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Roger W Giese

Publications and source records attributed to Roger W Giese.

13 recordsLinked to original sources
PubMed2006

Calibration by NMR for quantitative analysis: p-toluenesulfonic acid as a reference substance.

We have demonstrated the usefulness of p-toluenesulfonic acid (TsOH) as a reference substance to calibrate a water-soluble standard by NMR for quantitative analysis. In order to make TsOH convenient for this purpose, we first of all established its molar extinction coefficient under these conditions (epsilon = 351 at 262 nm). This was done by comparing it by quantitative NMR (qNMR) with a compound of known molar extinction coefficient, guanosine monophosphate. TsOH was then used as the standard in a second qNMR experiment to measure an aqueous solution of phosphoglycolate, a metabolite of interest in our laboratory. Perhaps due to its content of water, the purity of this compound was found to be 82%, lower than the value of 94% from the manufacturer.

Benzenesulfonates↗
PubMed2006

4-(4'-Methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl bromide: a new electrophoric derivatizing reagent.

Commercially-available 4,4'-dimethyloctafluorobiphenyl was converted in a single step to 4-(4'-methyltetrafluorophenyl)-2,3,5,6-tetrafluorobenzyl bromide (MTFP-TFBBr) for the purpose of providing a new electrophoric derivatizing reagent. When reacted with this reagent, 2-fluoro-O6-(2'-hydroxyethyl)hypoxanthine, a model analyte, gave a mixture of isomeric products (apparently substituted at N7 and N9, analogous to its known reaction with pentafluorobenzyl bromide), and 53 femtograms of the mixture was detected at S/N = 10 by gas chromatography electron capture mass spectrometry (GC-EC-MS). As intended, the volatility of the MTFB-TFBBr derivative was much less (two-fold) than that of the corresponding pentafluorobenzyl derivative. It is anticipated that MTFB-TFBBr sometimes will be useful in providing an electrophoric derivative that encounters less background noise in analysis by electrophore derivatization/GC-EC-MS.

Benzyl Compounds↗
PubMed2006

Nuclease P1 digestion/high-performance liquid chromatography, a practical method for DNA quantitation.

We have developed a practical method for quantifying DNA. The method is practical in two ways. First, a single enzyme is used to digest the DNA to nucleotides that are then quantified by HPLC under ordinary conditions. Second, the method quantifies DNA even when it is impure. In our method, "nuclease P1/HPLC," the DNA is hydrolyzed by nuclease P1 and the resulting 2'-deoxynucleoside 5'-monophosphates are quantified by HPLC with UV detection. This method was applied to several kinds of genomic DNA in terms of origin and method by which it had been purified. Calf thymus DNA (purified by salt precipitation by the supplier), pig liver DNA (purified by phenolic extraction or by anion-exchange chromatography using a Genomic Tip from Qiagen) and mouse skin DNA (similarly purified) were tested. In some cases a given sample was purified by two of these methods. The values for the amount of DNA by our method were compared with those by three other methods: acid hydrolysis/HPLC (selected as a reference procedure), UV absorbance, and dye binding. Agreement for all DNA samples between the values by our method versus those provided by acid hydrolysis/HPLC was within 10% for amounts of DNA in the 19-54 microg range. In contrast, UV absorbance and the dye-binding assay gave differences up to 30-40% relative to the consistent values furnished by acid hydrolysis and our method. Overall, normalizing the concentrations of the DNA (thymus, liver, skin) by acid hydrolysis/HPLC in 10 samples to values of 1.0 gave the following, relative values and standard deviations: 1.01+/-.07 (nuclease P1/HPLC), 0.8+/-0.17 (dye binding), and 1.1+/-0.1 (UV). Since one cannot assume that any sample of DNA is pure, and determining purity of DNA is difficult, then nuclease P1/HPLC or acid hydrolysis/HPLC is recommended rather than the UV absorbance or dye binding for quantifying DNA whenever an accurate value is important.

Animals↗
PubMed2005

Measurement of N7-(2'-hydroxyethyl)guanine in human DNA by gas chromatography electron capture mass spectrometry.

An improved method is presented, based on gas chromatography-electron capture mass spectrometry (GC-EC-MS), for measuring N7-(2'-hydroxyethyl)guanine (N7-HEG) in DNA from an in vivo sample. The method was used to detect this adduct in amounts of human DNA ranging from 0.07 to 11.5 microg isolated from granulocytes. In this method, the DNA is spiked with a stable isotope internal standard (N7-HEG-d4) and heated in water to release the adduct in a nucleobase form. After the adduct is extracted into 1-butanol, it is purified by reverse phase HPLC and derivatized with HONO, pentafluorobenzyl bromide, and pivalic anhydride. Further purification by silica solid phase extraction and reverse phase HPLC is done prior to injection into a GC-EC-MS. Relatively clean GC-EC-MS chromatograms result, contributing to the high sensitivity that is observed. In the samples tested, from 1.6 to 240 N7-HEG adducts in 10(7) nucleotides were observed, a 150-fold range.

