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Dipeptides have recently attracted considerable attention due to their newly found biological functions and potential biomarkers of diseases. Global analysis of dipeptides (400 common dipeptides in total number) in samples of complex matrices would enable functional studies of dipeptides and biomarker discovery. In this work, we report a method for high-coverage detection and accurate relative quantification of dipeptides. This method is based on differential chemical isotope labeling (CIL) of dipeptides with dansylation and liquid chromatography Orbitrap tandem mass spectrometry (LC-Orbitrap-MS). An optimized LC gradient ensured the separation of dansyl-dipeptides, including positional isomers (e.g., leucine- and isoleucine-containing dipeptides). MS/MS collision energy in Orbitrap MS was optimized to provide characteristic fragment ion information to sequence dansyl-dipeptides. Using the optimized conditions, a CIL standard library consisting of retention time, MS, and MS/MS information of a whole set of 400 dansyl-dipeptides was constructed to facilitate rapid dipeptide identification. For qualitative analysis of dipeptides in real samples, IsoMS data processing software's parameters were tuned to improve the coverage of dipeptide annotation. Data-dependent acquisition was also carried out to improve the reliability of dipeptide identification. As examples of applications, we successfully identified a total of 321 dipeptides in rice wines and 105 dipeptides in human serum samples. For quantitative analysis, we demonstrated that the intensity ratios of the peak pairs from 96% of the dansyl-dipeptides detectable in a 1:1 mixture of 12 C- and 13 C-labeled rice wine samples were within ±20% of an expected value of 1.0. More than 90% of dipeptides were detected with a relative standard deviation of less than 10%, showing good performance of relative quantification.

We report a segmented spectrum scan method using Orbitrap MS in chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) for improving the metabolite detection efficiency. In this method, the full m / z range is divided into multiple segments with the scanning of each segment to produce multiple narrow-range spectra during the LC data acquisition. These segmented spectra are separately processed to extract the peak pair information with each peak pair arising from a differentially labeled metabolite in the analysis of a mixture of 13 C and 12 C reagent-labeled samples. The sublists of peak pairs are merged to form the final peak pair list from the LC-MS run. Various experimental conditions, including automatic gain control (AGC) values, mass resolutions, segment m / z widths, number of segments, and total data acquisition time in the LC run, were examined to arrive at an optimal setting in the segment scan for increasing the number of detectable metabolites while maintaining the same analysis time as in the full scan. The optimal method used a segment width of 120 m / z with 60k resolution for a 16 min CIL LC-MS run. Using dansyl-labeled human urine samples as an example, we demonstrated that this method could detect 5867 peak pairs or metabolites (not features), compared to 3765 peak pairs detectable in a full scan, representing a 56% gain. Out of 5867 peak pairs, 5575 (95.0%) could be identified or mass-matched. The relative quantification accuracy was slightly reduced (81% peak pairs were within ±25% of the expected peak ratio of 1.0 in full, compared to 87% in the full scan) due to the inclusion of more low-abundance peak pairs in the segment scan. The peak ratio measurement precision was not significantly affected by the segment scan. We also showed the increase of the peak pair number detectable from 3843 in the full scan to 7273 (89% gain) using the Orbitrap operated at 120k resolution with a 60 m / z segment width when multiple repeat sample injections were used. Thus, segment scan Orbitrap MS is an enabling method for detecting coeluting metabolites in CIL LC-MS for increasing the metabolomic coverage.

A reversible fluorescent probe DRhFe is devised by linking spirolactam rhodamine and dansylamide through an Fe 3+ ionophore N 2 -hydroxyethyldiethylenetriamine, where Fe 3+ chelation generating rhodamine B can switch intramolecular fluorescence resonance energy transfer for ratiometric Fe 3+ sensing. Probe DRhFe exhibits an Fe 3+ -specific emission shift from 483 to 576 nm, and this ratiometric response has been successfully applied to monitor labile Fe 3+ fluctuations in cells undergoing ferroptosis.

Blood metabolomics has been widely used for discovering potential metabolite biomarkers of various diseases. In this study, we report our investigation of the effects of freeze-thaw cycles (FTCs) of human serum samples on quantitative metabolomics using a differential chemical isotope labeling (CIL) LC-MS method. A total of 99 serum samples collected from healthy individuals (47 females and 52 males) were subjected to five FTCs, followed by 12 C-/ 13 C-dansylation labeling LC-MS analysis. A total of 2790 peak pairs or metabolites were relatively quantified among the 495 comparative samples, including 150 positively identified metabolites, 235 high-confident putatively identified metabolites and 1949 mass-matched metabolites from database searches. Multivariate analysis of the metabolome data showed a clustering of the third to fifth FTC samples in contrast to the separation of the first and second FTC samples, indicating that the extent of FTC-induced metabolome changes became smaller after the third cycle. The changing patterns among the FTC-effected metabolites were found to be complex. Using sex as a biological factor for grouping, we observed a clear separation of males and females when the samples were subjected to the same number of FTCs. However, when the male- and female-samples with different numbers of FTCs were compared, the number of significant metabolites found in male-female comparison increased dramatically, indicating that FTC effects could lead to a large number of false positives in biomarker discovery. Finally, we proposed a method of detecting the FTC effects by reanalyzing the original samples after subjecting them to an additional FTC.

Calix[4]pyrrole phosphonate-cavitands were used as receptors for the design of supramolecular sensors for creatinine and its lipophilic derivative hexylcreatinine. The sensing principle is based on indicator displacement assays of an inherently fluorescent guest dye or a black-hole quencher from the receptor's cavity by means of competition with the creatinine analytes. The systems were thermodynamically and kinetically characterized regarding their 1:1 binding properties by means of nuclear magnetic resonance spectroscopy ( 1 H and 31 P NMR), isothermal titration calorimetry, and optical spectroscopies (UV/vis absorption and fluorescence). For the use of the black-hole indicator dye, the calix[4]pyrrole was modified with a dansyl chromophore as a signaling unit that engages in Förster resonance energy transfer with the indicator dye. The 1:1 binding constants of the indicator dyes are in the range of 10 7 M -1 , while hexylcreatinine showed values around (2-4) × 10 5 M -1 . The competitive displacement of the indicators by hexylcreatinine produced supramolecular fluorescence turn-on sensors that work at micromolar analyte concentrations that are compatible with those observed for healthy as well as sick patients. The limit of detection for one of the systems reached submicromolar ranges (110 nM).

The abnormal location or generation of superoxide radical anion (O 2 •- ) are implicated in many diseases, including cancers; thus, development of an efficient method to detect O 2 •- is of great importance. Inspired by the fluorophore-governed selective manner to O 2 •- and peroxynitrite (ONOO - ) of previously reported phosphinate-based fluorescence probes, in this contribution, a phosphinothioate-containing probe, TPP , was designed. The probe exhibited easy accessibility through a one-step sequence and good photostability and biocompatibility. Interestingly, TPP showed high specificity and sensitivity to O 2 •- over other reactive oxygen species/nitrogen species including ONOO - . Furthermore, with the assistance of two-photon microscopy, TPP was successfully applied for imaging endogenous O 2 •- in live cells and tissues.

