Microfluidic genetic analysis with an integrated a-Si:H detector.

We have developed an integrated hydrogenated amorphous silicon (a-Si:H) fluorescence detector for microfluidic genetic analysis. It consists of a half-ball lens, a ZnS/YF3 multilayer optical interference filter with a pinhole, and an annular a-Si:H PIN photodiode allowing the laser excitation to pass up through the central aperture in the photodiode and the filter. Microfluidic separations of multiplex PCR products generated from methicillin-resistant/sensitive Staphylococcus aureus (MRSA/MSSA) DNA on microfluidic capillary electrophoresis (CE) devices are successfully detected with the integrated detector. Similarly, multiplex PCR amplicons from the kanamycin resistant and K12 serotype-specific genes of E. coli cells are detected. The direct detection of multiplex PCR amplicons indicates that the fluorescence detector can be successfully coupled with current microfluidic PCR-CE platforms. This work establishes that the integrated a-Si:H detector provides relevant limits of detection for point-of-care genetic and pathogen analysis with microfluidic devices.

Integrated portable genetic analysis microsystem for pathogen/infectious disease detection.

An integrated portable genetic analysis microsystem including PCR amplification and capillary electrophoretic (CE) analysis coupled with a compact instrument for electrical control and laser-excited fluorescence detection has been developed. The microdevice contains microfabricated heaters, temperature sensors, and membrane valves to provide controlled sample positioning and immobilization in 200-nL PCR chambers. The instrument incorporates a solid-state laser and confocal fluorescence detection optics, electronics for sensing and powering the PCR reactor, and high-voltage power supplies for conducting CE separations. The fluorescein-labeled PCR products are amplified and electrophoretically analyzed in a gel-filled microchannel in <10 min. We demonstrate the utility of this instrument by performing pathogen detection and genotyping directly from whole Escherichia coli and Staphylococcus aureus cells. The E. coli detection assay consists of a triplex PCR amplification targeting genes that encode 16S ribosomal RNA, the fliC flagellar antigen, and the sltI shigatoxin. Serial dilution demonstrates a limit of detection of 2-3 bacterial cells. The S. aureus assay uses a femA marker to identify cells as S. aureus and a mecA marker to probe for methicillin resistance. This integrated portable genomic analysis microsystem demonstrates the feasibility of performing rapid high-quality detection of pathogens and their antimicrobial drug resistance.

High-pressure gel loader for capillary array electrophoresis microchannel plates.

Microfabricated capillary array electrophoresis (microCAE) microchannel plates are the next generation of bioanalytical separation devices. To fully exploit the capabilities of microCAE devices, supporting technology such as robotic sample loading, gel loading, microplate washing, and data analysis must be developed. Here, we describe a device for loading gel into radial capillary array electrophoresis microplates and for plate washing and drying. The microplates are locked into a loading module, and high-pressure helium is used to drive aqueous separation media or wash solutions into the microchannels through fixtures connected to the central anode reservoir. Microplates are rapidly (30 s to 5 min) loaded with separation media, such as 3%-4.8% linear polyacrylamide or 0.7%-3.0% hydroxyethyl cellulose, for electrophoresis. The effective and rapid gel-filling and plate-cleaning methods together with short electrophoretic analysis times (2-30 min) make microCAE systems versatile and powerful nucleic acid analysis platforms.

High-performance genetic analysis using microfabricated capillary array electrophoresis microplates.

This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.

Genotyping energy-transfer-cassette-labeled short-tandem-repeat amplicons with capillary array electrophoresis microchannel plates.

BACKGROUND: Genetic analysis of microsatellite DNA is a powerful tool used in linkage analysis, gene mapping, and clinical diagnosis. To address the expanding needs of studies of short tandem repeats (STRs), we demonstrated high-performance STR analysis on a high-throughput microchannel plate-based platform. METHODS: Energy-transfer-cassette-labeled STR amplicons were separated and typed on a microfabricated 96-channel radial capillary array electrophoresis (CAE) microchannel plate system. Four-color detection was accomplished with a laser-excited confocal fluorescence rotary scanner. RESULTS: Multiplex STR analysis with single base-pair resolution was demonstrated on denaturing polyacrylamide gel media. The high-throughput multiplex capabilities of this genetic analysis platform were demonstrated by the simultaneous separation of STR amplicons representing 122 samples in ninety-six 5.5-cm-long channels in <8 min. Sizing values obtained for these amplicons on the CAE microchannel plate were comparable to those measured on a conventional commercial CAE instrument and exhibit <1% sizing variance. CONCLUSIONS: Energy-transfer-cassette labeling and microfabricated CAE microchannel plates allow high-performance multiplex STR analyses.

