High-throughput simultaneous detection of point mutations and large-scale rearrangements by CE

The detection of unknown mutations is important both in population genetics research and in diagnosis. At present, two different methods must be used to detect either point mutations or large-scale genetic rearrangements, which is costly and time-consuming. We describe here a new method for the simultaneous detection of these two types of mutations. It is based on electrophoretic heteroduplex analysis (HDA) using enhanced mismatch mutation analysis (EMMA) and semiquantitative multiplexed PCR conditions. The use of such conditions allows the simultaneous search of any kind of mutation in up to five different fragments per capillary, in a single or multi-CE system. The method was validated on patient samples with mutations in the breast predisposition gene BRCA1. It leads to highly reliable and high-throughput mutation detection at low cost, as compared with classical methods.     

Electrophoretically mediated microanalysis

This review describes the existing developments in the use of the capillary electrophoretic microanalytical technique for the in-line study of enzyme reaction, electrophoretically mediated microanalysis (EMMA). The article is divided into a number of parts. After an introduction, the different modes, basic principle, procedure, and some mathematical treatments of EMMA methodology are discussed and illustrated. The applications of EMMA for enzyme assay and for non-enzymatic determination are summarized into two tables. In addition to classical capillary electrophoresis (CE) instrument EMMA, special emphasis is given to a relatively new technique: EMMA on CE microchip. Finally, conclusions are drawn.     

Advances in capillary electrophoretically mediated microanalysis: an update

This review, as a continuation of an earlier report, gives an overview of recent developments, over the period from 2003 until now, in the use of capillary electrophoretic techniques for the in-line study of enzymatic reactions, derivatization, and chemical reactions. The article is divided into two parts: (i) in-line enzymatic reactions and (ii) in-line derivatization and chemical reactions. The first part introduces electrophoretically mediated microanalysis (EMMA) and discusses and illustrates the different modes of EMMA. A literature overview on enzymatic reactions is provided. The second part starts with an introduction of the procedures and the nomenclature used in the area of in-line derivatization and chemical reactions based on EMMA. Reported derivatization and chemical reaction procedures are discussed and summarized.     

Advances in capillary electrophoretically mediated microanalysis

Recent developments in the use of capillary electrophoretic techniques for the in-line study of enzyme reactions and derivatization protocols are reviewed. The article is divided into two parts: (i) in-line enzyme reactions and (ii) in-line derivatization. The first part introduces electrophoretically mediated microanalysis (EMMA) and discusses and illustrates the different modes of EMMA. A literature overview is provided, starting from 1996, and the investigated enzymes are classified into two tables based on the mode of engagement (i.e., continuous or transient) of the developed EMMA-based assay. The second part starts with an introduction of the procedures and the nomenclature used in the area of in-line derivatization protocols based on EMMA. Reported derivatization procedures are discussed and classified in tables, according to the functional group that is derivatized.     

Electrophoretically mediated microanalysis of gentamicin with in-capillary derivatization and UV detection.

This paper describes a system for integration of a one-step-microscale chemical derivatization and analysis by a methodology known as electrophoretically mediated microanalysis (EMMA). Differential electrophoretic mobility between an analyte, reagent, and their product offers EMMA a unique capability to selectively carry out electrophoretic mixing, control product formation, and separation. This system was successfully applied to perform derivatization and separation of the multicomponent aminoglycoside antibiotic gentamicin using 1,2-phthalic dicarboxaldehyde and mercaptoacetic acid as labeling reagents. A multivariate approach based on central composite experimental design was used to optimize the derivative yield. Full automation of the derivatization and analytical procedure, high derivatization efficiency, high sample throughput, and precision are the excellent features of the present method. In addition, this methodology offers short analysis time, as well as selectivity and sensitivity suitable for impurities determination. Separation of gentamicin C1, C1a, C2, C2a, C2b, sisomicin, and several minor components was achieved. For the first time separation and identification of three impurities, namely garamine, 2-deoxystreptamine, and paromamine are described.     