Chromatography, High Pressure Liquid↗
PubMed2004

Phenolic extraction of DNA from mammalian tissues and conversion to deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides.

Towards a goal of detecting scaled-up DNA adducts as altered deoxynucleotides by mass spectrometry, we have set up a practical and general method for isolating DNA-derived deoxyribonucleoside-5'-monophosphates devoid of ribonucleotides starting with a 1 g sample of mammalian tissue. The method is practical because costs have been minimized, and it is general because it can be applied to a more difficult sample such as mouse skin or non-fresh calf liver. The procedure, consisting of a series of steps that were largely gleaned and tuned from prior literature, proceeds as follows: (1) homogenize the tissue in sodium dodecyl sulfate; (2) digest with ribonuclease A, ribonuclease TI, alpha-amylase and proteinase K; (3) partition between water and phenol; (4) precipitate the DNA with ethanol followed by redissolving and dialysis; and (5) digest with nuclease P1 and phosphodiesterase I followed by ultrafiltration and boric acid gel chromatography. The yellow to brown color of DNA from difficult tissues only persisted up to the ultrafiltration step. Apparently this DNA was contaminated with iron-containing proteins. Residual ribonucleotides were not observable (<0.1%) by HPLC in the final sample. Without boric acid gel chromatography, residual contamination by ribonucleotides was about 1% even when the DNA was purified before digestion by phenol partitioning followed by use of a Genomic Tip kit from Qiagen.

Animals↗
PubMed2004

Trace detection of glycolic acid by electrophore labeling gas chromatography-electron capture mass spectrometry.

As little as 10 pg of standard glycolic acid (glycolate) was detected in a method comprising the following sequence of steps: (1) add glycolate-2,2-d(2) as an internal standard and exchange the carboxylate oxygens in hot HCl/[(18)O]water; (2) form an amide derivative with a water-soluble carbodiimide and the electrophoric amine, AMACE1; (3) purify by bypass HPLC; (4) derivatize the residual hydroxy with butyric anhydride; (5) partition with acetonitrile/2 M NaCl; and (6) detect by GC-ECMS. At an intermediate stage in method development, 1 pg of glycolate-2,2,-d(2) could be detected by subjecting it to the above steps 2-6, forming product in an overall, absolute yield of 76%. Step 1 was added after an effort to fully overcome background contamination by glycolate was unsuccessful. For example, background contamination by glycolate could increase rather than decrease when the methanol reagent in the procedure was "carefully purified." The work extends the sensitivity for glycolate detection by approximately 100-fold and provides high-performance conditions for the analytical steps employed.

Gas Chromatography-Mass Spectrometry↗
PubMed2003

Handling and detection of 25 amol of near-infrared dye deoxynucleotide conjugates by capillary electrophoresis with laser-induced fluorescence detection.

Near-infrared dyes are attractive as labeling reagents to enhance sensitivity in trace analysis largely because background fluorescence is low in this spectral region. Here we demonstrate, towards a goal of detecting DNA adducts in small biological samples, that some near-infrared (IR) dye-labeled deoxynucleotides can be separated and detected with high sensitivity by capillary electrophoresis (CE)-laser-induced fluorescence detection (LIF) in a realistic way (handling detection limit of 25 amol) for near-IR dye-labeled deoxynucleotides. This detection limit is achieved by polarity-switching injection of 2.0 microl from a volume of 5.0 microl, in which the compounds are 5 x 10(-12) mol/l in 50% aqueous methanol. Although the adenine and cytosine-containing conjugates co-migrated, the other three (guanine, N2-ethylguanine and thymine) were resolved.

Coloring Agents↗
PubMed2003

Measurement of endogenous estrogens: analytical challenges and recent advances.

Recent developments in the analysis of endogenous estrogens (including both free and conjugated estrogens) are reviewed. Largely due to urging by some cancer researchers, new demands are now being placed on such measurements in terms of sensitivity, throughput, multi-analyte detection and accuracy. Especially high sensitivity is required for detecting estrogens in serum from postmenopausal women, children and men, where concentrations at the low pg/ml level are encountered, and one would prefer to test much less than 1 ml of serum. Aside from throughput, meeting all of these demands may be beyond the reach of immunoassay, the method that has created and continues to dominate this field. Both HPLC and GC versions of mass spectrometry are emerging that have some potential to improve the testing of physiological samples for endogenous estrogens. The following topics are covered in this review: related analyses (e.g. detection of estrogens in environmental samples such as water, where 1-1 samples can be collected to provide ng amounts of estrogens); structure and metabolism of estrogens; biological actions (with an emphasis on their role in cancer); immunoassays; HPLC with electrochemical detection; GC-ECD; and various forms of mass spectrometry.

Adult↗
PubMed2002

Xanthamide fluorescent dyes.