Conversion of capillary electrophoresis microchip genotyping data for analysis with Genetic Profiler software.

The collection and conversion of 4-color fluorescent genotyping data from capillary array electrophoresis microchip devices and its conversion to a format easily and rapidly analyzed by Genetic Profiler genotyping software is presented. Microchip fluorescence intensity data are acquired and stored as 4-color tab-delimited text. These files are converted to electrophoretic signal data (ESD) files using a utility program (TEXT-to-ESD) written in C. TEXT-to-ESD generates an ESD file by converting text data to binary data and then appending a 632-byte ESD-file trailer. Up to 96 ESD files are then assembled into a run folder and imported into Genetic Profiler, where data are reduced to 4-color electropherograms and analyzed. In this manner, DNA fragment sizing data acquired with our high-speed electrophoretic microchip devices can be rapidly analyzed using robust commercial software. Additionally, the conversion program allows sizing of data with Genetic Profiler that have been preprocessed using other third-party software, such as BaseFinder.

Radial capillary array electrophoresis microplate and scanner for high-performance nucleic acid analysis.

The design, fabrication, and operation of a radial capillary array electrophoresis microplate and scanner for high-throughput DNA analysis is presented. The microplate consists of a central common anode reservoir coupled to 96 separate microfabricated separation channels connected to sample injectors on the perimeter of the 10-cm-diameter wafer. Detection is accomplished by a laser-excited rotary confocal scanner with four color detection channels. Loading of 96 samples in parallel is achieved using a pressurized capillary array system. High-quality separations of 96 pBR322 restriction digest samples are achieved in < 120 s with the microplate system. The practical utility and multicolor detection capability is demonstrated by analyzing 96 methylenetetrahydrofolate reductase (MTHFR) alleles in parallel using a noncovalent 2-color staining method. This work establishes the feasibility of performing high-throughput genotyping separations with capillary array electrophoresis microplates.

Ultra-high throughput rotary capillary array electrophoresis scanner for fluorescent DNA sequencing and analysis.

We have constructed a rotary confocal fluorescence scanner and capillary array electrophoresis system that is designed to analyze over 1000 DNA sequencing or fragment sizing separations in parallel. Capillaries are arranged around the surface of a cylinder and a rotating objective in the middle of the cylinder excites and collects fluorescence from labeled DNA fragments as they pass the capillary detection window. The capillaries are pressure-filled with a replaceable matrix and the samples are electrokinetically injected in parallel from a stainless steel microtiter plate at the cathode end. We demonstrate that the instrument is capable of producing four-color data from all capillaries at a scan rate of 4 Hz (corresponding to a linear scan velocity of 121 cm/s). M13 sequencing data were obtained using a 128 capillary array mounted in half of the first quadrant of the scanner. In this initial run, read lengths greater than 500 bases were obtained in over 60% of the capillaries.

DNA sequencing using a four-color confocal fluorescence capillary array scanner.

The design, construction and operation of a four-color capillary array electrophoresis scanner are presented. The use of sensitive energy transfer primers facilitates four-color detection of the DNA sequencing fragments following excitation at a single laser wavelength (488 nm). This scanner collects fluorescence data from up to 25 capillaries in parallel. The resulting four-color image files are automatically reduced to four-color line plots, and a base-calling program (Sax) is used to call the sequence. The performance of this system for DNA sequencing is demonstrated by examining twelve different motifs of the hypervariable region I of human mitochondrial (mt) DNA obtained from a Sierra Leone population.

Design and synthesis of fluorescence energy transfer dye-labeled primers and their application for DNA sequencing and analysis.