A one-component array-based sensor consisting of a dansyl-modified polylysine (PLL-Dnc) is capable of discriminating the types and compositional ratios of human cells using varying buffer conditions. The PLL-Dnc sensor array, which affords turn-on fluorescence responses against analyte cells that depend on the pH value and the ionic strength, generates differential fluorescence signatures of cells and successfully discriminates eight types of human cell lines (2.0 × 10 4 cells/mL) with 100% accuracy using multivariate analysis. The array also allows differentiation of the composition of the cell mixtures that contain cells with the same tissue origin but of different subtypes. The good discrimination ability and simple platform of our "one-component"-based array allows an easy and rapid sensing of cells without requiring any information on specific biomarkers.

High-performance chemical isotope labeling (CIL) LC-MS is an important tool for profiling chemical-group-based submetabolomes using different labeling chemistries for quantitative metabolomics. Metabolites containing carboxylic acid groups are a class of molecules playing diverse and significant roles in many metabolic pathways. We report a relatively simple and convenient method for analyzing the carboxyl submetabolome with high coverage. Dansylhydrazine (DnsHz) labeling of the carboxylic acid group in metabolites is used to improve both separation and ionization in LC-MS. Using differential 12 C- and 13 C-DnsHz reagents for labeling individual samples and a reference sample (e.g., a pooled sample), accurate relative quantification of individual metabolites among comparative samples can be achieved. DnsHz labeling of carboxylic acids could be carried out at room temperature in water-containing solution in 2 h. A labeled-carboxyl-standard library consisting of 193 endogenous human metabolites was constructed for metabolite identification, which covers more than 55 pathways. To demonstrate the performance of this method, analysis of triplicate human urine samples with duplicate injections ( n = 6) was carried out. A total of 2266 peak pairs or metabolites were commonly detected in all six runs; among them, 81 peak pairs were positively identified and 517 and 1445 peak pairs were matched in the zero- and one-reaction MyCompoundID metabolome libraries, respectively, on the basis of accurate mass search. The possibility of using this method for comprehensive profiling of the carboxyl submetabolome in real world samples was demonstrated in metabolome comparison of 30 urine samples of female and male individuals as well as in absolute quantification of two urinary acids.

The environment-sensitive probe 2 with turn-on switch for Mcl-1 protein was developed herein. After careful evaluation, this small molecule fluorescent probe revealed a selective binding affinity with Mcl-1 protein with a K i value of 2.6 μM and can be well applied to imaging Mcl-1 protein or detecting the cellular distribution of Mcl-1 protein inhibitors. Compared with other imaging approaches, such as the immunofluorescence and fluorescent protein-based techniques, this fluorescent method is rapid, convenient, and affordable, especially since a washing procedure is no longer needed. This environment-sensitive "off-on" design strategy may present a case in point for developing small-molecule fluorescent probe of Bcl-2 family proteins.

Human sweat is an excellent biofluid candidate for metabolomics due to its noninvasive sample collection and relatively simple matrix. We report a simple and inexpensive method for sweat collection over a defined period (e.g., 24 h) based on the use of a nonocclusive style sweat patch adhered to a skin. This method was combined with differential chemical isotope labeling (CIL) LC-MS for mapping the metabolome profiles of sweat samples collected from skins of the left forearm, lower back, and neck of 20 healthy volunteers. Three 24-h sweat samples were collected at three different days from each subject for examining day-to-day metabolome variations. A total of 342 LC-MS runs were carried out (two runs were discarded due to instrumental issue), resulting in the detection and relative quantification of 3140 sweat metabolites with 84 metabolites identified and 2716 metabolites mass-matched to metabolome databases. Multivariate and univariate analyses of the metabolome data revealed a location-dependence characteristic of the sweat metabolome, offering a possibility of mapping the sweat metabolic differences according to skin locations. Significant differences in male and female sweat metabolomes could be detected, demonstrating the possibility of using the sweat metabolome to reveal biological variations among different comparative groups. Thus, the combination of noninvasive sweat collection and CIL LC-MS is a robust analytical tool for sweat metabolomics with potential applications including daily monitoring of the sweat metabolome as health indicators, discovering sweat-based disease biomarkers, and metabolomic mapping of sweat collected from different areas of skin with and without injuries or diseases.

Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential 12 C- and 13 C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with 12 C-labeling and spiked with a 13 C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 12 C-/ 13 C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that 12 C-/ 13 C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.

Milk is a complex sample containing a variety of proteins, lipids, and metabolites. Studying the milk metabolome represents an important application of metabolomics in the general area of nutritional research. However, comprehensive and quantitative analysis of milk metabolites is a challenging task due to the wide range of variations in chemical/physical properties and concentrations of these metabolites. We report an analytical workflow for in-depth profiling of the milk metabolome based on chemical isotope labeling (CIL) and liquid chromatography mass spectrometry (LC-MS) with a focus of using dansylation labeling to target the amine/phenol submetabolome. An optimal sample preparation method, including the use of methanol at a 3:1 ratio of solvent to milk for protein precipitation and dichloromethane for lipid removal, was developed to detect and quantify as many metabolites as possible. This workflow was found to be generally applicable to profile milk metabolomes of different species (cow, goat, and human) and types. Results from experimental replicate analysis (n = 5) of 1:1, 2:1, and 1:2 12 C-/ 13 C-labeled cow milk samples showed that 95.7%, 94.3%, and 93.2% of peak pairs, respectively, had ratio values within ±50% accuracy range and 90.7%, 92.6%, and 90.8% peak pairs had RSD values of less than 20%. In the metabolomic analysis of 36 samples from different categories of cow milk (brands, batches, and fat percentages) with experimental triplicates, a total of 7104 peak pairs or metabolites could be detected with an average of 4573 ± 505 (n = 108) pairs detected per LC-MS run. Among them, 3820 peak pairs were commonly detected in over 80% of the samples with 70 metabolites positively identified by mass and retention time matches to the dansyl standard library and 2988 pairs with their masses matched to the human metabolome libraries. This unprecedentedly high coverage of the amine/phenol submetabolome illustrates the complexity of the milk metabolome. Since milk and milk products are consumed in large quantities on a daily basis, the intake of these milk metabolites even at low concentrations can be cumulatively high. The high-coverage analysis of the milk metabolome using CIL LC-MS should be very useful in future research involving the study of the effects of these metabolites on human health. It should also be useful in the dairy industry in areas such as improving milk production, developing new processing technologies, developing improved nutritional products, quality control, and milk product authentication.

A key step in metabolomics is to perform accurate relative quantification of the metabolomes in comparative samples with high coverage. Hydroxyl-containing metabolites are an important class of the metabolome with diverse structures and physical/chemical properties; however, many of them are difficult to detect with high sensitivity. We present a high-performance chemical isotope labeling liquid chromatography mass spectrometry (LC-MS) technique for in-depth profiling of the hydroxyl submetabolome, which involves the use of acidic liquid-liquid extraction to enrich hydroxyl metabolites into ethyl acetate from an aqueous sample. After drying and then redissolving in acetonitrile, the metabolite extract is labeled using a base-activated 12 C- or 13 C-dansylation reaction. A fast step-gradient LC-UV method is used to determine the total concentration of labeled metabolites. On the basis of the concentration information, a 12 C-labeled individual sample is mixed with an equal mole amount of a 13 C-labeled pool or control for relative metabolite quantification. The 12 C-/ 13 C-labeled mixtures are individually analyzed by LC-MS, and the resultant peak pairs of labeled metabolites in MS are measured for relative quantification and metabolite identification. A standard library of 85 hydroxyl compounds containing MS, retention time, and MS/MS information was constructed for positive metabolite identification based on matches of two or all three of these parameters with those of an unknown. Using human urine as an example, we analyzed samples of 1:1 12 C-/ 13 C-labeled urine in triplicate with triplicate runs per sample and detected an average of 3759 ± 45 peak pairs or metabolites per run and 3538 ± 71 pairs per sample with 3093 pairs in common (n = 9). Out of the 3093 peak pairs, 2304 pairs (75%) could be positively or putatively identified based on metabolome database searches, including 20 pairs positively identified using the dansylated hydroxyl standards library. The majority of detected metabolites were those containing hydroxyl groups. This technique opens a new avenue for the detailed characterization of the hydroxyl submetabolome in metabolomics research.

