Biomedical subjects

Jennifer S Brodbelt

Publications and source records attributed to Jennifer S Brodbelt.

At least 37 records · Page 2Linked to original sources

PubMed2005

Influence of initial charge state on fragmentation patterns for noncovalent drug/DNA duplex complexes.

The charge state-dependent dissociation of various DNA duplexes and drug/duplex complexes has been investigated using collisionally activated dissociation (CAD) in a quadrupole ion trap mass spectrometer (QIT-MS). Several non-self-complementary 14-residue oligonucleotides were employed, in addition to an array of known DNA-interactive ligands, including the intercalators daunomycin and nogalamycin, as well as the minor groove binding agents distamycin, netropsin, 4',6-diamidino-2-phenylindole, and Hoechst 33342. In general, the dissociation pathways exhibited by both the duplexes and the drug/duplex complexes were found to be markedly sensitive to initial charge state. Time- and activation voltage-independent duplex strand separation predominated for higher charge states, which was interpreted to be a result of internal Coulombic repulsion or partial unzipping in the interface, while time- and activation voltage-dependent covalent cleavage predominated for lower charge states. The identity of the drug and the sequence of the duplex were both found to affect the competition between different dissociation processes. The dissociation pathways for the lower charge state complexes are probably more reflective of specific drug-DNA interactions because Coulombic and/or conformational effects are less marked for these precursors.

Benzimidazoles↗

PubMed2005

Charge state-dependent fragmentation of oligonucleotide/metal complexes.

Collision-activated dissociation (CAD) has been employed to assess the gas-phase fragmentation behavior of a series of 1:1 oligodeoxynucleotide (ODN):metal complexes over a range of charge states, using several ten-residue ODNs and a wide array of alkali, alkaline earth, and transition metals. For parent species in low to intermediate charge states, complexation with Ca(+2), Sr(+2), or Ba(+2) altered the relative intensity of M-B species, promoting loss of cytosine over loss of guanine. The relative intensities of sequence ions were largely unaffected. This behavior was most prevalent for isomeric sequences with complementary residues at the 5'- and 3'-termini, suggesting that metal complexation may change the gas-phase conformation and/or conformational dynamics for some sequences. In higher charge states, some ODN/Ba(+2) complexes produced abundant fragment ions corresponding to metallated a(n)(-m) species, which are not commonly observed in CAD mass spectra for deprotonated ODNs. The formation of these ions was most favored for complexes between Ba(+2) and ODN sequences with a thymine residue at Position 6. Literature precedent exists for the formation of a(n)(-m) ions from sequences in which covalent modification generates one or more neutral sites along the phosphate backbone. ODN/metal adducts in high charge states possess only a few acidic protons, and the juxtaposition of these neutral phosphate groups near thymine residues and the bound Ba(+2) ion may direct formation of the metallated a(n)(-m) species.

Base Sequence↗

PubMed2005

Threshold dissociation and molecular modeling of transition metal complexes of flavonoids.

The relative threshold dissociation energies of a series of flavonoid/transition metal/auxiliary ligand complexes of the type [MII (flavonoid - H) auxiliary ligand]+ formed by electrospray ionization (ESI) were measured by energy-variable collisionally activated dissociation (CAD) in a quadrupole ion trap (QIT). For each of the isomeric flavonoid diglycoside pairs, the rutinoside (with a 1-6 inter-saccharide linkage) requires a greater CAD energy and thus has a higher dissociation threshold than its neohesperidoside (with a 1-2 inter-saccharide linkage) isomer. Likewise, the threshold energies of complexes containing flavones are higher than those containing flavanones. The monoglycoside isomers also have characteristic threshold energies. The flavonoids that are glycosylated at the 3-O- position tend to have lower threshold energies than those glycosylated at the 7-O- or 4'-O- position, and those that are C- bonded have lower threshold energies than the O- bonded isomers. The structural features that substantially influence the threshold energies include the aglycon type (flavanone versus flavone), the type of disaccharide (rutinose versus neohesperidose), and the linkage type (O- bonded versus C- bonded). Various computational means were applied to probe the structures and conformations of the complexes and to rationalize the differences in threshold energies of isomeric flavonoids. The most favorable coordination geometry of the complexes has a plane-angle of about 62 degrees , which means that the deprotonated flavonoid and 2,2'-bipyridine within a complex do not reside on the same plane. Stable conformations of five cobalt complexes and five deprotonated flavonoids were identified. The conformations were combined with the point charges and helium accessible surface areas to explain qualitatively the differences in threshold energies for isomeric flavonoids.