Rapid screening of aminopeptidase N inhibitors by capillary electrophoresis with electrophoretically mediated microanalysis

In this work, an electrophoretically mediated microanalysis (EMMA) method with a partial‐filling technique was setup to evaluate the inhibitory potency of novel compounds toward aminopeptidase N (APN). It was necessary to optimize the electrophoretic conditions with respect to the kinetic constraints and for attaining high sensitivity. In our setup, a part of the capillary was filled with the incubation buffer for the enzyme reaction, whereas the rest was filled with a suitable BGE for the separation of substrates and products. To monitor the performance of the newly developed method, the kinetic constants (K_m and V_max) for the catalyzed dissociation of l ‐Leucine‐p‐nitroanilide in the presence of APN as well as the inhibition constant (IC₅₀) of a known competitive inhibitor, that is bestatin, were determined and these results were compared with those obtained by a classical spectrophotometric assay. The developed EMMA method was subsequently applied to the screening of 30 APN inhibitors. Whereas the inhibition potency of these inhibitors (expressed in IC₅₀ values) were significantly underestimated by the EMMA method, the order of the inhibitory potential of these various compounds was found in agreement with the literature.     

Determination of kanamycin by electrophoretically mediated microanalysis with in-capillary derivatization and UV detection

An electrophoretically mediated microanalysis (EMMA) approach, used to perform on-line chemistry between two small molecules, has been characterized and optimized. The plug-plug type EMMA method involved electrophoretic mixing and subsequent reaction of nanoliter plugs of kanamycin-containing samples and 1,2-phthalic dicarboxaldehyde and mercaptoacetic acid within the confines of the capillary column, which acts as a microreactor. Analyses were performed by pressure-injecting a plug of kanamycin sandwiched in two reagent plugs. A potential of 375 Vcm(-1) was then applied to electrophoretically mix the two reactants, and an incubation time of up to 5 min allowed the reaction to proceed prior to the application of a separation potential of 588 Vcm(-1). UV detection was at 335 nm. The background electrolyte was 30 mM sodium tetraborate at pH 10.0, containing 16% of methanol. The method was validated in terms of linearity, limits of quantitation and detection, and precision. The method allows determination of kanamycin in bulk samples as a fully automated procedure.     

Electrophoretically mediated microanalysis of beta-galactosidase on microchips.

Electrophoretically mediated microanalysis (EMMA) is a method of accomplishing chemical analyses, typically in an open-tubular capillary, due to the difference in the electrophoretic mobility between the particular reagents. This work reports on combining this technique onto microfabricated systems. Two methods of this technique were applied, constant potential and zero potential EMMA onto chips. A dosage response curve was run using this constant potential mode that resulted in a linear response over three orders of substrate concentration magnitude. The chemical system used here is beta-galactosidase (beta-Gal) as the enzyme and fluorescein mono-beta-D-galactopyranoside (FMG) as the substrate. The zero potential mode was used to amplify product turnover using various incubation times. Using this technique and a 10 min incubation, approximately 40000 enzyme molecules could be detected. The zero potential mode is also used in conjunction with an internal standard to show how one can quantitate using this method. The power and ease of utility of this technique is described.     

Detection of the 35S promoter in transgenic maize via various isothermal amplification techniques: a practical approach

In 2003 the European Commission introduced a 0.9 % threshold for food and feed products containing genetically modified organism (GMO)-derived components. For commodities containing GMO contents higher than this threshold, labelling is mandatory. To provide a DNA-based rapid and simple detection method suitable for high-throughput screening of GMOs, several isothermal amplification approaches for the 35S promoter were tested: strand displacement amplification, nicking-enzyme amplification reaction, rolling circle amplification, loop-mediated isothermal amplification (LAMP) and helicase-dependent amplification (HDA). The assays developed were tested for specificity in order to distinguish between samples containing genetically modified (GM) maize and non-GM maize. For those assays capable of this discrimination, tests were performed to determine the lower limit of detection. A false-negative rate was determined to rule out whether GMO-positive samples were incorrectly classified as GMO-negative. A robustness test was performed to show reliable detection independent from the instrument used for amplification. The analysis of three GM maize lines showed that only LAMP and HDA were able to differentiate between the GMOs MON810, NK603, and Bt11 and non-GM maize. Furthermore, with the HDA assay it was possible to realize a detection limit as low as 0.5 %. A false-negative rate of only 5 % for 1 % GM maize for all three maize lines shows that HDA has the potential to be used as an alternative strategy for the detection of transgenic maize. All results obtained with the LAMP and HDA assays were compared with the results obtained with a previously reported real-time PCR assay for the 35S promoter in transgenic maize. This study presents two new screening assays for detection of the 35S promoter in transgenic maize by applying the isothermal amplification approaches HDA and LAMP.     

