thick) including soft, pyrex and tempered. Greater than 50% yield of useable knives averaging more than 50% of flawless edge, as judged at a magnification of 220 and by ultrathin sectioning, has been obtained with the device. The instrument design and technique facilitate controllably reducing the fracturing velocity to significantly increase the width of stress-free knife edge obtained. Details of the technique, optional attachments and modifications are outlined.     

"Molded" rods of macroporous polymer for preparative separations of biological products

A continuous rod of porous poly(glycidy1 methacrylate-co-ethylene dimethacrylate) has been prepared by a free radical polymerization within the confines of a 16-mm-i.d. glass column. The epoxide groups of the rod have been modified in situ by their reaction with diethylamine to afford the ionizable weak base 1-N,N-diethylamino-2-hydroxypropyl functionalities that are required for the ion-exchange chromatographic mode. The bimodal pore size distribution curve typical for other molded separation media also prevail for the preparative-size rod. The column has been used successfully for the chromatographic separation of a mixture of standard proteins and yeast enzymes. The column exhibits a dynamic capacity that exceeds 420 mg of bovine serum albumin at a flow velocity of 60 cm/h. (c) 1995 John Wiley & Sons, Inc.     

A vertical submarine electrophoresis apparatus for polyacrylamide minigels

A vertical submarine electrophoresis apparatus for use with minislab polyacrylamide gels is described. The design allows polyacrylamide gels to be run with the same ease and convenience that agarose gels are run with horizontal submarine apparatuses. The vertical submarine features a single buffer chamber with a restriction between the upper and the lower portions of the chamber. Acrylamide gels, cast between 9 X 10-cm glass slides, are inserted into the restriction and are completely immersed in buffer. Thus, current flows primarily through the gel itself, but some current flows through the buffer in the restriction surrounding the gel. Because water-tight separation of buffer chambers is not necessary, time-consuming and/or expensive procedures such as sealing with agarose or using fragile notched glass plates are eliminated. The apparatus can be set up to run a gel in less than 30 s. It is versatile in that gels of varying thickness (0.5, 0.8, 1.5, and 3 mm) can be run on a single apparatus. The apparatus has been used for sodium dodecyl sulfate gels, low ionic strength native gels for nucleoprotein complexes, and composite acrylamide-agarose gels.     

Xylan-Containing supports used to separate xylanase from the cellulases of aspergillus terreus F-413

The separation of xylanase from cellulolytic enzymes of A. terreus F-413 by affinity chromatography on xylan-containing supports was investigated. Xylanase purified over tenfold was obtained after column chromatography on xylan bound to controlled porous glass. The molecular weight of the purified enzyme has been found to be 140 000 daltons, and it is homogeneous in polyacrylamide gel electrophoresis. Purified xylanase also showed residual celluloytic activity (perhaps cross-specificity) with cellulosic substrates.     

Precise localization of several covalent RNA-RNA cross-link in Escherichia coli 16S RNA

The RNA-RNA cross-linking reagent N-acetyl-N'-(p-glyoxylyl-benzoyl)cystamine, which reacts via its glyoxal residue with guanines not involved in G X C base pairs, has been used to introduce reversible RNA-RNA cross-links into Escherichia coli 16S rRNA. A two-dimensional gel method has been devised for the separation of the cross-linked oligonucleotides, and the precise location of guanines involved in four of these cross-links has been determined by sequencing the oligonucleotides. One cross-link involves guanosines 1315 and 1360 situated in two hairpin end loops of domain III. The other cross-links involves pairs of guanosine situated within the same hairpin end loops.     

Parallel plate equipment for preparation of uniform gel sheets

A method for the preparation of uniform gel-disks for enzyme and cell immobilisation, as well as for characterisation of gel mechanical stability, is described. The apparatus comprises a stainless steel base unit and glass parallel plates, designed to permit easy and fast production of multiple homogeneous gel sheets of variable thickness.     