Electrochemistry↗

PubMed2004

Screening flavonoid metabolites of naringin and narirutin in urine after human consumption of grapefruit juice by LC-MS and LC-MS/MS.

The main flavonoids in grapefruit juice, naringin and narirutin, were quantified by LC-MS with structural differentiation by LC-MS/MS. After human consumption of grapefruit juice, urine samples were collected for 24 hours and screened for flavonoid metabolites by LC-MS. The metabolite structures (glucuronides, sulfates, and glucuronide sulfates) were then confirmed via their unique fragmentation patterns by LC-MS/MS. To further verify the identity of the common aglycon (naringenin) shared by the metabolites, enzymatic hydrolysis was performed and the resulting products were analyzed. This work demonstrates that LC-MS and LC-MS/MS techniques can be used for fast metabolite screening without extensive sample preparation.

Adult↗

PubMed2004

Enhancing Hoogsteen interactions: a pyrrole-containing purine nucleoside that competes with guanosine self-assembly.

A pyrrole-appended purine nucleoside 1 is described that can form an "extended" three-point Hoogsteen-type interaction due to the stabilization of the donor-acceptor-acceptor (DAA) motif. Nucleoside 1 is shown to bind guanosine 10 (a classic ADD motif) to form ensemble I. This interaction competes effectively with guanosine self-assembly and, as such, is capable of disrupting guanosine quadruplex formation.

Binding, Competitive↗

PubMed2004

Gas-phase hydrogen/deuterium exchange and conformations of deprotonated flavonoids and gas-phase acidities of flavonoids.

Gas-phase hydrogen/deuterium (H/D) exchange was used to probe the conformations, gas-phase acidities, and sites of deprotonation of isomeric flavonoid aglycons and glycosides. The flavonoids in each isomer series were differentiated on the basis of their relative rate constants and total numbers of exchanges. For example, flavonoids that possess neohesperidose-type disaccharides may undergo faster and far more extensive exchange than isomeric rutinoside flavonoids. The structural factors that promote or prevent H/D exchange were identified and correlated with collisionally activated dissociation (CAD) patterns and/or molecular modeling data (both high-level ab initio acidity calculations and conformational analysis with molecular dynamics (MD) simulations), thus providing a framework for the use of H/D exchange reactions in the structural elucidation of new flavonoids.

Carbohydrates↗

PubMed2004

Collisionally activated dissociation and infrared multiphoton dissociation of oligonucleotides in a quadrupole ion trap.

Infrared multiphoton dissociation (IRMPD) of deprotonated and protonated oligonucleotides ranging from 5 to 40 residues has been performed in a quadrupole ion trap mass spectrometer at normal operating pressure and temperature. Only moderate exposure times and laser powers were required to achieve efficient dissociation. In general, IRMPD and collisionally activated dissociation (CAD) produce comparable sequencing information, indicating that IRMPD is a viable alternative to CAD for oligonucleotide analysis in the quadrupole ion trap. Two major characteristics distinguish CAD and IRMPD spectra for a given parent ion. First, structurally uninformative M-B ions that dominate CAD spectra are generally only low-intensity species in IRMPD spectra because nonresonant activation causes these species to dissociate to backbone cleavage products. Second, phosphate and nucleobase ions can be observed directly in IRMPD experiments because the low-mass cutoff can be set to trap small fragment ions. For this reason IRMPD can sometimes facilitate analysis of sequences containing modified bases.

