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Biomedical subjects

L B McGown

Publications and source records attributed to L B McGown.

At least 19 recordsLinked to original sources
PubMed2001

Open-tubular capillary electrochromatography of bovine beta-lactoglobulin variants A and B using an aptamer stationary phase.

DNA aptamers that form a G-quartet conformation were covalently attached to a capillary surface for open-tubular capillary electrochromatographic separation of bovine beta-lactoglobulin variants A and B, which vary by 2 of their 162 amino acid residues. Separation was achieved using a 4-plane, G-quartet aptamer stationary phase with tris(hydroxymethyl)aminomethane (Tris) or phosphate buffer as the mobile phase. In control experiments, separation did not occur using either an oligonucleotide of similar base composition but which does not form a G-quartet structure, or using capillary zone electrophoresis on a bare capillary under similar experimental conditions. Separation was achieved using a capillary coated only with the covalent linker molecule. In phosphate buffer, the separations were similar for aptamer-coated and linker-only stationary phases, while in Tris buffer, retention times were almost doubled for the linker-only capillary. When Tris buffer is the mobile phase, there appears to be weaker interactions between the proteins and the stationary phase that may result in a gentler, less denaturing separation than is commonly achieved using hydrocarbon-based stationary phases.

Animals↗
PubMed2001

Comparison of sieving matrices for on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments.

Commercially available, replaceable sieving matrices and their solvent modulated forms were evaluated for use in on-the-fly fluorescence lifetime detection of dye-labeled DNA fragments in capillary electrophoresis. The fragments were labeled with dyes that can be excited by the 488 nm line of an argon ion laser and have lifetimes in the range of 0.8 ns to 3.8 ns. The sieving matrices and buffer systems included poly(vinylpyrrolidone) (PVP), poly(ethyleneoxide) (PEO), hydroxyethylcellulose (HEC), Tris-borate-EDTA (TBE) and Tris-TAPS-EDTA buffers modified with DMSO and formamide. Selection of the optimal sieving matrix is based on the separation efficiency and the enhancement of lifetime resolution of DNA fragments. Best results for both electrophoretic resolution and lifetime detection were obtained using a poly(ethyleneoxide)/TBE gel buffer in the presence of 10% formamide.

Base Sequence↗
PubMed2000

DNA sequencing by capillary electrophoresis with four-decay fluorescence detection.

A scheme for multiplex detection of dye-labeled DNA fragments in DNA sequencing is described in which on-the-fly, frequency-domain fluorescence lifetime detection is used to discriminate among the dye-labeled fragments of the four terminal bases in a single-lane CE separation. Two four-dye systems were evaluated, one excited at 488 nm and the other, at 514 nm. The 488 nm system proved successful for four-decay detection. Base calling was achieved either directly from on-the-fly lifetimes or from lifetime-resolved electropherograms recovered for each base from the electropherogram of the mixture of sequencing reaction products. The latter method was found to be more accurate (99% for two bases and 98.5% for three bases) and could achieve longer read lengths, but it was unsuccessful for sequencing of all four bases. The first method gave a base-calling accuracy of 96% for four-base sequencing over the fragment length range of 41-220 bases.

Base Sequence↗
PubMed2000

Fluorescence lifetime for on-the-fly multiplex detection of DNA restriction fragments in capillary electrophoresis.

This paper describes the first use of frequency-domain fluorescence lifetime for multiplex detection of DNA restriction fragments in capillary electrophoresis (CE). The fragments were labeled with monomeric intercalating dyes that can be excited by either the 488- or 514-nm line of an argon ion laser and have lifetimes in the range of 0.5-2.5 ns. We were able to achieve multiplex lifetime detection in the CE separation of a restriction fragment digest and a DNA size ladder in the same run, for fragments shorter than 700 bp. Different gel buffer systems, including a modified polyacrylamide gel and several tris-borate-EDTA/hydroxyethylcellulose (TBE/HEC) gels, were investigated for separation and detection of the dye-labeled DNA fragments. Best results for both electrophoretic resolution and lifetime detection were obtained using a gel containing 1% high molecular weight (90,000-105,000) HEC and 0.3% low molecular weight (24,000-27,000) HEC in TBE buffer.

DNA↗
PubMed2000

Separation of nontarget compounds by DNA aptamers.

