Optimization of sequencing conditions using near-infrared lifetime identification methods in capillary gel electrophoresis

We have investigated the sample preparation and electrophoresis conditions necessary to prepare DNA sequencing samples appropriate for use with near-infrared (IR) fluorescent labels with dye identification accomplished via lifetime techniques. It was found that several sample preparation protocols required attention to maximize the fluorescence yields of the labeling dyes, such as thermal cycling conditions, choice of counter ion used for the ethanol precipitation step and also, dye-primer versus dye-terminator chemistries. In addition, several different sieving matrices were investigated for their effects on both the fluorescence properties of the labeling dyes and electrophoretic resolution. Extended times used for the high temperature denaturing of duplexed DNA fragments during cycle sequencing produced cleavage products, in which the covalently attached dye to the sequencing primer was released through attack by dithiothreitol (DTT). Even under optimized thermal cycling conditions, free dye was generated that masked readable data from the sequencing traces. Ethanol precipitation was necessary to remove this free dye with the proper choice of counter ion (sodium). The results using different sieving matrices indicated that linear polyacrylamides (LPAs) were appropriate for any fluorescence measurement, since they could readily be replaced between runs minimizing deleterious memory effects associated with cross-linked polyacrylamide gels. After investigation of several different sieving LPAs, the commercially available POP6 was found to be particularly attractive, since it produced good electrophoretic resolution, single exponential behavior for the near-IR dye series investigated herein, and also, discernible lifetime differences within the dye set. Finally, dye-terminator chemistry was also found to minimize bleeding in the gel matrix produced by large amounts of unextended dye-primer within the gel lane.     

Interdigitated array microelectrode based impedance immunosensor for detection of avian influenza virus H5N1

Continuous outbreaks of avian influenza (AI) in recent years with increasing threat to animals and human health have warranted the urgent need for rapid detection of pathogenic AI viruses. In this study, an impedance immunosensor based on an interdigitated array (IDA) microelectrode was developed as a new application for sensitive, specific and rapid detection of avian influenza virus H5N1. Polyclonal antibodies against AI virus H5N1 surface antigen HA (Hemagglutinin) were oriented on the gold microelectrode surface through protein A. Target H5N1 viruses were then captured by the immobilized antibody, resulting in a change in the impedance of the IDA microelectrode surface. Red blood cells (RBCs) were used as biolabels for further amplification of the binding reaction of the antibody-antigen (virus). The binding of target AI H5N1 onto the antibody-modified IDA microelectrode surface was further confirmed by atomic force microscopy. The impedance immunosensor could detect the target AI H5N1 virus at a titer higher than 10³ EID₅₀/ml (EID₅₀: 50% Egg Infective Dose) within 2 h. The response of the antibody-antigen (virus) interaction was shown to be virus titer-dependent, and a linear range for the titer of H5N1 virus was found between 10³ and 10⁷ EID₅₀/ml. Equivalent circuit analysis indicated that the electron transfer resistance of the redox probe [Fe(CN)₆]^3−/4− and the double layer capacitance were responsible for the impedance change due to the protein A modification, antibody immobilization, BSA (bovine serum albumin) blocking, H5N1 viruses binding and RBCs amplification. No significant interference was observed from non-target RNA viruses such as Newcastle disease virus and Infectious Bronchitis disease virus. (The H5N1 used in the study was inactivated virus.)     

Nanoliter-scale sample preparation methods directly coupled to polymethylmethacrylate-based microchips and gel-filled capillaries for the analysis of oligonucleotides.

We are currently developing miniaturized, chip-based electrophoresis devices fabricated in plastics for the high-speed separation of oligonucleotides. One of the principal advantages associated with these devices is their small sample requirements, typically in the nanoliter to sub-nanoliter range. Unfortunately, most standard sample preparation protocols, especially for oligonucleotides, are done off-chip on a microliter-scale. Our work has focused on the development of capillary nanoreactors coupled to micro-separation platforms, such as micro-electrophoresis chips, for the preparation of sequencing ladders and also polymerase chain reactions (PCRs). These nanoreactors consist of fused-silica capillary tubes (10-20 cm x 20-50 microns I.D.) with fluid pumping accomplished using the electroosmotic flow generated by the tubes. These reactors were situated in fast thermal cyclers to perform cycle sequencing or PCR amplification of the DNAs. The reactors could be interfaced to either a micro-electrophoresis chips via capillary connectors micromachined in polymethylmethacrylate (PMMA) using deep X-ray etching (width 50 microns; depth 50 microns) or conventional capillary gel tubes using zero-dead volume glass unions. For our chips, they also contained an injector, separation channel (length 6 cm; width 30 microns; depth 50 microns) and a dual fiber optic, near-infrared fluorescence detector. The sequencing nanoreactor used surface immobilized templates attached to the wall via a biotin-streptavidin-biotin linkage. Sequencing tracks could be directly injected into gel-filled capillary tubes with minimal degradation in the efficiency of the separation process. The nanoreactor could also be configured to perform PCR reactions by filling the capillary tube with the PCR reagents and template. After thermal cycling, the PCR cocktail could be pooled from multiple reactors and loaded onto a slab gel or injected into a capillary tube or microchip device for fractionation.     

Photoelectron spectroscopic characterization of vapors over heated alkali metaborate solids

The He(I) photoelectron spectra of the gaseous metaborates of K, Rb, and Cs have been obtained using a modified high-temperature cylindrical-mirror electron spectrometer equipped with a resistance-heated sample oven. Attempts to acquire data for LiBO₂ and NaBO₂ were unsuccessful because of the high temperature required for volatilization (on the order of 1300–1400 K). The identities of the vapor-phase molecules were based on mass spectrometric and electron diffraction data. Spectral lines were assigned molecular-orbital origins through the use of MO calculations and by analogy with other compounds of similar type.     

The photoelectron spectroscopic characterization of vapors above heated alkali tetrafluoroaluminates,alkali tetrachloroaluminates,and ammonium tetrachloroaluminate

The high-temperature He(I) photoelectron spectra of gas-phase alkali tetrafluoroaluminates, alkali tetrachloroaluminates, and ammonium tetrachloroaluminate have been obtained. The identities of the vapor-phase entities were assigned from data derived by electron diffraction, mass spectrometry, and matrix-isolation and vapor infrared spectroscopies. The ionization energies observed in the spectra have been assigned molecular-orbital origins through the use of theoretical calculations and comparisons with analogous compounds.     

A simple method for urine estrogen determination of nonpregnant women

Summary A new method for quantitating urinary estrogen by gasliquid chromatography is described. A minimum of 50 cm³ of urine sample is required for the preliminary enzyme hydrolysis. The hydrolysate is extracted with a mixture of ether and ethyl acetate followed by multiple washes or rotary evaporation to eliminate interfering emulsions. The estrogen fractions are silylated, concentrated and chromatographed on a 3% OV-225 column. This method combines the advantages of several procedures while eliminating many of the adverse reactions previously encountered. The method is sufficiently sensitive to quantitate estrogens in the nanogram range.     

Tailoring plasmonic substrates for surface enhanced spectroscopies

Our understanding of how the geometry of metallic nanostructures controls the properties of their surface plasmons, based on plasmon hybridization, is useful for developing high-performance substrates for surface enhanced spectroscopies. In this tutorial review, we outline the design of metallic nanostructures tailored specifically for providing electromagnetic enhancements for surface enhanced Raman scattering (SERS). The concepts developed for nanoshell-based substrates can be generalized to other nanoparticle geometries and scaled to other spectroscopies, such as surface enhanced infrared absorption spectroscopy (SEIRA).