Human sweat can be noninvasively collected and used as a media for diagnosis of certain diseases as well as for drug detection. However, because of very low concentrations of endogenous metabolites present in sweat, metabolomic analysis of sweat with high coverage is difficult, making it less widely used for metabolomics research. In this work, a high-performance method for profiling the human sweat submetabolome based on chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is reported. Sweat was collected using a gauze sponge style patch, extracted from the gauze by centrifugation, and then derivatized using CIL. Differential (12)C- and (13)C-dansylation labeling was used to target the amine/phenol submetabolome. Because of large variations in the total amount of sweat metabolites in individual samples, sample amount normalization was first performed using liquid chromatography with UV detection (LC-UV) after dansylation. The (12)C-labeled individual sample was then mixed with an equal amount of (13)C-labeled pooled sample. The mixture was subjected to LC-MS analysis. Over 2707 unique metabolites were detected across 54 sweat samples collected from six individuals with an average of 2002 ± 165 metabolites detected per sample from a total of 108 LC-MS runs. Using a dansyl standard library, we were able to identify 83 metabolites with high confidence; many of them have never been reported to be present in sweat. Using accurate mass search against human metabolome libraries, we putatively identified an additional 2411 metabolites. Uni- and multivariate analyses of these metabolites showed significant differences in the sweat submetabolomes between male and female, as well as between early and late exercise. These results demonstrate that the CIL LC-MS method described can be used to profile the human sweat submetabolome with high metabolomic coverage and high quantification accuracy to reveal metabolic differences in different sweat samples, thereby allowing the use of sweat as another human biofluid for comprehensive and quantitative metabolomics research.

A large number of polyphenols are consumed with the diet and may contribute to the prevention of chronic diseases such as cardiovascular diseases, diabetes, cancers, and neurodegenerative diseases. More comprehensive methods are needed to measure exposure to this complex family of bioactive plant compounds in epidemiological studies. We report here a novel method enabling the simultaneous measurement in urine of 38 polyphenols representative of the main classes and subclasses found in the diet. This method is based on differential (12)C-/(13)C-isotope labeling of polyphenols through derivatization with isotopic dansyl chloride reagents and on the analysis of the labeled polyphenols by tandem mass spectrometry. This derivatization approach overcomes the need for costly labeled standards. Different conditions for enzyme hydrolysis of polyphenol glucuronides and sulfate esters, extraction, and dansylation of unconjugated aglycones were tested and optimized. Limits of quantification varied from 0.01 to 1.1 μM depending on polyphenols. Intrabatch coefficients of variation varied between 3.9% and 9.6%. Interbatch variations were lower than 15% for 31 compounds and lower than 29% for 6 additional polyphenols out of the 38 tested. Thirty seven polyphenols were validated and then analyzed in 475, 24 h urine samples from the European Prospective Investigation on Cancer and Nutrition (EPIC) study. Thirty four polyphenols could be detected and successfully estimated and showed large interindividual variations of concentrations (2-3 orders of magnitude depending on the compound), with median concentrations spanning from 0.01 to over 1000 μM for all 34 compounds.

An analytical method is presented here that is sensitive to the parts-per-quadrillion (pg/L) for estrogens in surface water. The estrogens included for study were estrone, 17β-estradiol, estriol, 17α-ethinylestradiol, and equilin. The method consisted of the small-scale liquid-liquid extraction of surface water followed by derivation with dansyl chloride. Analyte separation and detection were performed by high-pressure liquid-chromatography and tandem mass-spectrometry. A large volume (100 μL) of the sample was injected on-column to increase the analyte mass sent to the detector. The detection limits of the method were 0.045 ng/L for estrone, 0.086 ng/L for 17β-estradiol, 0.030 ng/L for estriol, 0.049 ng/L for 17α-ethinylestradiol, and 0.13 ng/L for equilin. The whole-method accuracy ranged from 93 ± 5.8% to 105 ± 4.5% for all the analytes at two different spike levels. Similarly, the precision of the method was less than 8.0% relative standard deviation. The final method was used to analyze a series of samples from the Mississippi River spanning 51 river miles. Estrone was detected in all of the samples and 17β-estradiol was detected in one. Concentrations of estrone ranged from between the detection and quantification limits up to 0.63 ng/L. Increases in the concentration of estrone could be observed downstream from potential sources including a drinking water treatment plant. 17β-estradiol was detected below its quantitation limit in a sample taken downstream from a wastewater treatment plant.

A reaction-based probe 1 for hypochlorite signaling was designed by the conjugation of two fluorophores, rhodamine and dansyl moieties, by the reaction of rhodamine B base with dansylhydrazine. Probe 1 exhibited pronounced hypochlorite-selective chromogenic and fluorescent signaling behavior over other oxidants used in practical applications, such as hydrogen peroxide, peracetic acid, and ammonium persulfate, as well as commonly encountered metal ions and anions. Signaling was attributed to the hypochlorite-induced oxidative cleavage of the sulfonhydrazide linkage of the probe. In particular, favorable ratiometric fluorescence signaling was possible by utilizing the emissions of the two fluorophores. A detection limit of 1.13 × 10(-6) M (0.058 ppm) was estimated for the determination of hypochlorite. A paper-based test strip was prepared and was used as a semiquantitative indicator for the presence of hypochlorite in aqueous solutions. The probe was also successfully applied for the determination of hypochlorite in practical tap water samples.

Artifical metalloenzymes combine the reactivity of small molecule catalysts with the selectivity of enzymes, and new methods are required to tune the catalytic properties of these systems for an application of interest. Structure-based computational design could help to identify amino acid mutations leading to improved catalytic activity and enantioselectivity. Here we describe the application of Rosetta Design for the genetic optimization of an artificial transfer hydrogenase (ATHase hereafter), [(η(5)-Cp*)Ir(pico)Cl] ⊂ WT hCA II (Cp* = Me5C5(-)), for the asymmetric reduction of a cyclic imine, the precursor of salsolsidine. Based on a crystal structure of the ATHase, computational design afforded four hCAII variants with protein backbone-stabilizing and hydrophobic cofactor-embedding mutations. In dansylamide-competition assays, these designs showed 46-64-fold improved affinity for the iridium pianostool complex [(η(5)-Cp*)Ir(pico)Cl]. Gratifyingly, the new designs yielded a significant improvement in both activity and enantioselectivity (from 70% ee (WT hCA II) to up to 92% ee and a 4-fold increase in total turnover number) for the production of (S)-salsolidine. Introducing additional hydrophobicity in the Cp*-moiety of the Ir-catalyst provided by adding a propyl substituent on the Cp* moiety yields the most (S)-selective (96% ee) ATHase reported to date. X-ray structural data indicate that the high enantioselectivity results from embedding the piano stool moiety within the protein, consistent with the computational model.

Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use.

The intracellular Ca²⁺ concentration is an important regulator of many cellular functions. The small acidic protein calmodulin (CaM) serves as a Ca²⁺ sensor and control element for many enzymes. Nitric oxide synthase (NOS) is one of the proteins that is activated by CaM and plays a major role in a number of key physiological and pathological processes. Previous studies have shown CaM to act like a switch that causes a conformational change in NOS to allow for the electron transfer between the reductase and oxygenase domains through a process that is thought to be highly dynamic. We have analyzed the structure and dynamics of complexes formed by peptides based on inducible NOS (iNOS) and endothelial NOS (eNOS) with CaM at Ca²⁺ concentrations that mimic the physiological basal (17 and 100 nM) and elevated levels (225 nM) found in mammalian cells using fluorescence techniques and nuclear magnetic resonance spectroscopy. The results show the CaM-NOS complexes have similar structures at physiological and fully saturated Ca²⁺ levels; however, their dynamics are remarkably different. At 225 nM Ca²⁺, the CaM-NOS complexes show overall an increase in backbone dynamics, when compared to the dynamics of the complexes at saturating Ca²⁺ concentrations. Specifically, the N-lobe of CaM in the CaM-iNOS complex displays a lower internal mobility (higher S²) and higher exchange protection compared to those of the CaM-eNOS complex. In contrast, the C-lobe of CaM in the CaM-eNOS complex is less dynamic. These results illustrate that structures of CaM-NOS complexes determined at saturated Ca²⁺ concentrations cannot provide a complete picture because the differences in intramolecular dynamics become visible only at physiological Ca²⁺ levels.

We describe herein a novel approach for the fluorescent detection of small molecules using a sandwich-type aptamer strategy based on a signaling macrocyclic host-dye system. One split adenosine aptamer fragment was 5'-conjugated to a β-cylodextrin (CD) molecule while the other nucleic acid fragment was labeled at the 3'-end by a dansyl molecule prone to be included into the macrocycle. The presence of the small target analyte governed the assembly of the two fragments, bringing the dye molecule and its specific receptor in close proximity and promoting the inclusion interaction. Upon the inclusion complex formation, the microenvironment of dansyl was modified in such a way that the fluorescent intensity increased. Concomitantly, this supplementary interaction at the aptamer extremities induced stabilizing effects on the ternary complex. We next proposed a bivalent signaling design where the two extremities of one split aptamer fragment were conjugated to the β-CD molecule while those of the other fragment were tagged by the dansyl dye. The dual reporting dye inclusion promoted an improvement of both the signal-to-background change and the assay sensitivity. Owing to the vast diversity of responsive host-macrocycle systems available, this aptasensor strategy has potential to be extended to the multiplexed analysis and to other kinds of transducers (such as electrochemical).

Human fecal samples contain endogenous human metabolites, gut microbiota metabolites, and other compounds. Profiling the fecal metabolome can produce metabolic information that may be used not only for disease biomarker discovery, but also for providing an insight about the relationship of the gut microbiome and human health. In this work, we report a chemical isotope labeling liquid chromatography-mass spectrometry (LC-MS) method for comprehensive and quantitative analysis of the amine- and phenol-containing metabolites in fecal samples. Differential (13)C2/(12)C2-dansyl labeling of the amines and phenols was used to improve LC separation efficiency and MS detection sensitivity. Water, methanol, and acetonitrile were examined as an extraction solvent, and a sequential water-acetonitrile extraction method was found to be optimal. A step-gradient LC-UV setup and a fast LC-MS method were evaluated for measuring the total concentration of dansyl labeled metabolites that could be used for normalizing the sample amounts of individual samples for quantitative metabolomics. Knowing the total concentration was also useful for optimizing the sample injection amount into LC-MS to maximize the number of metabolites detectable while avoiding sample overloading. For the first time, dansylation isotope labeling LC-MS was performed in a simple time-of-flight mass spectrometer, instead of high-end equipment, demonstrating the feasibility of using a low-cost instrument for chemical isotope labeling metabolomics. The developed method was applied for profiling the amine/phenol submetabolome of fecal samples collected from three families. An average of 1785 peak pairs or putative metabolites were found from a 30 min LC-MS run. From 243 LC-MS runs of all the fecal samples, a total of 6200 peak pairs were detected. Among them, 67 could be positively identified based on the mass and retention time match to a dansyl standard library, while 581 and 3197 peak pairs could be putatively identified based on mass match using MyCompoundID against a Human Metabolome Database and an Evidence-based Metabolome Library, respectively. This represents the most comprehensive profile of the amine/phenol submetabolome ever detected in human fecal samples. The quantitative metabolome profiles of individual samples were shown to be useful to separate different groups of samples, illustrating the possibility of using this method for fecal metabolomics studies.

A new cationic dansyl derivative-based (DIlSD) fluorescence probe was designed and synthesized. Its combination with anionic surfactant SDS assemblies shows enhanced fluorescence intensity and blue-shifted maximum wavelength. Its fluorescence can be slightly quenched by Cu(2+); however, the fluorescence quenching efficiency by Cu(2+) is highly increased upon titration of arginine (Arg). As a result, the ternary system containing the cationic fluorophore, anionic surfactant, and Cu(2+) functions as a highly sensitive and selective sensor to Arg. The optimized sensor system displays a detection limit of 170 nM, representing the highest sensitivity to Arg in total aqueous solution by a fluorescent sensor. Control experiments reveal that the imidazolium groups in the fluorophore, the anionic surfactant, and Cu(2+) all play important roles in the process of sensing Arg. The electrostatic interaction between the cationic fluorophore and anionic surfactants facilitates the binding of imidazolium rings with Cu(2+), the surfactant surface-anchored Cu(2+) is responsible for further binding of Arg, and the electrostatic interaction between anionic surfactants and positively charged amino acids accounts for the selective responses to Arg.

Metabolomics involves the comparison of the metabolomes of individual samples from two or more groups to reveal the metabolic differences. In order to measure the metabolite concentration differences accurately, using the same amount of starting materials is essential. In this work, we describe a simple and rapid method for sample amount normalization. It is based on dansylation labeling of the amine and phenol submetabolome of an individual sample, followed by solvent extraction of the labeled metabolites and ultraviolet (UV) absorbance measurement using a microplate reader. A calibration curve of a mixture of 17 dansyl-labeled amino acid standards is used to determine the total concentration of the labeled metabolites in a sample. According to the measured concentrations of individual samples, the volume of an aliquot taken from each sample is adjusted so that the same sample amount is taken for subsequent metabolome comparison. As an example of applications, this dansylation metabolite assay method is shown to be useful in comparative metabolome analysis of two different E. coli strains using a differential chemical isotope labeling LC-MS platform. Because of the low cost of equipment and reagents and the simple procedure used in the assay, this method can be readily implemented. We envisage that, this assay, which is analogous to the bicinchoninic acid (BCA) protein assay widely used in proteomics, will be applicable to many types of samples for quantitative metabolomics.