Method for the characterization of size-exclusion chromatography media for preparative purification of DNA restriction fragments

A protocol has been developed to characterize the potential of size exclusion chromatography media for the separation of DNA fragments at a preparative scale. A standard DNA mixture composed of -DNA cut with the restriction enzymes, AluI and HaeIII, was chromatographed on a column packed with the gel of interest. Fractions were collected and examined by PAGE. A digitized image of the gel was analyzed with the aid of a computer software program to determine the DNA fractionation range and selectivity curve for each chromatography gel. Four gels were characterized using this protocol. The effect of the elution buffer ionic strength on the fractionation of DNA was also investigated.The US Government right to retain a non-exclusive royalty-freelicense in and to any copyright is acknowledged.     

Application of centrifugal force to the extraction and separation of parasorboside and gerberin from Gerbera hybrida

A method for the separation of parasorboside and gerberin from the ornamental plant Gerbera hybrida (Asteraceae) has been developed. The two closely related glucosides were extracted using an Extrachrom instrument, a prototype multi-functional separation tool equipped with an extraction chamber. The rotation planar extraction procedure was compared with that of a medium pressure solid-liquid extraction system. The resulting extracts were pre-purified using rotation planar chromatography and the results compared with those obtained using medium pressure liquid chromatography with silica gel as the stationary phase and a mobile phase of methanol:ethyl acetate:tetrahydrofuran at selectivity point Ps = 111 with 1% formic acid as modifier. The title compounds were isolated from the purified extracts by TLC and their structures confirmed by 1H- and 13C-NMR spectroscopy.     

Large scale library generation for high throughput sequencing

Background

Large efforts have recently been made to automate the sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols.

Methodology/Principal Findings

In this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions.

Conclusions/Significance

The method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.     

Measuring gene expression by quantitative proteome analysis

Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis for protein separation, visualization, and quantification and mass spectrometry for protein identification. Over the past year, exceptional progress has been made towards developing a new technology base for the precise quantification and identification of proteins in complex mixtures, that is, quantitative proteomics.     

Reversed-phase HPLC separation of proteins on chemically bonded silica gel columns

Reversed-phase high-performance liquid chromatographic (RP-HPLC) separation of proteins on chemically bonded silica gel columns is described. Efficiency of nonporous alkylsilyl bonded silica gel is compared with that of a macroporous gel that has been widely used for the purpose. A comparative study of the separation under conventional and fast separation conditions is also given. The fast separation technique on the nonporous reversed-phase column has the advantage of improving the recovery of late-eluting hydrophobic and large proteins, such as ovalbumin and apoferritin.     

Chromatographic properties of human leukocyte alpha-interferon A on sorbents with sepharose and silochrome matrices

Chromatography on immobilized monoclonal antibodies NK-2 from a bacterial strain-producer resulted in a pure human leukocyte alpha-interferon A (alpha-INF-A) homogeneous upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate and reverse phase high performance liquid chromatography. The chromatographic properties of partially purified alpha-INF-A on synthetic and commercial sorbents containing immobilized dyes, aromatic dipeptides, chelating and hydrophobic ligands as well as on porous glass have been investigated. In most cases, [125I]alpha-INF-A was used as an inner standard. The chromatographic behaviour of native and [125I]-labeled alpha-INF-A was practically the same. alpha-INF-A was most effectively chromatographed on porous glass, L-Trp-L-Trp-Sepharose 4B and Cu2+-chelate sorbents. In the latter case, the feasibility of substitution of the Sepharose matrix for the silochrome one has been demonstrated. It has been proposed that alpha-INF-A has a hydrophobic "pocket" with exposed aromatic amino acid residues which are capable of selective binding to aromatic dipeptides.     

Methods for increasing the resolution of two-dimensional protein electrophoresis

A two-dimensional gel elctrophoresis protocol has been developed which provides for a 1.5-to 3-fold increase in the resolution of proteins compared to other frequently used methods. The major variations from previous protocols include increased pore size in the isoelectric focusing gels; cholamidopropyldimethylhydroxypropanesulfonate, a zwitterionic detergent, replaces most of the Nonidet P-40, a nonionic detergent, in the isoelectric focusing gels; no equilibration step is employed between the first and second dimensional separation. The use of a stacking gel in the second dimension has been eliminated; a more efficient and evenly distributed cooling system has been designed for the molecular mass separation, allowing faster migration with higher current. Finally, the crosslinker diacrylylpiperazine is employed which improves protein separation and detection with ammoniacal silver staining. Silver-stained two-dimensional gel electrophoretograms of human plasma and hamster brain tissues and autoradiographs of rat liver cells are compared to the results obtained from previous methods.     