Electrophoretically mediated microanalysis with small molecules: the Jaffé method for creatinine carried out in a capillary tube

An eletrophoretically mediated microanalysis (EMMA) approach, used to perform online chemistry between two small molecules, has been characterized and optimized. The "plug-plug" type EMMA method involved electrophoretic mixing and subsequent reaction of nanoliter plugs of creatinine-containing samples and alkaline picrate (Jaffe reaction) within the confines of the capillary column, which acts as a microreactor. Analyses were performed by pressure injecting a plug of picrate followed by a plug of the creatinine-containing sample. A potential was then applied to electrophoretically mix the two reactants, and an incubation time of up to 6 min allowed the reaction to proceed prior to the application of a 27 kV separation potential with absorbance detection at 485 nm. The use of a 50 microm inner diameter(ID) extended light path capillary (150 microm pathlength) was found to be adequate for determining elevated levels of creatinine in human blood sera, but could not be used to quantify normal levels. Quantification of both normal and elevated levels of creatinine in sera was possible with a 75 microm ID high-sensitivity cell (1200 microm pathlength). Calibration plots using the latter for creatinine in human blood sera spanned the expected clinical range and were linear between 40 microM and 1.2 mM (r2 = 0.996) with an estimated limit of detection of 17 microM (signal-to-noise ratio S/N = 3). A quantitative comparison of results obtained with the reported EMMA method and accepted clinical methodology correlated very well (slope = 1.001).     

Asymmetric Diels–Alder and Inverse‐Electron‐Demand Hetero‐Diels–Alder Reactions of β,γ‐Unsaturated α‐Ketoesters with Cyclopentadiene Catalyzed by N,N′‐Dioxide Copper(II) Complex

Highly enantioselective Diels–Alder (DA) and inverse‐electron‐demand hetero‐Diels–Alder (HDA) reactions of β,γ‐unsaturated α‐ketoesters with cyclopentadiene catalyzed by chiral N,N′‐dioxide–Cu(OTf)₂ (Tf=triflate) complexes have been developed. Quantitative conversion of β,γ‐unsaturated α‐ketoesters and excellent diastereoselectivities (up to 99:1) and enantioselectivities (up to >99 % ee) were observed for a broad range of substrates. Both aromatic and aliphatic β,γ‐unsaturated α‐ketoesters were found to be suitable substrates for the reactions. Moreover, the chemoselectivity of the DA and HDA adducts were improved by regulating the reaction temperature. Good to high chemoselectivity (up to 94 %) of the DA adducts were obtained at room temperature, and moderate chemoselectivity (up to 65 %) of the HDA adducts were achieved at low temperature. The reaction also featured mild reaction conditions, a simple procedure, and remarkably low catalyst loading (0.1–1.5 mol %). A strong positive nonlinear effect was observed.     

聚二甲基硅氧烷芯片自由酶反应器检测葡萄糖

应用电泳中介微分析(EMMA)技术,构建聚二甲基硅氧烷(PDMS)芯片自由酶反应器, 在线检测葡萄糖(Glu),在十字形的芯片通道上,采用自制的碳纤维微电极检测葡萄糖氧化酶(GOD)催化氧化Glu生成的H2O2,并对检测电位、GOD浓度、GOD进样时间、分离电压等参数进行了优化,测定了该自由酶反应器的线性范围和检出限,考察了其重现性及稳定性.结果表明,此自由酶反应器制作方便,操作简单,重现性好,Glu浓度在0.1～20 mmol/L之间有较好的线性关系(r=0.997),检出限为19.8 μmol/L(S/N=3).     

Speciation of chromium by in-capillary derivatization and electrophoretically mediated microanalysis

An electrophoretic method for chromium speciation analysis--as Cr(III) and Cr(VI)--based on in-capillary derivatization with 1,5-diphenylcarbazide (DPC) is here proposed. As Cr(III) does not react with DPC, it was oxidized also in-capillary to Cr(VI) by Ce(IV). For this purpose, a capillary electrophoresis (CE) mode called electrophoretically mediated microanalysis (EMMA) based on sequential injection of sample and reagents--namely, DPC, sample and Ce(IV)--was employed. The conditions of both reactions--Cr(III) oxidation and Cr(VI)-DPC derivatization--were optimized in order to quantify separately the Cr(VI)-DPC complex from the original Cr(VI) in the sample and that from oxidation of Cr(III) to Cr(VI). The electrophoretic conditions were independently optimized for variables influencing the resolution and those affecting sensitivity. The method thus developed was applied to the determination of Cr(III) and Cr(VI) in glass material, for which different sample preparation methods--namely, EPA method 3060A, ultrasound-assisted leaching and microwave-assisted digestion--were tested. Microwave-assisted digestion was found to be the best sample preparation alternative in terms of efficiency of the step--99.6 and 98.3% for Cr(VI) and Cr(III), respectively--and procedure time--20 min. The complete method was validated with the certified reference material BAM-S004.     