We report herein the synthesis and photophysical studies on a new multicomponent chemosensor dyad comprising two fluorescing units, dansylamide (DANS) and nitrobenzoxadiazole (NBD). The system has been developed to investigate receptor-analyte binding interactions in the presence of both cations and anions in a single molecular system. A dimethyl amino (in the DANS unit) group is used as a receptor for cations, and acidic hydrogens of sulfonamide and the NBD group are used as receptors for anions. The system is characterized by conventional analytical techniques. The photophysical properties of this supramolecular system in the absence and presence of various metal ions and nonmetal ions as additives are investigated in an acetonitrile medium. Utility of this system in an aqueous medium has also been demonstrated. The absorption and fluorescence spectrum of the molecular system consists of a broad band typical of an intramolecular charge-transfer (ICT) transition. A low quantum yield and lifetime of the NBD moiety in the present dyad indicates photoinduced electron transfer (PET) between DANS and the NBD moiety. The fluorescence intensity of the system is found to decrease in the presence of fluoride and acetate anions; however, the quenching is found to be much higher for fluoride. This quenching behavior is attributed to the enhanced PET from the anion receptor to the fluorophore moiety. The mechanistic aspect of the fluoride ion signaling behavior has also been studied by infrared (IR) and (1)H NMR experiments. The hydrogen bonding interaction between the acidic NH protons of the DPN moiety and F(-) is found to be primarily responsible for the fluoride selective signaling behavior. While investigating the cation signaling behavior, contrary to anions, significant fluorescence enhancement has been observed only in the presence of transition-metal ions. This behavior is rationalized by considering the disruption of PET communication between DANS and the NBD moiety due to transition-metal ion binding. Theoretical (density functional theory) studies are also performed for the better understanding of the receptor-analyte interaction. Interestingly, negative cooperativity in binding is observed when the interaction of this system is studied in the presence of both Zn(2+) and F(-). Fluorescence microscopy studies also revealed that the newly developed fluorescent sensor system can be employed as an imaging probe in live cells.

A novel fluorescent thrombin binding aptamer (TBA), conjugated with the environmentally sensitive dansyl probe at the 3'-end and a β-cyclodextrin residue at the 5'-end, has been efficiently synthesized exploiting Cu(I)-catalyzed azide-alkyne cycloaddition procedures. Its conformation and stability in solution have been studied by an integrated approach, combining in-depth NMR, CD, fluorescence, and DSC studies. ITC measurements have allowed us to analyze in detail its interaction with human thrombin. All the collected data show that this bis-conjugated aptamer fully retains its G-quadruplex formation ability and thrombin recognition properties, with the terminal appendages only marginally interfering with the conformational behavior of TBA. Folding of this modified aptamer into the chairlike, antiparallel G-quadruplex structure, promoted by K(+) and/or thrombin binding, typical of TBA, is associated with a net fluorescence enhancement, due to encapsulation of dansyl, attached at the 3'-end, into the apolar cavity of the β-cyclodextrin at the 5'-end. Overall, the structural characterization of this novel, bis-conjugated TBA fully demonstrates its potential as a diagnostic tool for thrombin recognition, also providing a useful basis for the design of suitable aptamer-based devices for theranostic applications, allowing simultaneously both detection and inhibition or modulation of the thrombin activity.

A dansyl derivative (Ds-DAB) was prepared and used as a fluorescent probe for peroxynitrite (ONOO(-)) detection. The results showed that the addition of peroxynitrite to the aqueous solution of Ds-DAB would result in obvious fluorescence enhancement. This probe is highly specific for peroxynitrite in aqueous solution, avoiding interference from other reactive oxygen species (ROS) and nitrogen species (RNS). The advantages of high selectivity, fast reaction rate, and peroxynitrite bioimaging render Ds-DAB suitable for peroxynitrite detection.

We show that interactions of fatty acids with the central cavity of potassium channel KcsA can be characterized using the fluorescence probe 11-dansylaminoundecanoic acid (Dauda). The fluorescence emission spectrum of Dauda bound to KcsA in bilayers of dioleoylphosphatidylcholine contains three components, which can be attributed to KcsA-bound and lipid-bound Dauda together with unbound Dauda. The binding of Dauda to KcsA was characterized by a dissociation constant of 0.47 ± 0.10 μM with 0.94 ± 0.06 binding site per KcsA tetramer. Displacement of KcsA-bound Dauda by the tetrabutylammonium (TBA) ion confirmed that the Dauda binding site was in the central cavity of KcsA. Dissociation constants for a range of fatty acids were determined by displacement of Dauda: binding of fatty acids increased in strength with an increasing chain length from C14 to C20 but then decreased in strength from C20 to C22. Increasing the number of double bonds in the chain from one to four had little effect on binding, dissociation constants for oleic acid and arachidonic acid, for example, being 2.9 ± 0.2 and 3.0 ± 0.4 μM, respectively. Binding of TBA to KcsA was very slow, whereas binding of Dauda was fast, suggesting that TBA can enter the cavity only through an open channel whereas Dauda can bind to the closed channel, presumably entering the cavity via the lipid bilayer.

Cystic fibrosis is a genetic disease caused by mutations in the gene for the cystic fibrosis transmembrane conductance regulator (CFTR) protein. In vitro experiments have demonstrated that 4-methyl-2-(5-phenyl-1H-pyrazol-3-yl)phenol (VRT-532, 1) is able to partially restore the function of mutant CFTR proteins. To help elucidate the nature of the interactions between 1 and mutant CFTR, molecular probes based on the structure of 1 have been prepared. These include a photoreactive aryl azide derivative 11 and a fluorescent dansyl sulfonamide 15. Additionally, a method for hydrogen isotope exchange on 1 has been developed, which could be used for the incorporation of radioactive tritium. Using iodide efflux assays, the probe molecules have been demonstrated to modulate the activity of mutant CFTR in the same manner as 1. These probe molecules enable a number of biochemical experiments aimed at understanding how 1 rescues the function of mutant CFTR. This understanding can in turn aid in the design and development of more efficacious compounds which may serve as therapeutic agents in the treatment of cystic fibrosis.

Interaction of a few dansyl-naphthalimide conjugates 1a-e linked through polymethylene spacer groups with various metal ions was investigated through absorption, fluorescence, NMR, isothermal calorimetric (ITC), and laser flash photolysis techniques. The characteristic feature of these dyads is that they exhibit competing singlet-singlet energy transfer (SSET) and photoinduced electron transfer (PET) processes, both of which decrease with the increase in spacer length. Depending on the spacer group, these dyads interact selectively with divalent Cu(2+) and Zn(2+) ions, as compared to other mono- and divalent metal ions. Jobs plot analysis showed that these dyads form 2:3 complexes with Cu(2+) ions, while 1:1 complexes were observed with Zn(2+) ions. The association constants for the Zn(2+) and Cu(2+) complexes were determined and are found to be in the order 10(3)-10(5) M(-1). Irrespective of the length of the spacer group, these dyads interestingly act as fluorescence ratiometric molecular probes for Cu(2+) ions by altering the emission intensity of both dansyl and naphthalimide chromophores. In contrast, only the fluorescence intensity of the naphthalimide chromophore of the lower homologues (n = 1-3) was altered by Zn(2+) ions. (1)H NMR and ITC measurements confirmed the involvement of both sulfonamide and dimethylamine groups in the complexation with Cu(2+) ions, while only the latter group was involved with Zn(2+) ions. Laser excitation of the dyads 1a-e showed formation of a transient absorption which can be attributed to the radical cation of the naphthalimide chromophore, whereas only the triplet excited state of the dyads 1a-e was observed in the presence of Cu(2+) ions. Uniquely, the complexation of 1a-e with Cu(2+) ions affects both PET and SSET processes, while only the PET process was partially inhibited by Zn(2+) ions in the lower homologues (n = 1-3) and the higher homologues exhibited negligible changes in their emission properties. Our results demonstrate that the spacer length dependent variations of the photophysical properties of these novel conjugates not only enable the selective detection of Cu(2+) and Zn(2+) ions but also aid in discriminating these two biologically important metal ions.