Two derivatives of fluorescein, termed "xanthamides," were prepared from fluorescein, an inexpensive dye. Relative to fluorescein, which contains a 6-phenolic OH and a 2'-carboxyl, the first derivative (5) contains a carboxymethyl ether at the 6-position and a secondary amide of dimethylamine at the 2'-position. The second derivative (8) contains a corresponding 6-methyl ether and a secondary amide of isonipecotic acid at the 2'-position. Thus, both derivatives contain a single carboxyl group, making them monofunctional. Especially 8 is much more photostable (about 10 times) than either fluorescein or BODIPY FL dye when exposed to ordinary light (tungsten light bulb). When tested for relative response in a capillary electrophoresis instrument fitted with an argon ion laser detector (488 nm) and a broad band emission filter, 8 was found to be 4-fold less bright than fluorescein. Both xanthamides, consistent with prior literature on 6-O-alkylated fluorescein, exhibit relatively pH-independent fluorescence (pH 4-10 was tested here). Because they possess two absorbance maximums, the xanthamides can be excited over a broader wavelength range than fluorescein or BODIPY. These collective properties of the xanthamides will make them advantageous over fluorescein and BODIPY dyes for some applications.

Boron Compounds↗
PubMed2002

Handling and detection of 0.8 amol of a near-infrared cyanine dye by capillary electrophoresis with laser-induced fluorescence detection.

We are interested in the detection of DNA adducts and other trace analytes by labeling them with a fluorescent tag followed by use of capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) for high resolution and sensitivity. Towards this goal, here we report the following: (1) synthesis and handling properties of a near-IR, carboxyl-substituted heptamethine cyanine dye; (2) modification of an existing ball lens LIF detector to provide near-LIF detection with excitation at 785 nm for CE; and (3) corresponding handling and detection of as little as 0.8 amol of the dye by enrich-injection of 4.7 microl of 1 x 10(-13) mol/l dye in methanol from an 8-microl volume into a corresponding CE-LIF system. The electrolyte for the separation was methanol-40 mmol/l aqueous sodium borate (98:2, v/v). This finding encourages further exploration of the dye by functionalization of its carboxyl group for chemical labeling purposes.

Carbocyanines↗
PubMed2002

Bypass high-performance liquid chromatography for purification of trace analytes.

technique that we have termed "bypass HPLC" is introduced as a noncontaminating way to define the retention time of a trace analyte for purification purposes on an HPLC column when the amount of the analyte in real samples is too low for on-line detection. The technique employs two HPLC columns ("calibration" and "purification") of the same type that are connected in parallel, with appropriate valving, along with use of two accessory compounds. By injecting ordinary (on-line detectable) amounts of authentic analyte plus the two accessory compounds on the calibration column, and similarly the two accessory compounds onto the purification column, one can predict the retention of the analyte on the latter column without contaminating this column, as follows. The migration times of the first accessory compound provide a reference time on each column; the migration times of the second accessory compound are normalized on each column by subtracting the corresponding reference times; and then the retention time of analyte can be calculated on the second column since the ratio of its normalized retention times on the two columns equals the corresponding ratio for the second accessory compound.

Calibration↗
PubMedDate not supplied

Synthesis of releasable electrophore tags for applications in mass spectrometry.

Releasable electrophore mass tags (electrophore tags) are compounds for use as labels in ligand assays such as hybridization assays and immunoassays. In such assays, the electrophore-tagged reagent (e.g., DNA probe or antibody) is quantified at the conclusion of the assay by cleaving a bond in the attached tag so that the electrophore part can be brought into the gas phase (usually thermally) for detection by electron capture mass spectrometry (EC-MS) or a related technique. Interest in these tags is promoted mainly by their potential to provide highly sensitive and multiplexed assays. The high multiplexing arises from the opportunity to measure many such tags simultaneously in the mass spectrometer, where each tag has an electrophore part with a unique mass. In this study five precursors of electrophore mass tags are presented. Each precursor can lead to a large library of electrophore tags in a practical way, since each precursor can be converted to many different electrophore tags by reaction with commonly available phenols that provide a variation in mass. The phenol-reactive part of the tag is either a polyfluorobiphenyl or a benzyl chloride moiety. Representative library compounds are prepared and detected in an inert ester form by gas chromatography electron capture mass spectrometry (GC-EC-MS). Further, one tag is conjugated to DNA, and the resulting product is detected by laser-induced electron capture time-of-flight mass spectrometry on a silver surface. A calculation by the semiempirical method AM1 for an ion formed by one of the electrophores suggests that ring rotation promotes dissociative electron capture. The features of practical synthesis, simple composition, physicochemical stability, high multiplicity, high sensitivity, and potential for high throughput detection make releasable electrophore mass tags attractive for highly multiplexed assays. This includes their use in SNP assays or dideoxy DNA sequencing for detection of mutations in individuals, where the combination of high accuracy and speed is essential.

Combinatorial Chemistry Techniques↗