We have designed and synthesized fluorescent oligonucleotide primers having improved fluorescence and electrophoretic properties by exploiting the concept of resonance fluorescence energy transfer (ET). These primers carry a fluorescein derivative at the 5' end as a common fluorescence donor and other fluorescein and rhodamine derivatives attached to a modified thymidine within the primer sequence as acceptors. These primers all have strong absorption at a common excitation wavelength (448 nm) and fluorescence emission maxima of 525, 555, and 605 nm. The fluorescence emission intensity of the ET primers increases as the spacing between the donor and acceptors is increased, and of the spacings studied the strongest fluorescence was observed when the number of nucleotides between the donor and acceptors is 10. The electrophoretic mobilities of the primers were also found to be a function of the spacing between the donor and the acceptors, and mobilities of the single base extension DNA fragments generated with primers (F10F, F10J, F10T, and F10R) is 2- to 14-fold greater than that of the corresponding primers labeled with only one dye. The increased fluorescence intensity of the ET primers and the substantially similar mobilities of the DNA fragments generated with the four ET primers allow four-color DNA sequencing on a capillary electrophoresis DNA sequencer using a single laser line at 488 nm for excitation and without applying mobility shift adjustments. With single-stranded M13mp18 DNA as the template, a typical run with the ET primers on a commercial sequencer provided DNA sequences with 99-100% accuracy in the first 500 bases using 8-fold less DNA template than that typically required using T7 DNA polymerase.

On the position of the hydro-phobic/philic boundary in lipid bilayers.

The sensitivity of calculated structural dimensions of hydrated lipids to the position of the hydrophobic/hydrophilic boundary is reviewed. The position of this boundary is critical in determining the extent of hydration and location of water in the bilayer. A calculation of the dimensions of the hydrophilic and hydrophobic parts of the phosphatidylcholine and ethanolamine bilayer from literature values of the x-ray long spacing shows that the choice of boundary in phospholipids is not arbitrary and is best placed at the average position of the first CH(2) group in the hydrocarbon chains. Calculated dimensions of the hydrocarbon core and the water accessible regions agree with neutron and x-ray diffraction measurements. Hydration differences between phosphatidylcholines and phosphatidylethanolamines are readily explained from derived estimates of the layers of water which cover these headgroups.

Dependence of lipid chain and head group packing of the inverted hexagonal phase on hydration.

A model which positions the hydrophobic/hydrophilic boundary in phosphatidylethanolamine lipids at the first CH(2) group in the acyl or alkyl chain is used to calculate the surface area per lipid, the mean chain and head-group dimensions and diameters of the hydrophilic tubes of the inverted hexagonal phase of didodecylphosphatidylethanolamine. The calculated surface areas compare favorably with areas obtained for the lamellar liquid crystal phase of the same lipid using the same boundary. Placement of the boundary within the lipid structure permits a determination of the maximum headgroup packing at hydration levels down to complete dehydration. The headgroup dimensions are consistent with a 5 A diam void at the center of a hydrophilic tube at zero hydration. The calculated mean fluid chain length is approximately 2 A smaller than the mean chain length of the lamellar phase at comparable levels of hydration. Comparison of the calculated mean fluid chain length and distances between hydrophobic boundaries shows that the fluid chains are interdigitated between adjacent tubes, and not interdigitated in the central space between three tubes. At low hydration the chains interdigitate in both spaces. The number of lipids packed around a tube at low hydration is only a function of the headgroup geometry, whereas at high hydration, it is a function of the number of carbon atoms in the chains.

The partial molar volume of water in biological membranes.

A new algorithm is presented for interpreting the hydration dependence of x-ray diffraction measurements. The method assumes that the volume of the hydrocarbon phase of the lipid bilayer is not affected by hydration and that the volume expansion between bilayers at maximum hydration is caused by incorporation of water molecules whose partial molar volume is that of pure bulk water. These simple assumptions lead to a determination of the area expansion (and hence change in hydrocarbon-phase thickness) as a function of hydration. An analysis is made of x-ray data of the L alpha and L beta' phases of dimyristoyl phosphatidylcholine and the L alpha phase of egg phosphatidylcholine. The partial molar volume of water depends critically on the degree of lipid hydration and the presence of voids between the head groups of adjacent lipids. The calculated head-group spacings at minimum hydration are consistent with those obtained from neutron diffraction and indicate that the methyl groups of the choline are almost in contact with corresponding groups in the opposing bilayer. This calls into question the origin of the repulsive forces observed in dehydration experiments.

Effects of chain packing and chain mobility on the Raman spectra of biomembranes.

The degree of lateral crystal-like order between hydrocarbon chains in biomembrane systems can be estimated from Raman measurements in the C-H stretching region. Observations of the temperature dependence of the Raman spectra of crystalline n-C16H34 and the urea clathrate of n-C16H34 have enabled us to separate to some extent the overlapping effects of chain packing and chain mobility, effects that are normally not distinguished in considering lateral order. The mobility is associated with the freedom of an extended chain to rotate and twist about its long axis. A high degree of such motion must be ascribed to n-C16H34 in a urea clathrate in order to explain the unusual temperature behavior observed for Raman bands at 2885 and 1174 cm-1. Comparison of the temperature behavior of the Raman spectra of the clathrate with that of crystalline n-C16H34 permits the effects due to packing and to mobility to be distinguished. The same effects can be expected to be present in the Raman spectra of biomembranes.