蛋白质二硫键异构酶的纯化和活力测定

 从500g新鲜牛肝制得蛋白质二硫键异构酶(PDI,EC 5.3.4.1)98mg。该酶制剂在SDS-聚丙烯酰胺凝胶电泳中表现为亚基分子量62,000的均一条带。在260nm追踪,因二硫键错接而失活的牛胰核糖核酸酶A,经PDI作用使其二硫键重排恢复活力,从而催化酵母RNA的水解来测定PDI活力。这种单波长法比文献中介绍的追踪A_(260)—A_(280)的双波长法更为灵敏方便。酶的克分子消光系数ε_M=1.03×10~5(pH7.5),其比活性为1400单位/克蛋白质。     

Microfabricated polymer chip for capillary gel electrophoresis

A polymer (PDMS: poly(dimethylsiloxane)) microchip for capillary gel electrophoresis that can separate different sizes of DNA molecules in a small experimental scale is presented. This microchip can be easily produced by a simple PDMS molding method against a microfabricated master without the use of elaborate bonding processes. This PDMS microchip could be used as a single use device unlike conventional microchips made of glass, quartz or silicon. The capillary channel on the chip was partially filled with agarose gel that can enhance separation resolution of different sizes of DNA molecules and can shorten the channel length required for the separation of the sample compared to capillary electrophoresis in free-flow or polymer solution format. We discuss the optimal conditions for the gel preparation that could be used in the microchannel. DNA molecules were successfully driven by an electric field and separated to form bands in the range of 100 bp to 1 kbp in a 2.0% agarose-filled microchannel with 8 mm of effective separation length.     

A rapid, high resolution DNA sequencing gel system

We have developed a simple method which significantly increases the efficiency of manual DNA sequencing. This method increases both the ease of gel preparation and the quality of fragment resolution. Our system involves (i) casting of gels horizontally, without sealing around the plates; (ii) the use of a self-forming buffer gradient to stack bands in the lower part of the gel; (iii) separation of the samples on two 0.2-mm-thick acrylamide gels (4.5 and 4%) with overlapping readings; (iv) "nonsmiling" electrophoresis with very simple, self-made electrophoresis stands; and (v) prior to exposure in situ dry fixation of the gel matrix to the glass support without previous covalent binding of the gel. On average, we are able to read from nucleotide position 50 to position 600 without ambiguity.     

The electrophoresis of histones in polyacrylamide gel and their quantitative determination

1. A new method has been devised for the separation of the histone fractions of calf thymus by electrophoresis in polyacrylamide gel at pH2.4. 2. The fractions have been characterized by their relative mobilities with respect to a marker protein, bovine plasma albumin. 3. A method has been developed for the quantitative determination of the separated histone fractions by measuring the colour yields of dye-histone complexes formed in the gel.     

Preparative separation of hemoglobins A and S by gel electrofocusing, using selective zone elution by gel transposition between suitable anolytes and catholytes.

Preparative electrofocusing on polyacrylamide gels has been limited, until recently, to excision of gel slices, diffusion, and collection of the slice diffusates. An advance was made by the introduction of a method of selective electrophoretic zone recovery by specific changes of anolyte (A. McCormick, L. E. M. Miles, and A. Chrambach, 1976, Anal. Biochem.75, 314–324). It was shown (a) that selective zone recovery could be achieved by transposition of the gels into either isoelectric ampholytes or charged buffers, (b) that it could be applied to the gram scale, and (c) that zone elution could proceed either continuously or discontinuously. The early study was, however, limited to a trivial model problem, the separation of hemoglobin from bovine serum albumin (BSA). The present study was an attempt to apply a similar selective zone recovery method to a more demanding separation problem, the separation of hemoglobin A from hemoglobin S as well as from other minor components contained in a sickle-trait human hemolysate. The study shows that selective electrophoretic zone elution from a electrofocusing gel 18 mm in diameter is capable of yielding hemoglobin A, separated from hemoglobin S, differing by only 0.2 pH units in isoelectric point. The recovery of hemoglobin A was 70%, with a load of 32 mg of hemoglobin mixture per gel, using discontinuous zone elution into a collection cup.