In the Parkinson's disease-associated state, α-synuclein undergoes large conformational changes, forming ordered, β-sheet-containing fibrils. To unravel the role of specific residues during the fibril assembly process, we prepared single-Cys mutants in the disordered (G7C and Y136C) and proximal (V26C and L100C) fibril core sites and derivatized them with environmentally sensitive dansyl (Dns) fluorophores. Dns fluorescence exhibits residue specificity in spectroscopic properties as well as kinetic behavior; early kinetic events were revealed by probes located at positions 7 and 136 compared to those at positions 26 and 100.

Fluorescent dyes (e.g., dansyl, fluoresceine isothiocyanate, or naphthalimide groups) are widely used as markers to study biological properties of drugs. In order to evaluate possible mediated cytotoxicity, we attached three molecules each to 1,3,5-tris(3-propylamino)benzene initially synthesized as core molecule for the design of dendrimers. Cytotoxic effects were only observed for the NO(2)-substituted naphthalimide conjugate. The intracellular distribution was visualized via confocal fluorescence microscopy and pointed to an accumulation in the endosome or nucleus, dependent on the cell line used.

In this work we report the synthesis of a set of labeled ligands targeting the human 5-HT(6) receptor (h5-HT(6)R). Among the synthesized compounds, fluorescent probe 10 (K(i) = 175 nM and Φ(f) = 0.21) and biotinylated derivative 15 (K(i) = 90 nM) deserve special attention because they enable direct observation of the h5-HT(6)R in cells. Thus, they represent the first molecular probes for 5-HT(6)R visualization. These results are the starting point for introducing a variety of tags in these or other 5-HT(6)R ligand scaffolds aimed at the development of optimized probes with tailored profiles in terms of fluorescence, affinity, or selectivity.

Chemical derivatization is useful for improving the ionization characteristics of poorly or nonionizable analytes in liquid chromatography-mass spectrometry (LC-MS). Dansyl chloride has been widely used as a derivatizing reagent for fluorescence detection and for facilitating the MS detection of phenols and amines, but not for general alcohols. A new dansylation method for improving the mass spectral sensitivity of unactivated alcohols was developed. The dansylated derivative was formed after incubation of the test compound cholesterol and excess dansyl chloride in CH(2)Cl(2) in the presence of 4-(dimethylamino)-pyridine (DMAP) plus N,N-diisopropylethylamine at 65 °C for 1 h, with an overall yield of 96%. The versatility of dansylation was investigated by utilizing representative lipid compounds (containing different numbers of hydroxy groups) for dansylation. All dansylated derivatives of the selected compounds were detected by LC-MS/MS in the electrospray ionization (ESI) positive ion mode. Validation of the method was established in terms of the sensitivity, stability, and repeatability of dansylation. The method was then applied to characterizing the P450 7A1 oxidation product (dansylated 7α-hydroxycholesterol) in human liver extracts using an LC-MS metabolomics/isotopic labeling approach (Tang, Z.; Guengerich, F. P. Anal. Chem. 2009, 81, 3071-3078). The dansylated derivative of the product was identified, with the signal increased by 10(3)-fold compared with a previous method (derivatization with succinic anhydride and ESI negative ion MS). Quantitation of testosterone in human liver extracts was also done as an example of the application of the dansylation method. Thus, dansylation is a potential method of modifying many alcohols for detection by fluorescence and LC-MS analysis.

Here, we report on the first synthesis of fluorescent-labeled epidermal growth factor receptor-DNA targeting combi-molecules, and we studied the influence of P-glycoprotein status of human sarcoma MES-SA cells on their growth inhibitory effect and cellular uptake. The results showed that 6, bearing a longer spacer between the quinazoline ring and the dansyl group, was more stable and more cytotoxic than 4. In contrast to the latter, it induced significant levels of DNA damage in human tumor cells. Moreover, in contrast to doxorubicin, a drug known to be actively effluxed by P-gp, the more stable combi-molecule 6 induced almost identical levels of drug uptake and DNA damage in P-gp-proficient and -deficient cells. Likewise, in contrast to doxorubicin, 4 and 6 exerted equal levels of antiproliferative activity against the two cell types. The results in toto suggest that despite their size, the antiproliferative effects of 4 and 6 were independent of P-gp status of the cells.

Site-directed tryptophan fluorescence has been successfully used to determine the solution structure of tear lipocalin. Here, the technique is extended to measure the binding energy landscape. Single Trp mutants of tear lipocalin are bound to the native ligand and an analogue tagged with a quencher group to both populate and discriminate the excited protein states. Steady-state and time-resolved fluorescence quenching data reveal the intracavitary state of the ligand. The static components of fluorescence quenching identify the residues where nonfluorescence complexes form. An asymmetric distribution of the ligand within the cavity reflects the complex energy landscape of the excited protein states. These findings suggest that the excited protein states are not unique but consist of many substates. The roughness of the binding energy landscape is about 2.5kBT. The excited protein states originate primarily from conformational selections of loops AB and GH, a portal region. In contrast to static quenching, the dynamic components of fluorescence quenching by the ligand are relevant to both local side chain and ligand dynamics. Apparent bimolecular rate constants for collisional quenching of Trp by the nitroxide moiety are approximately 1 / 5 x 10(12) M(-1) s(-1). Estimations made for effective ligand concentrations establish actual rate constants on the order of 12 x 10(9) M(-1) s(-1). Prior to exit from the cavity of the protein, ligands explore binding sites in nanoseconds. Although microsecond fluctuations are rate-limiting processes in ligand binding for many proteins, accompanying nanosecond motion may be necessary for propagation of ligand binding.

We report a new quantitative metabolome profiling technique based on differential (12)C-/(13)C-isotope dansylation labeling of metabolites, fast liquid chromatography (LC) separation and electrospray ionization Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) detection. An isotope reagent, (13)C-dansyl chloride, can be readily synthesized. This reagent, along with (12)C-dansyl chloride, provides a simple and robust means of labeling metabolites containing primary amine, secondary amine, or phenolic hydroxyl group(s). It is shown that dansylation labeling offers 1-3 orders of magnitude ESI signal enhancement over the underivatized counterparts. Dansylation alters the chromatographic behaviors of polar and ionic metabolites normally not retainable on a reversed phase (RP) column to an extent that they can be retained and separated by RPLC with high efficiency. There is no isotopic effect on RPLC separation of the differential isotope labeled metabolites, and (12)C-/(13)C-labeled isoforms of metabolites are coeluted and detected by MS for precise and accurate quantification and confident metabolite identification. It is demonstrated that, in the analysis of 20 amino acids, a linear response of over 2 orders of magnitude is achieved for relative metabolite quantification with an average relative standard deviation (RSD) of about 5.3% from replicate experiments. A dansylation standard compound library consisting of 121 known amines and phenols has been constructed and is proven to be useful for absolute metabolite quantification and MS-based metabolite identification in biological samples. As an example, the absolute concentrations of 93 metabolites, ranging from 30 nM to 2510 microM, can be determined from a pooled sample of human urines collected in 5 consecutive days labeled with (12)C-dansylation and spiked with the 121 (13)C-dansylated standards. Relative concentration variations of these metabolites in individual urine samples can also be monitored by mixing the (13)C-dansylated pooled urine sample with the (12)C-dansylated individual sample. With a 12 min fast LC separation combined with FTICR MS, 672 metabolites were detected in a human urine sample with each metabolite peak having a signal-to-noise ratio of greater than 20; the identities of most of the metabolites remain to be determined. This work illustrates that dansylation labeling and fast LC/FTICR MS can be a powerful technique for quantitative profiling of at least 672 metabolites in urine samples in 12 min.