The ability of DNA aptamers to separate nontarget compounds is demonstrated. Two G-quarter forming aptamers, a 15-mer and a 20-mer, were covalently linked to fused silica capillary columns to serve as stationary-phase reagents in capillary electrochromatography. Separations of binary mixtures of amino acids (D-trp and D-tyr), enantiomers (D-trp and L-trp), and polycyclic aromatic hydrocarbons were achieved. Aptamers offer several attractive features for stationary-phase reagents, including ease of synthesis and of attachment to surfaces and modification of their binding properties through minor changes in sequence.

DNA↗
PubMed2000

Improving signal to background ratio for on-the-fly fluorescence lifetime detection in capillary electrophoresis.

On-the-fly fluorescence lifetime detection (OFLD) in capillary electrophoresis (CE) was previously demonstrated using a commercial multiharmonic Fourier transform (MHF) spectrofluorometer interfaced to a commercial CE system. This paper discusses optimization of the interface design for minimization of background fluorescence and scattered light, thereby maximizing the signal-to-background ratio (S/B) of the dynamic measurement. Strategies included using various combinations of optical filters including a holographic filter and longpass or bandpass filters, tilting the capillary relative to the incident laser beam, employing a confocal design and adding an iris to remove out-of-focus light, using a microscope objective in the emission beam to increase the collection efficiency, and using square instead of ciruclar capillary columns. Significant improvements in S/B for on-column, on-the-fly detection of fluorescein in CE were achieved with most modifications.

Electrophoresis, Capillary↗
PubMed1999

Effects of gel material on fluorescence lifetime detection of dyes and dye-labeled DNA primers in capillary electrophoresis.

Investigations of fluorescence lifetimes of the dye 6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]hexanoic acid (NBD-HA) and of DNA M13 primers labeled with NBD-HA, Cy3, rhodamine green and 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene++ +-3-propionic acid (BODIPY-FL) dyes in polyacrylamide gels of various degrees of crosslinking and different crosslinkers, and in a cellulose sieving buffer with different organic modifiers, are described. The dependence of fluorescence lifetime on gel matrix and on experimental conditions was studied in order to identify which factors may be important for optimization of multiplex fluorescence lifetime detection. Lifetimes were determined in both batch solution and on-the-fly, on-column in CE. Results show that lifetimes of the primer-attached dyes remain constant in gels of different composition. Additionally, multiexponential fluorescence decays are observed for primer-attached dyes in batch solutions of the cellulose sieving buffers but are reduced to monoexponential decays when measured on-the-fly, on-column in CE. Lifetime detectability can be improved by addition of an organic modifier to the gel matrix.

Acrylic Resins↗
PubMed1998

On-the-fly fluorescence lifetime detection of dye-labeled DNA primers for multiplex analysis.

Mixtures of dye-labeled, M13-forward DNA primers were separated by capillary gel electrophoresis and detected on-the-fly, using fluorescence lifetime measurements, to evaluate four-decay detection for multiplex DNA sequencing. Three different four-dye systems were used, two that were excited at 488 nm and one that was excited at 514 nm. Each dye-labeled primer was identified on the basis of the lifetime of the conjugated dye using nonlinear least squares or the maximum entropy method to analyze the lifetime data. Overlapping electrophoretic peaks were generated by making multiple injections of mixtures of the dye-labeled primers. The overlapping peaks were resolved by fitting the data to two-, three- or four-component lifetime models used in nonlinear least-squares analysis in which each lifetime component was fixed to the predetermined lifetime of the corresponding dye-labeled primer. In two of the dye systems, the lifetimes of the four dye-labeled primers were sufficiently different to allow peak resolution. In the other dye system, addition of 10% DMSO to the run buffer changed the lifetime of one dye-labeled primer, allowing it to be resolved from another dye-labeled primer with similar lifetime.

DNA Primers↗
PubMed1998

Spectroscopic studies of single-stranded DNA ligands and oxazole yellow dyes.

Interactions between short single-stranded DNA ligands and fluorescent DNA indicator dyes were used to investigate binding selectivity of the ligands. Conformational differences among four DNA ligands of different sequence and structure, including two that form a G-quartet and two that do not, were confirmed by circular dichroism spectroscopy. Their interactions with indicator dyes YO-pro-1 iodide (YO) and YOYO-1 iodide (YOYO) were probed using measurements of dye absorbance; induced circular dichroism; and fluorescence spectra, anisotropy, and lifetime. Equilibrium binding constants and stoichiometry were determined as well. Results indicate significant differences among the dye interactions and binding stoichiometries of the four ligands. One of the G-quartet forming ligands, a 20-mer of sequence 5'-GGTTTTGGTTTTGGTTTTGG-3', shows distinctly different interactions from the other three ligands, all of which are 15-mers. These studies illustrate the importance of sequence and conformation in determining the binding interactions of short single-stranded DNA.

