MALDI‐MS detection of noncovalent interactions of single stranded DNA with Escherichia coli single‐stranded DNA‐binding protein

The Escherichia coli single‐stranded DNA binding protein (SSB) selectively binds single‐stranded (ss) DNA and participates in the process of DNA replication, recombination and repair. Different binding modes have previously been observed in SSB?ssDNA complexes, due to the four potential binding sites of SSB. Here, chemical cross‐linking, combined with high‐mass matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry (MS), is used to determine the stoichiometry of the SSB?ssDNA complex. SSB forms a stable homotetramer in solution, but only the monomeric species (m/z 19 100) can be detected with standard MALDI‐MS. With chemical cross‐linking, the quaternary structure of SSB is conserved, and the tetramer (m/z 79 500) was observed. We found that ssDNA also functions as a stabilizer to conserve the quaternary structure of SSB, as evidenced by the detection of a SSB?ssDNA complex at m/z 94 200 even in the absence of chemical cross‐linking. The stability of the SSB?ssDNA complex with MALDI strongly depends on the length and strand of oligonucleotides and the stoichiometry of the SSB?ssDNA complex, which could be attributed to electrostatic interactions that are enhanced in the gas phase. The key factor affecting the stoichiometry of the SSB?ssDNA complex is how ssDNA binds to SSB, rather than the protein‐to‐DNA ratio. This further suggests that detection of the complex by MALDI is a result of specific binding, and not due to non‐specific aggregation in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

Comparative studies of poly(dimethyl siloxanes) using automated GPC-MALDI-TOF MS and on-line GPC-ESI-TOF MS

In this study we compare on-line gel permeation chromatography (GPC) electrospray ionization (ESI) time-of-flight (TOF) mass spectrometry (MS) to automated GPC matrix assisted laser desorption ionization (MALDI) TOF MS for poly (dimethylsiloxane) (PDMS) analysis. Average mass values for a hydroxyl-terminated PDMS (OH-PDMS) sample were obtained and compared to traditional GPC that was calibrated with narrow polystyrene standards, by direct ESI and MALDI MS analysis, by a summation of mass spectra of all GPC fractions, and also by the recalibration method determined by both mass spectrometric methods. Quantitatively, the difference noted here between these hyphenated techniques is that GPC-ESI-TOF MS effectively reports the low-mass oligomers and underestimates the high-mass oligomers, while GPC-MALDI-TOF MS effectively reports the high-mass oligomers and underestimates the low-mass oligomers. In the GPC-ESI-TOF MS experiments, ion current suppression was observed in the high molecular weight region. The suppression effect was confirmed by repeatable sample runs and by injecting different PDMS samples. Higher chromatographic resolution was observed for GPC-ESI-TOF MS compared to GPC-MALDI-TOF MS. In fact, truly mono-disperse oligomers were observed in the low molecular weight range from GPC-ESI MS experiments.     

The Detection and Stability of DNA Duplexes Probed by MALDI Mass Spectrometry

Matrix‐assisted laser desorption/ionization (MALDI) with nonacidic matrices is shown to generate intact gas‐phase ions of double‐stranded DNA. Control experiments show that specific DNA duplexes are detected by this method, while nonspecific adducts form only when high monomer concentrations are present in the MALDI sample. The relative intensity of the duplex‐ion signal is found to reflect the solution‐phase stability of the double‐stranded DNA.     

Reactivity profiles of ligands of mammalian retinoic acid receptors: A preliminary COREPA analysis

Retinoic acid and associated derivatives comprise a class of endogenous hormones that bind to and activate different families of retinoic acid receptors (RARs, RXRs), and control many aspects of vertebrate development. Identification of potential RAR and RXR ligands is of interest both from a pharmaceutical and toxicological perspective. The recently developed COREPA (COmmon REactivity PAttern) algorithm was used to establish reactivity profiles for a limited data set of retinoid receptor ligands in terms of activation of three RARs ( f , g , n ) and an RXR ( f ). Conformational analysis of a training set of retinoids and related analogues in terms of thermodynamic stability of conformers and rotational barriers showed that these chemicals tend to be quite flexible. This flexibility, and the observation that relatively small energy differences between conformers can result in significant variations in electronic structure, highlighted the necessity of considering all energetically reasonable conformers in defining common reactivity profiles. The derived reactivity patterns for three different subclasses of the RAR ( f , g , n ) were similar in terms of their global electrophilicity (nucleophilicity) and steric parameters. However, the profile of active chemicals with respect to interaction with the RXR- f differed qualitatively from that of the RARs. Variations in reactivity profiles for the RAR versus RXR families would be consistent with established differences in their affinity for endogenous retinoids, likely reflecting functional differences in the receptors.     