The activation of a lipopolysaccharide (LPS) with 1-cyano-4-dimethylaminopyridinium tetrafluoroborate (CDAP) in the presence of a surfactant allows an efficient conjugation with dansyl hydrazine or horseradish peroxidase (HRP) in an aqueous medium maintaining its biological activity. In order to promote the reaction a series of amphiphilic compounds were tested, sodium deoxycholate being the most suitable. The method presents several advantages: it is carried out in a mild environment, good conjugation ratios are obtained, it is suitable for any label bearing amino, hydrazine, or hydrazide groups, and the LPS endotoxic and HRP enzymatic activities are preserved. The HRP conjugate is applied in an amperometric competitive assay for the detection of lipopolysaccharides in an electrode array combined with a multipotentiostat able to carry out simultaneous determinations. The system is able to detect samples in concentrations as low as 100 pg mL(-1) of LPS.

Reactive metabolite formation has been associated with drug-induced liver, skin, and hematopoietic toxicity of many drugs that has resulted in serious clinical toxicity, leading to clinical development failure, black box warnings, or, in some cases, withdrawal from the market. In vitro and in vivo screening for reactive metabolite formation has been proposed and widely adopted in the pharmaceutical industry with the aim of minimizing the property and thus the risk of drug-induced toxicity (DIT). One of the most common screening methods is in vitro thiol trapping of reactive metabolites. Although it is well-documented that many hepatotoxins form thiol adducts, there is no literature describing the adduct formation potential of safer drugs that are widely used. The objective of this study was to quantitatively assess the thiol adduct formation potential of 50 drugs (10 associated with DIT and 40 not associated) and document apparent differences in adduct formation between toxic and safer drugs. Dansyl glutathione was used as a trapping agent to aid the quantitation of adducts following in vitro incubation of drugs with human liver microsomes in the presence and absence of NADPH. Metabolic turnover of these drugs was also monitored by LC/UV. Overall, 15 out of the 50 drugs screened formed detectable levels of thiol adducts. There were general trends toward more positive findings in the DIT group vs the non-DIT group. These trends became more marked when the relative amount of thiol adducts was taken into account and improved further when dose and total daily reactive metabolite burdens were considered. In conclusion, there appears to be a general trend between the extent of thiol adduct formation and the potential for DIT, which would support the preclinical measurement and minimization of the property through screening of thiol adduct formation as part of an overall discovery optimization paradigm.

In this paper, we report the synthesis on Merrifield's resin of alkyl-bis-o-aminobenzamides labeled with a fluorescent dansyl group for use in metal ion recognition. The influence of alkyl groups with different long chains (n = 1, 2, 4, 6) on the spectral fluorescence characteristics was studied. The sensing properties of the beads were evaluated by packing the resins into a flow-through cell for use in a FIA (flow injection analysis)format. Results demonstrated that for those materials with a longer alkyl chain, the fluorescence emission increased upon Li+, Na+, K+, Ca2+, and Mg2+ addition with a higher sensitivity for Mg2+. On the contrary,a fluorescence quenching was observed when Cu2+, Fe3+, or Zn2+ ions were added. The potential applicability of the sensing approach described in this paper for magnesium ions and the sensing response mechanism are outlined.

A new efficient and highly selective fluorescent chemosensor for determination of Pb (2+) has been obtained by covalent attachment of two pendent proton-ionizable dansylcarboxamide groups to the calix[4]arene preorganized in the partial cone conformation. This geometry of the calixarene moiety was chosen on the basis of the prior (1)H NMR study of conformations adopted by the flexible dansyl-containing prototype upon complexation with lead ion. In acidic MeCN-H2O (1:1 v/v) solutions, the partial cone fluoroionophore allowed for detection of Pb (2+) at the levels as low as 2.5 ppb, which is totally compatible with the regulations of the U.S. Environmental Protection Agency and the World Health Organization on the limiting content of this hazardous pollutant in drinking water.

A series of new fluorescent probes bearing tren-spaced rhodamine B and dansyl groups have been synthesized. Compound 1 exhibits selective changes in the absorption and the emission spectra toward Cu2+ ion over miscellaneous metal cations. Among 1-3, 1 shows the best FRET efficiency through dansyl emission to rhodamine absorption for the Cu2+ ion.

Dimaleimide fluorogens are being developed for application to fluorescent protein labeling. In this method, fluorophores bearing two maleimide quenching groups do not fluoresce until both maleimide groups have undergone thiol addition reactions with the Cys residues of the target protein sequence [J. Am. Chem. Soc. 2005, 127, 559-566]. In this work, a new convergent synthetic route was developed that would allow any fluorophore to be attached via a linker to a dimaleimide moiety in a modular fashion. Series of dimaleimide and dansyl derivatives were thus prepared conveniently and used to elucidate the mechanism of maleimide quenching. Intersystem crossing was ruled out as a potential quenching pathway, based on the absence of a detectable triplet intermediate by laser flash photolysis. Stern-Volmer rate constants were measured with exogenous dimaleimide quenchers and found to be close to the diffusion-controlled limits, consistent with electron transfer being thermodynamically favorable. The thermodynamic feasibility of the photoinduced electron transfer (PET) quenching mechanism was verified by cyclic voltammetry. The redox potentials measured for dansyl and maleimide confirm that electron transfer from the dansyl excited state to a pendant maleimide group is exergonic and is responsible for fluorescence quenching of the fluorogens studied herein. Taking this PET quenching mechanism into account, future fluorogenic protein labeling agents will be designed with spacers of variable length and rigidity to probe the structure-property PET efficiency relationship.

Nitration of protein tyrosine residues is very often regarded as a molecular signal of peroxynitrite formation during development, oxidative stress, and aging. However, protein nitration might also have biological functions comparable to protein phosphorylation, mainly in redox signaling and in signal transduction. The major challenge in the proteomic analysis of nitroproteins is the need to discriminate modified proteins, usually occurring at substoichiometric levels from the large amount of nonmodified proteins. Moreover, precise localization of the nitration site is often required to fully describe the biological process. Existing methodologies essentially rely on immunochemical techniques either using 2D-PAGE fractionation in combination with western blot analyses or exploiting immunoaffinity procedures to selectively capture nitrated proteins. Here we report a totally new approach involving dansyl chloride labeling of the nitration sites that rely on the enormous potential of MSn analysis. The tryptic digest from the entire protein mixture is directly analyzed by MS on a linear ion trap mass spectrometer. Discrimination between nitro- and unmodified peptide is based on two selectivity criteria obtained by combining a precursor ion scan and an MS3 analysis. This new procedure was successfully applied to the identification of 3-nitrotyrosine residues in complex protein mixtures.