变性高效液相色谱法在α-血红蛋白稳定蛋白基因检测中的应用

建立了采用变性高效液相色谱(DHPLC)对α-血红蛋白稳定蛋白(AHSP)基因进行基因分型和突变筛查的新方法。将AHSP基因序列分成6个片段,因第一、二、四、六个片段均含有1～2个常见单核苷酸多态性(single nucleotide polymorphism, SNP)位点,需单个标本分别进行检测;第三、五个片段不含有常见SNP位点,采用DHPLC结合DNA(脱氧核糖核酸)池的方法进行检测。以基因测序为金标准对所建立的AHSP基因检测方法进行方法学评价,结果显示: 40个样品的DHPLC检测结果与测序结果之间完全吻合,说明所建立的检测方法能对AHSP基因6种常见SNP进行准确基因分型。应用DHPLC对365个样品的AHSP基因进行检测,发现2个罕见SNP(11810 G＞A和12802 C＞T);同时还发现2个错义突变(AHSP D29V和AHSP V56G), AHSP D29V突变为新突变,AHSP V56G为罕见突变。结果表明采用DHPLC法可有效地对AHSP基因进行基因分型和突变筛查。     

Water's polyamorphic transitions and amorphization of ice under pressure

Transformations of water's high density amorph (HDA) to low density amorph (LDA) and of LDA's to cubic ice (Ic) have been studied by in situ thermal conductivity kappa measurements at high pressures. The HDA to LDA transformation is unobservable at p of 0.07 GPa, indicating that, for a fixed heating rate, an increase in pressure increases the temperature of HDA to LDA transformation and decreases that of LDA to ice Ic, causing thereby the two transformations to merge, and HDA appears to convert directly to ice Ic. Thus either LDA forms but converts extremely rapidly to ice Ic, or LDA does not form. At a fixed p and T, in the range of pressure amorphization of hexagonal ice, kappa continues to decrease with time. Therefore, the amorphization of ice Ih is kinetically controlled. When HDA at 1 GPa was heated from 130 to 157 K and densified to very HDA, its kappa increased by 3%. Our findings and a scrutiny of earlier reports show that a reversible transition between HDA and LDA does not occur at approximately 135 K and approximately 0.2 GPa. Since there is no unique HDA, it is difficult to justify the conjecture for a second critical point for water.     

Capillary electrophoretic approach to screen for enzyme inhibitors in natural extracts

This paper demonstrates development of electrophoretically mediated micro analysis (EMMA), for screening protein tyrosine phosphatase (PTP) inhibitors in natural extracts. It is demonstrated that capillary electrophoresis (CE) separation of the substrate and the product allows for using the assay in an on-column format to monitor the reaction without typically used fluorogenic substrates. Michaelis-Menten kinetics parameters calculated based on the EMMA results (Km = 1.2-1.5 microM) were in a good agreement (Km = 1.0-1.5 microM) obtained using an off-line CE functional assay (CE FA). EMMA of PTP titrated with different concentrations of ligand demonstrated the peak-shift phenomenon normally seen in affinity capillary electrophoresis. This feature of EMMA gives an indication of the binding affinity of the ligand in addition to its functional activity, providing another dimension in characterization of the protein-inhibitor interaction. It was demonstrated that simultaneous screening of the primary PTP target and a secondary, counter target (PTP-C) using the EMMA format can be used to prioritize hits based on their specificity.     