Removal of I(2)absorption lines from 514-nm excited Raman spectra.

The intense excitation of an Ar(+) laser operating at 514 nm enhances the grating ghosts and general stray light within most double monochromators at wavelengths close to the exciting line. The I(2) filter technique provides an effective means of reducing this interference and, in so doing, makes possible the measurement of Raman bands close to the exciting line. However, at an instrument resolution less than 3 cm(-1), the I(2) absorption spectrum seriously interferes with the Raman spectrum. Ratioing the Raman spectrum with a white light absorption spectrum of I(2) removes the I(2) absorption lines. However, with slit widths <3 cm(-1), the wavelength reproducibility of the monochromator on successive scans is not high enough to insure successful ratioing. A technique is described for obtaining, approximately within the same time interval, the Raman spectra and white light spectrum at each wavelength that data are acquired. This procedure accurately removes the I(2) absorption spectrum.

Resonance Raman spectra of iron(III)-, copper(II)-, cobalt(III)-, and manganese(III)-transferrins and of bis(2,4,6-trichlorophenolato)diimidazolecopper(II) monohydrate, a possible model for copper(II) binding to transferrins.

Fe(III), Cu(II), Co(III), and Mn(III) complexes of ovo- and human serum transferrins show resonance enhanced Raman bands near 1600, 1500, 1270, and 1170 cm-1 upon excitation with laser frequencies which fall within the visible absorption bands of those metalloproteins. Comparison of the visible absorption and resonance Raman spectra of the Cu(II)-transferrin complexes with those for the Cu(II) model compound, bis(2,4,6-trichlorophenolato)diimidazolecopper(II) monohydrate, indicates that the resonance Raman bands are due to enhancement of phenolic vibrational modes. For the model (Cu(II) compound, a normal coordinate analysis was used to aid our assignment of the observed resonance bands at 1562, 1463, 1311, and 1122 cm-1 to A1 vibrational modes of the 2,4,6-trichlorophenolato moiety. These assignments are consistent with those made for Cu(II)-transferrins. The latter assignments were based upon calculated A1 frequencies for p-methylphenol (Cummings, D.L., and Wood, J.L. (1974), J. Mol. Struct. 20, 1). The wavelength shifts in the resonance bands for the model compound from those for Cu(II)-transferrins are due to the influence of the chloro substituents on the planar vibrations of phenol. These results clearly identify tyrosine as a ligand in copper binding to transferrins.

Raman spectra of a solid antifreeze glycoprotein and its liquid and frozen aqueous solutions.

Raman spectroscopy was used to study the anomalous decrease in the freezing temperature of water produced by an antifreeze glycoprotein obtained from the sera of an Antarctic fish. An active fraction of this glycoprotein has a molecular weight of approximately 18,000 by equilibrium sedimentation compared to an apparent weight of 20 by freezing temperature depression. The Raman spectra of water present in a 1% antifreeze glycoprotein solution and of ice frozen from this solution were indistinguishable from the spectra of pure water and ice, respectively. These results indicate that the bulk properties of water and ice are unaffected by the presence of the antifreeze glycoprotein. Raman measurements on ice grown slowly, using as seed an oriented single crystal of ice in contact with 1% glycoprotein solutions, showed that the active glycoprotein was not excluded from the ice phase. On the other hand, we found that a smaller, inactive glycoprotein was excluded. Comparison of the Raman spectra of active and inactive glycoprotein components as solids, in 5% solutions, and rapidly frozen 5% solutions, showed that the two components differ in conformation and possibly in the environment of their carbohydrate hydroxyls. These observations suggest that hydrogen bonding of the carbohydrate hydroxyls of the active glycoprotein at the ice-solution interface may physically prevent growth of the ice lattice.

On-line acquisition of data from Raman and infrared spectrometers with a time-sharing computer.

Considerations leading to the interface and software design of an on-line data acquisition system are presented. The system makes extensive use of conversation mode programing and the nature and extent of the operator-computer program interactions are discussed. The system employs close-loop control of the acquisition process with the possibility of operator intervention at any stage. Control actions and data reduction may be initiated asynchronous to the data acquisition process. An illustration of the use of the system for correcting relative Raman intensities is given.