Infrared Rays↗

PubMed2004

Comparison of sustained off-resonance irradiation collisionally activated dissociation and multipole storage-assisted dissociation for top-down protein analysis.

Tandem mass spectrometric data acquired for small (8-18 kDa) intact proteins by sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD) and multipole storage-assisted dissociation (MSAD) were compared, and the results indicate that the two activation methods do not always provide the same fragmentation patterns. In MSAD experiments, the charge state distribution made available by the ionization conditions may dictate the range of fragment ions that can be generated. In addition, conditions of high space charge within the hexapole impair transmission and/or trapping of high m/z species, which can result in loss of important precursor and product ions. Finally, the non-resonant nature of activation in MSAD can provide access to secondary dissociation processes that are not available by SORI. Because of these considerations, MSAD is less reliable than SORI for generating sequence tag data. However, it appears that MSAD samples 'preferred' cleavage processes (i.e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses.

Amino Acid Sequence↗

PubMed2004

MS(n) characterization of protonated cyclic peptides and metal complexes.

MS(n) experiments involving low energy collisionally activated dissociation (CAD) in a quadrupole ion trap were used to characterize the fragmentation of alkali, alkaline earth and transition metal complexes of five cyclic peptides, and the results were compared with those obtained for protonated cyclic peptides. Complexes with metal ions produced enhanced abundances of the most diagnostic fragments for elucidating the primary structures. For cyclosporin A, nickel and lithium complexes gave additional sequence information compared with the protonated peptide. For depsipeptides, sodium and lead complexes were superior to the protonated peptide or other metal complexes for sequencing residues, and CAD of the lead complexes led to preferential cleavage of two residues at a time. For cyclic lipopeptides, complexes with silver, nickel and strontium ions provided enhanced abundances of key fragment ions.

Anti-Bacterial Agents↗

PubMed2004

Determination of the glycosylation site of flavonoid monoglucosides by metal complexation and tandem mass spectrometry.

Metal complexation and tandem mass spectrometry were used to differentiate C- and O-bonded flavonoid monoglucoside isomers. Electrospray ionization of solutions containing a flavonoid glycoside and a metal salt led to the generation of the key [M(II) (L) (L-H)](+) complexes, where M is the metal ion and L is the flavonoid glycoside. Thirteen flavonoid monoglucosides were examined in combination with Ca(II), Mg(II), Co(II), Ni(II), and Cu(II). Collisional activated dissociation (CAD) of the [M(II) (L) (L-H)](+) complexes resulted in diagnostic mass spectra, in contrast to the CAD mass spectra of the protonated, deprotonated, and sodium-cationized flavonoid glucosides. Five common sites of glycosylation could be predicted based on the fragmentation patterns of the flavonoid glucoside/magnesium complexes, while flavonoid glucoside/calcium complexes also were effective for location of the glycosylation site when MS(3) was employed. Cobalt, nickel and copper complexation had only limited success in this application. The metal complexation methods were also applied for characterization of a flavonoid rhamnoside, and the dissociation pathways of the metal complexes indicate that flavonoid rhamnosides have distinctive dissociation features from flavonoid glucosides.

Binding Sites↗

PubMed2004

Evaluation of complexes of DNA duplexes and novel benzoxazoles or benzimidazoles by electrospray ionization mass spectrometry.

Electrospray ionization mass spectrometry is used to compare the metal ion binding and metal-mediated DNA binding of benzoxazole (1, 2, 3, 4) and benzimidazole (5) compounds and to elucidate the putative binding modes and stoichiometries. The observed metal versus non-metal-mediated DNA binding, as well as the specificity of DNA binding, is correlated with the biological activities of the analogs. The ESI-MS spectra for the antibacterial benzoxazole and benzimidazole analogs 4 and 5 demonstrated non-specific and non-metal-mediated binding to DNA, with the appearance of DNA complexes containing multiple ligands. The anticancer analog 2 demonstrates a clear preference for metal-mediated DNA interactions, with an apparent selectivity for Ni2+ -mediated binding over the more physiologically relevant Mg2+ or Zn2+ cations. Complexation between DNA and the biologically inactive analog 1 was not observed, either in the absence or presence of metal cations.