Sample stacking capillary electrophoretic microdevice for highly sensitive mini Y short tandem repeat genotyping

Lab‐on‐a‐chip provides an ideal platform for short tandem repeat (STR) genotyping due to its intrinsic low sample consumption, rapid analysis, and high‐throughput capability. One of the challenges, however, in the forensic human identification on the microdevice is the detection sensitivity derived from the nanoliter volume sample handling. To overcome such a sensitivity issue, here we developed a sample stacking CE microdevice for mini Y STR genotyping. The mini Y STR includes redesigned primer sequences to generate smaller‐sized PCR amplicons to enhance the PCR efficiency and the success rate for a low copy number and degraded DNA. The mini Y STR amplicons occupied in the 5‐ and 10‐mm stacking microchannels are preconcentrated efficiently in a defined narrow region through the optimized sample stacking CE scheme, resulting in more than tenfold improved fluorescence peak intensities compared with that of a conventional cross‐injection microcapillary electrophoresis method. Such signal enhancement allows us to successfully analyze the Y STR typing with only 25 pg of male genomic DNA, with high background of female genomic DNA, and with highly degraded male genomic DNA. The combination of the mini Y STR system with the novel sample stacking CE microdevice provides the highly sensitive Y STR typing on a chip, making it promising to perform high‐performance on‐site forensic human identification.     

Electronic structures and hydrogen bond network of high-density and very high-density amorphous ices

Electronic structures of hexagonal ice (ice Ih), high-density amorphous ice (HDA), and very high-density amorphous ice (VHDA) are investigated using ab initio density functional theory (DFT) at 77 K under a pressure of 0.1 MPa, focusing on band structure, density of states (DOS), partial density of states (PDOS), and electron density. It is found that the integration intensity of the O-2p bonding band in HDA is 1.53 eV wider than that in the VHDA. Because more 2p electrons in HDA participate the 2p-1s hybridization of O-H. The classical molecular dynamics (MD) method has further been carried out to analyze the hydrogen bond network of HDA and VHDA with larger numbers of water molecules under the same temperature, pressure, and boundary conditions used as those during the DFT calculation. MD results show that there exists some water molecules with five hydrogen bonds in both HDA (4.1 +/- 0.1%) and VHDA (2.8 +/- 0.1%), as compared with the LDA, being consistent with the integration intensity results of PDOS. This result can be used to interpret the physical nature of the similar transition temperature of HDA and VHDA to LDA with different heating rates.     

Strain discrimination of Yersinia pestis using a SERS-based electrochemically driven melting curve analysis of variable number tandem repeat sequences

Strain discrimination within genetically highly similar bacteria is critical for epidemiological studies and forensic applications. An electrochemically driven melting curve analysis monitored by SERS has been utilised to reliably discriminate strains of the bacterial pathogen Yersinia pestis, the causative agent of plague. DNA amplicons containing Variable Number Tandem Repeats (VNTRs) were generated from three strains of Y. pestis: CO92, Harbin 35 and Kim. These amplicons contained a 10 base pair VNTR repeated 6, 5, and 4 times in CO92, Harbin 35 and Kim respectively. The assay also included a blocker oligonucleotide comprising 3 repeats of the 10-mer VNTR sequence. The use of the blocker reduced the effective length of the target sequence available to bind to the surface bound probe and significantly improved the sensitivity of the discrimination. The results were consistent during three replicates that were carried out on different days, using different batches of PCR product and different SERS sphere segment void (SSV) substrate. This methodology which combines low cost, speed and sensitivity is a promising alternative to the time consuming current electrophoretic methods.     

Chromatographic determination of amines in biological fluids with special reference to the biological monitoring of isocyanates and amines. IV. Determination of 1,6-hexamethylenediamine in human urine using capillary gas chromatography and selective ion monitoring

A capillary gas chromatographic (GC) method was developed for the determination of 1,6-hexamethylenediamine (HDA) in hydrolysed human urine. The method was based on a derivatization procedure with heptafluorobutyric anhydride. The amides formed were determined using capillary GC with selected ion monitoring in the chemical ionization mode with ammonia as reagent gas. The overall recovery was 34% for a concentration of 100 micrograms/l of HDA in urine. The minimum detectable concentration in urine was below 0.5 microgram/l. The precision of the method was 5% (n = 9). Deuterium-labelled HDA [H2NC2H2(CH2)4C2H2NH2] was used as the internal standard. A male subject was exposed to hexamethylene diisocyanate (HDI) for 7.5 h in a test chamber. The average air concentration of HDI was ca. 30 micrograms/m3, which corresponds to ca. 85% of the threshold limit value in Sweden (35 micrograms/m3). The half time of urinary levels of HDA was ca. 1.4 h and more than 90% of the urinary elimination was completed within 4 h after the exposure. The amount of HDA excreted in urine was ca. 10 micrograms, corresponding to ca. 10% of the estimated inhaled dose of HDI.