The interaction between the bovine pancrease trypsin (Tryp) and its competitive inhibitor benzamidine (1), in solution and the gas phase, is investigated using nanoflow electrospray ionization (nanoES) and Fourier transform ion cyclotron resonance mass spectrometry. In a recent study (Clark, S.M.; Konermann L. Anal. Chem. 2004, 76, 7077-7083), it was reported that the (Tryp + 1) complex could not be detected by ES-MS. Here, it is shown that, with gentle sampling conditions, it is possible to detect gaseous protonated ions of the (Tryp + 1) complex with nanoES-MS. However, the relative abundance of the detected (Tryp + 1)n+ ions is lower than expected, based on solution composition, which suggests that dissociation of (Tryp + 1)n+ ions occurs during MS sampling. The dissociation pathways and corresponding Arrhenius parameters for the protonated (Tryp + 1)n+ ions, at n = 7-9, are determined from time-resolved thermal dissociation experiments, implemented with the blackbody infrared radiative dissociation technique. The gaseous (Tryp + 1)n+ ions are found to have short lifetimes, e.g., <0.6 s, at temperatures of >100 degrees C. The use of solution additives, including polyols, carbohydrates, amino acids, and small organic molecules, to stabilize the (Tryp + 1)n+ ions during nanoES-MS analysis is investigated. Notably, the addition of imidazole to the nanoES solution is shown to preserve the (Tryp + 1)n+ ions. The Kassoc value, (1.9 +/- 0.2) x 104 M-1, determined for the (Tryp + 1) complex by the direct ES-MS method is in agreement with values determined by other analytical methods. The stabilizing effect of imidazole in nanoES-MS is further demonstrated for the interaction between carbonic anhydrase II and 5-(dimethylamino)naphthalene-1-sulfonamide. The stabilizing effect of imidazole may be due to enhanced evaporative cooling achieved by the dissociation of molecules of imidazole, bound nonspecifically, from the protein-ligand complex in the ion source.

This article describes a new two-step methodology for preparing thiol monolayers having artificial recognition sites for dansylated amino acids on gold optical biosensor surfaces. Nepsilon-Dansyl-L-lysine (DK) was used as the template molecule to form molecularly imprinted monolayers (MIMs). Impact factors that were studied were the concentration of DK in step one (template deposition) and the time and method for thiol monolayer formation in step two (backfilling). Compared to a prior method that used the simultaneous adsorption of the template and thiol from solution, this new approach provides the flexibility to imprint template molecules that have low binding energies on gold. Control over the surface density of imprinting sites can be achieved by this approach, and rebinding studies done using surface plasmon resonance spectroscopy confirmed that the MIMs prepared against DK showed selectivity for that template over didansyl-L-lysine.

Anthrancenyl and dansyl fluorophore ligands [AnCH2pipCS(2)K (1), Ds-Hen (2), Ds-HAMP (3), Ds-HAQ (4), and Ds-HAPP (5)] were prepared for coordination to Cu(II). Five Cu complexes, [Cu(AnCH2pipCS2)2] (6), [Cu(Ds-en)2] (7), [Cu(Ds-AMP)2] (8), [Cu(Ds-AQ)2] (9), and [Cu(Ds-APP)(OTf)] (10), were synthesized as candidates for detecting nitric oxide (NO) by fluorescence and characterized by X-ray crystallography. A decrease in fluorescence compared to that of the free ligands (1-5) was measured following the formation of the corresponding five Cu(II) complexes 6-10. Fluorescence was restored in the presence of NO in CH3OH/CH2Cl2 solutions of the compounds. Complexes 7, 8, and 10 exhibited a fluorescence response to NO in pH 7.0 or 9.0 buffered aqueous solutions. Spectroscopic studies revealed that NO-induced fluorescence enhancement in these Cu(II) complexes occurs by reduction to Cu(I). The present studies demonstrate that Cu(II) complexes are effective as fluorescent probes for detecting NO in both organic and aqueous environments.

The pH dependence of the PHM-catalyzed monooxygenation of dansyl-YVG was studied in two different buffer systems in the pH range of 4-10. The pH-activity profile measured in a sulfonic acid buffer exhibited a maximum at pH 5.8 and became inactive at pH >9. The data could be fit to a model that assumed a protonated unreactive species A, a major reactive species B, and a less reactive species C. B formed in a deprotonation step with pK(a) of 4.6, while C formed and decayed with pK(a)s of 6.8 and 8.2, respectively. The pH dependence was found to be dominated by k(cat), with K(m)(dansyl-YVG) remaining pH-independent over the pH range of 5-8. Acetate-containing buffers shifted the pH maximum to 7.0, and the activity-pH profile could be simulated by formation and decay of a single active species with pK(a)s of 5.8 and 8.3, respectively. The pH-dependent changes in activity could be correlated with a change in the Debye-Waller factor for the Cu-S(met) (M314) component of the X-ray absorption spectrum which underwent a transition from a tightly bound inactive "met-on" form to a conformationally mobile active "met-off" form with a pK(a) which tracked the formation of the active species in both sulfonic acid and acetate-containing buffer systems. The data suggested that the conformational mobility of the bound substrate relative to the copper-superoxo active species is critical to catalysis and further suggested the presence of an accessible vibrational mode coupling Cu-S motion to the H tunneling probability along the Cu-O...H...C coordinate.

Formation of a luminescent device by the Huisgen 1,3-dipolar cycloaddition reaction between a Eu(III) complex and dansyl azide is reported. This reaction is catalyzed by a common biological copper(I) complex [GS--Cu(I)], and the resultant copper(I) catalytic sensor shows a 10-fold enhancement of europium luminescence emission.

Treatment of cis-Pt(Me2SO)2Cl2 with DNSH-tren afforded [Pt(DNSH-tren)Cl]Cl and with DNSH-dienH, under increasingly more basic conditions, led to Pt(DNSH-dienH)Cl(2), Pt(DNSH-dien)Cl, and Pt(DNS-dien). (DNSH = 5-(dimethylamino)naphthalene-1-sulfonyl, linked via a sulfonamide group to tris(2-aminoethyl)amine (DNSH-tren) and diethylenetriamine (DNSH-dienH); the H's in DNSH-dienH designate protons sometimes lost upon Pt binding, i.e., sulfonamide NH for the dienH moiety and H8 for the DNSH moiety). Respectively, the three neutral DNSH-dienH-derived complexes are difunctional, monofunctional, and nonfunctional and exhibit decreasing fluorescence in this order as the dansyl group distance to Pt decreases. 2D NMR data establish that Pt(DNS-dien) has a Pt-C8 bond and a Pt-N(sulfonamido) bond. Pt(DNSH-dien)Cl and [Pt(DNSH-tren)Cl]Cl bind to N7 of 6-oxopurines (e.g., 5'-GMP, 3'-IMP, and 9-ethylguanine) and sulfur of methionine (met). Competition and challenge reactions for Pt(II) with met and 5'-GMP typically reveal that met binding is favored kinetically but that 5'-GMP binding is favored thermodynamically. This common type of behavior was found for [Pt(DNSH-tren)Cl]Cl. In contrast, Pt(DNSH-dien)Cl had reduced kinetic selectivity for met. This unusual behavior undoubtedly arises as a consequence of the bound Pt-N(sulfonamido) group, which donates strongly to Pt (as indicated by relatively upfield dien NH signals) and which places the bulky DNSH moiety close to the monofunctional reaction site. The decrease in the relatively upfield shifts of the DNSH group signals indicates that this group stacks with the purine. This stacking could explain the unprecedented, relatively low reactivity of a Pt complex bearing a dien-type ligand toward met vs 5'-GMP.