Anti-Bacterial Agents↗

PubMed2004

Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides.

Dissociation of protonated peptides via infrared multiphoton dissociation (IRMPD) provides more extensive sequence information than is obtained with collisionally activated dissociation (CAD) in a quadrupole ion trap due to the lack of the CAD low m/z cutoff and the ability to form secondary and higher order fragments with the non-resonant photoactivation technique. In addition, IRMPD is shown to be useful for the selective dissociation of phosphopeptides over those which are not phosphorylated because the greater photon absorption efficiency of the phosphorylated peptides leads to their more rapid dissociation. Finally, the selectivity of the IRMPD technique for phosphorylated species in complex mixtures is confirmed with the analysis of a mock peptide mixture and a tryptic digest of alpha-casein.

Amino Acid Sequence↗

PubMed2003

Structural characterization and detection of kale flavonoids by electrospray ionization mass spectrometry.

Sensitive and precise analytical methods are needed for flavonols, a subclass of flavonoids that has strong antioxidant activity. We report an improved method for identifying the predominant flavonols, quercetin and kaempferol, by collisionally activated dissociation (CAD) and quantifying them by high-performance liquid chromatography electrospray ionization mass spectrometry (HPLC-ESI-MS) in the selected ion monitoring mode. Practical applications of the method were demonstrated using several kale and biological samples. Two commercial kale samples were found to have 77 or 244 ppm quercetin and 235 or 347 ppm kaempferol (ppm = microg of quercetin/g of kale or microg of kaempferol/g of kale by fresh weight, 5-15% relative standard deviation). Blanching was found to reduce the flavonols to approximately 60% of the levels found in the unblanched kale. Isotopically labeled kale (cultivar Vates) grown in a greenhouse under an atmosphere of (13)CO(2) was found to have much lower flavonol levels. UV-A and UV-B supplementation during kale growth in the greenhouse was found to enhance both quercetin and kaempferol levels in Vates kale. The UV-B-supplemented kale not only produced more flavonols but the quercetin-to-kaempferol ratio was also higher than the UV-A-supplemented or the nonsupplemented kale. Recovery of flavonols from kale was approximately 60% based on spike and recovery trials with rutin, a glycoside of quercetin. Recovery of flavonols from biological samples spiked with rutin ranged from 96% for urine to 70% for plasma. Compared to UV detection, ESI-MS in the deprotonation mode provided lower detection limits, and both higher sensitivity and selectivity, in addition to structural characterization of the kale flavonols by CAD.

Brassica↗

PubMed2003

Novel guanosine-cytidine dinucleoside that self-assembles into a trimeric supramolecule.

[reaction: see text] Synthesis and assembly studies of a guanosine-cytidine dinucleoside 1 that self-assembles into a trimeric supramolecule (I) are presented. Dinucleoside 1 was obtained by utilizing two consecutive palladium-catalyzed cross-coupling reactions. Ensemble I was analyzed by ESI-MS, NMR spectroscopies, size exclusion chromatography (SEC), and vapor pressure osmometry (VPO).

Chromatography, Gel↗

PubMed2003

An equilibrium partitioning model for predicting response to host-guest complexation in electrospray ionization mass spectrometry.