Base Sequence↗
PubMed1998

Oxazole yellow dye interactions with short DNA oligomers of homogeneous base composition and their hybrids.

Interactions between short single-stranded DNA oligomers of homogeneous base composition and the fluorescent probes oxazole yellow (YO) and its homodimer YOYO are described. The oligomers included 15-mers and 30-mers of polydA, polydT, polydG, and polydC. Interactions between the dyes and DNA hybrids formed from complementary homogeneous strands of equal length were also investigated. No interactions were observed between the dyes and the monomeric monophosphate nucleosides A, G, T, or C. The dyes were found to interact much more strongly with the purine oligomers polydA and polydG than with the pyrimidine oligomers polydT and polydC. PolydA of both lengths has strong interactions with YOYO, whereas the polydG 30-mer interacts strongly with monomeric YO. The 15-mers of polydG and polydC of both lengths show little interaction with either dye. Interactions of the dyes with the polydA/polydT and polydG/polydC hybrids tend to be dominated by interactions with polydA and polydG, respectively. Although dye interactions generally were facilitated by hybridization, particularly for polydA/polydT, the interactions were similar to those with the single strands and different from those that have been observed in long double-stranded DNA.

Base Composition↗
PubMed1997

On-the-fly fluorescence lifetime detection of labeled DNA primers.

The first application of frequency-domain, on-the-fly fluorescence lifetime detection to the detection, identification and resolution of fluorescent labeled oligonucleotide primers in capillary electrophoresis is presented. These studies, which are directed towards the development of four-decay DNA sequencing, employed two common sequencing primers, SP6 and M13/pUC. The primers were each tagged by a derivative of either fluorescein or BODIPY. Fluorescence emission maxima and lifetimes of the free dyes and the labeled primers were determined both in batch mode and on-the-fly in capillary electrophoresis. Fluorescence intensity and lifetime electropherograms were extracted from dynamic lifetime data that were acquired at 0.1-s intervals during the CE separation. Lifetimes were recovered using either conventional non-linear least-squares analysis or the self-modeling maximum entropy method, which does not require prior knowledge of the system. Based on migration time and fluorescence lifetime, peaks could be detected and identified, and co-eluting peaks could be resolved. Interference from background impurities and scattered light was greatly reduced by the combination of physical separation and lifetime resolution.

DNA Primers↗
PubMed1997

Characterization of visible dyes for four-decay fluorescence detection in DNA sequencing.

Dyes of several classes were investigated as candidates for use in a multiplex, four-decay fluorescence detection scheme for DNA sequencing. The dyes include nitrobenzofuran dyes, rhodamine dyes, fluorescein dyes, cyanine dyes, Nile Red, and BODIPY dyes. Based on the results of fluorescence spectral and lifetime studies, an initial set of four dyes was selected for further study: NBD-aminohexanoic acid (NBD-HA, r = 1.1 ns), tetramethyl-rhodamine, methyl ester (r = 2.2 ns), rhodamine green (r = 4.3 ns), and BODIPY 505/515 (r = 5.9 ns). Limits of lifetime detection of the four dyes were investigated, and lifetime resolution was demonstrated for mixtures of the free dyes in batch solution. Lifetime of dye-labeled DNA primers also were determined in batch solution and detected on-the-fly in capillary electrophoresis (CE). Conjugation of the dyes to DNA improved the resolution of their individual lifetimes in mixtures in batch measurements. When attached to the primer, tetramethyl-rhodamine exhibited biexponential decay with a dominant lifetime of 3.8 ns, making it unsuitable for four-decay sequencing. Contact with the CE gel lengthened the lifetime of NBD-HA-labeled primer from 1.3 to 2.1 ns but did not affect the lifetimes of the other dyes. Lifetime detectability of labeled primers at individual points along an electrophoretic peak in the attomole range.

Evaluation Studies as Topic↗
PubMed1997

Temperature and quenching studies of fluorescence polarization detection of DNA hybridization.