While electrospray ionization mass spectrometry (ESI-MS) has become a powerful technique for analyzing many types of host-guest complexation, questions remain as to just how accurately ion abundances generated by ESI reflect the true distribution of species at equilibrium in solution. To better understand this relationship, an equilibrium partitioning model was developed to explain the various interactions that dictate how much of a particular host-guest complex is transferred from solution into the gas phase in the ESI process. By evaluating the simultaneous equilibria of the complexation reaction and the partitioning of species between the surface and interior of the ESI droplets, one can estimate the ion abundances generated. The predictions of this new model were evaluated and experimentally confirmed through the analysis of the complexes of 18-crown-6 with alkali metal cations in an ESI quadrupole ion trap mass spectrometer, and it was determined that binding constants alone may not give accurate predictions about the observed ESI-MS response to different host-guest complexes.

Journal Article↗

PubMed2003

Structural characterization and isomer differentiation of chalcones by electrospray ionization tandem mass spectrometry.

A series of chalcones were characterized by electrospray ionization tandem mass spectrometry (MS(n)). Several ionization modes were evaluated, including protonation, deprotonation and metal complexation, with metal complexation being the most efficient. Collision-activated dissociation (CAD) was used to characterize the structures, and losses commonly observed include H(2), H(2)O, CO and CO(2), in addition to methyl radicals for the methoxy-containing chalcones. CAD of the metal complexes, especially [Co(II) (chalcone-H) 2,2'-bipyridine](+), allowed the most effective differentiation of the isomeric chalcones with several diagnostic fragment ions appearing upon activation of the metal complexes. MS(n) experiments were performed to support identification of some fragment ions and to verify the proposed fragmentation pathways. In several cases, MS(n) indicated that specific neutral losses occurred by stepwise pathways, such as the neutral loss of 44 u as CH3* and HCO*, or CH(4) and CO, in addition to CO(2).

Chalcone↗

PubMed2003

Differentiation of flavonoid glycoside isomers by using metal complexation and electrospray ionization mass spectrometry.

The elucidation of flavonoid isomers is accomplished by electrospray ionization tandem mass spectrometry (ESI-MS/MS) via formation and collisional activated dissociation (CAD) of metal/flavonoid complexes containing an auxiliary ligand. Addition of a metal salt and a suitable neutral auxiliary ligand to flavonoids in solution results in the formation of [M(II) (flavonoid-H) ligand]+ complexes by ESI which, upon collisional activated dissociation, often result in more distinctive fragmentation patterns than observed for conventional protonated or deprotonated flavonoids. Previously, 2,2'-bipyridine was used as an auxiliary ligand, and now we compare and explore the use of alternative pyridyl ligands, including 4,7-diphenyl-1,10-phenanthroline. Using this technique, three groups of flavonoid glycoside isomers are differentiated, including glycosides of apigenin, quercetin, and luteolin.

2,2'-Dipyridyl↗

PubMed2003

Threshold dissociation energies of protonated amine/polyether complexes in a quadrupole ion trap.

Electrospray ionization mass spectrometry (ESI-MS) is increasingly used to probe the nature of noncovalent complexes; however, assessing the relevance of gas-phase results to structures of complexes in solution requires knowledge of the types of interactions that are maintained in a solventless environment and how these might compare to key interactions in solution. This study addresses the factors impacting the strength of hydrogen bonding noncovalent interactions in the gas phase. Hydrogen bonded complexes consisting of ammonium ions bound to polydentate ethers are transported to the gas phase with ESI, and energy-variable collisional activated dissociation (CAD) is used to map the relative dissociation energies. The measured relative dissociation energies are correlated with the gas-phase basicities and steric factors of the amine and polyether constituents. To develop correlations between hydrogen bonding strength and structural features of the donor and acceptor molecules, a variety of amines with different gas-phase basicities and structures were selected, including primary, secondary, and tertiary amines, as well as those that are bidentate to promote intramolecular hydrogen bonding. The acceptor molecules are polydentate ethers, such as 18-crown-6. Four primary factors influence the observed dissociation energies of the polyether/ammonium ion complexes: the gas-phase basicities of the polyether and amine, steric effects of the amines, conformational flexibility of the polyethers, and the inhibition of intramolecular hydrogen bonds of the guest ammonium ions in the resulting ammonium/polyether noncovalent complexes.

Journal Article↗