The effects of temperature and collisional quenching on fluorescence polarization detection of DNA hybridization were studied using measurements of fluorescence intensity and anisotropy and the dynamic decay of these properties. Three different tethers, 3, 6, and 12 carbons in length, were used to attach fluorescein label to the 5' end of the 33-base oligomers. Perrin plots showed that the effective rotating volume decreases with increasing tether length and approximately doubles upon hybridization. Hybridization increases the association between the tethered dye and the DNA for the shorter tethers but displaces the fluorescein on the 12C tether from the DNA, forcing it into greater contact with the bulk solution. The 6C tether appears to promote sequence-specific interaction between fluorescein label and the oligomer, which causes unexpectedly high anisotropy at higher temperatures and increased protection from collisional quenching. In all cases, there appear to exist several possible conformations for the tethered fluorescein. As temperature is increased, these conformations tend to collapse into a single, average or preferred, conformation. The results demonstrate the importance of the selection of tether, dye, and DNA probe in designing a polarization strategy for detection of DNA hybridization, particularly with respect to tether length and DNA probe sequence.

Anisotropy↗
PubMed1996

On-the-fly frequency-domain fluorescence lifetime detection in capillary electrophoresis.

On-the-fly fluorescence lifetime detection in capillary electrophoresis (CE) is demonstrated. Virtually continuous detection is achieved by interfacing a commercial CE instrument with a commercial, multiharmonic Fourier transform lifetime fluorometer (MHF). The CE capillary cartridge was modified to allow the capillary to pass through a specially constructed capillary column mount capable of micropositioning in the MHF sample chamber. Optimization of the CE/MHF interface was achieved through the incorporation of a focusing lens, appropriate alignment of the laser beam on the capillary, and use of appropriate optical filters in the emission beam. Both fluorescence intensity and lifetime are recovered from the dynamic MHF data, which is analyzed using either conventional nonlinear least-squares or the maximum entropy method, which allows for lifetime recovery without a priori knowledge of the system. Continuous, on-the-fly fluorescence lifetime detection using the MHF technology adds the dimension of fluorescence lifetime without sacrificing the resolution and speed of CE. Its application to the CE separation of a mixture of the fluorescent dyes NBD-hexanoic acid and fluorescein is demonstrated.

Electrophoresis, Capillary↗
PubMed1996

Maximum entropy method for frequency-domain fluorescence lifetime analysis. 2. Timing, mismatched intensity, and reference lifetime errors.

The maximum entropy method (MEM) provides a robust and unbiased solution to fluorescence lifetime data through the use of a broad window of decay terms fit by simultaneous minimization of the chi 2 goodness-of-fit parameter and maximization of a statistical entropy function. This work investigated the effects of three systematic errors, common in frequency-domain measurements, on fluorescence lifetime recovery by MEM. Through real and simulated data, the expression of the systematic errors in lifetime distributions recovered by MEM was compared to that in standard nonlinear least-squares (NLLS) analysis. Reference lifetime errors in the presence of random noise had similar effects on both MEM and NLLS results. Characteristic changes in the recovered lifetimes, fractional intensities, and peak shapes were related to the identification of the true reference lifetime. Compared to NLLS, MEM afforded significant improvements for the recovery of lifetimes and fractional intensities from data containing timing or mismatched intensity errors. These improvements are linked to the dynamic, self-modeling approach of MEM and the direction provided by the entropy criterion. These results speak to the utility of the maximum entropy approach in frequency-domain fluorescence lifetime recovery as well as in other applications.

Fluorescence↗
PubMed1995

Hybridization of fluorescein-labeled DNA oligomers detected by fluorescence anisotropy with protein binding enhancement.

Fundamental aspects of the application of fluorescence anisotropy to detect the hybridization of fluorescein-labeled DNA oligomers were explored. The oligomers included a binding site for the EcoRI restriction enzyme, which binds to double-stranded DNA and is used in this work to enhance the difference between the anisotropies of the single-stranded and double-stranded oligomers by increasing the effective volume of the latter. The fluorescence anisotropy increases upon hybridization and further upon binding of EcoRI to the double strand. By varying the length of the tether used to attach the fluorescein to the 5' end of the oligonucleotide, it was found that a 6-carbon tether was optimal, providing the most dramatic increases in anisotropy in the presence of EcoRI. Dynamic fluorescence anisotropy (DFA) provided insight into the increases in steady-state anisotropy. In most cases, the best fits to the DFA data were obtained using a biexponential decay model, which describes an anisotropic rotator. Upon hybridization, the faster rotational motion is more hindered, and the contribution of the slower rotational component is increased. This effect is enhanced by binding of EcoRI to the double strand, especially when the EcoRI binding site is near the fluorescein at the 5' end and the tether length is in the optimal range. Because the rotational correlation time of the slower anisotropy decay component is much longer than the fluorescence lifetime, it is possible in some cases to reduce the anisotropic rotator model to the special limiting case of a hindered rotator.

Base Sequence↗