Reactivity profiles of ligands of mammalian retinoic acid receptors: a preliminary COREPA analysis

Retinoic acid and associated derivatives comprise a class of endogenous hormones that bind to and activate different families of retinoic acid receptors (RARs, RXRs), and control many aspects of vertebrate development. Identification of potential RAR and RXR ligands is of interest both from a pharmaceutical and toxicological perspective. The recently developed COREPA (COmmon REactivity PAttern) algorithm was used to establish reactivity profiles for a limited data set of retinoid receptor ligands in terms of activation of three RARs (alpha, beta, gamma) and an RXR (alpha). Conformational analysis of a training set of retinoids and related analogues in terms of thermodynamic stability of conformers and rotational barriers showed that these chemicals tend to be quite flexible. This flexibility, and the observation that relatively small energy differences between conformers can result in significant variations in electronic structure, highlighted the necessity of considering all energetically reasonable conformers in defining common reactivity profiles. The derived reactivity patterns for three different subclasses of the RAR (alpha, beta, gamma) were similar in terms of their global electrophilicity (nucleophilicity) and steric parameters. However, the profile of active chemicals with respect to interaction with the RXR-alpha differed qualitatively from that of the RARs. Variations in reactivity profiles for the RAR versus RXR families would be consistent with established differences in their affinity for endogenous retinoids, likely reflecting functional differences in the receptors.     

Retinoid X receptor-antagonistic diazepinylbenzoic acids

Several dibenzodiazepine derivatives were identified as novel retinoid X receptor (RXR) antagonists on the basis of inhibitory activity on retinoid-induced cell differentiation of human promyelocytic leukemia cells HL-60 and transactivation assay using retinoic acid receptors (RARs) and RXRs in COS-1 cells. 4-(5H-2,3-(2,5-Dimethyl-2,5-hexano)-5-n- propyldibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX603, 6c) is an N-n-propyl derivative of an RXR pan-agonist HX600 (6a), and exhibited RXR-selective antagonistic activity. Similar RXR-antagonistic activities were observed with 4-(5H-2,3-(2,5-dimethyl-2,5-hexano)-5-methyl- 8-nitrodibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX531, 7a) and 4-(5H-10,11-dihydro-5,10-dimethyl-2,3-(2,5-dimethyl- 2,5-hexano)-dibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX711, 8b), which also inhibited transactivation of RARs induced by an RAR agonist, Am80. These compounds inhibited HL-60 cell differentiation induced by the combination of a low concentration of the retinoid agonist Am80 with an RXR agonist (a retinoid synergist, HX600). These results indicated that HX603 (6c), and the related RXR antagonists inhibit the activation of RAR-RXR heterodimers as well as RXR homodimers, which is a distinct characteristic different from that of the known RXR antagonist, LG100754 (9).     

Detection of specific noncovalent interaction of peptide with DNA by MALDI-TOF

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was used to obtain spectra of peptide-DNA complexes formed by basic domain (BD15) of c-Fos protein and DNA AP-1 site (5'-TGAGTCA-3'). The noncovalent interaction between single stranded DNA and BD15 was observed and confirmed to be an ionic one between the negatively charged sugar-phosphate backbone of DNA and positively charged side chains of Arg- and lys-rich peptides as demonstrated by Vertes and coworkers and Woods and coworkers. But the specific noncovalent interaction between DNA AP-1 site and the dimer of BD15 was firstly detected in this paper. Various different sequence DNAs were studied and it was found that this interaction is a sequence-specific one, and AP-1 site was essential for this interaction. This specific interaction depends on the matrix. It was only observed in the ATT matrix and not in the other two matrixes (CHCA and DHBA).     

Retinoidal pyrimidinecarboxylic acids. Unexpected diaza-substituent effects in retinobenzoic acids

Several pyridine- and pyrimidine-carboxylic acids were synthesized as ligand candidates for retinoid nuclear receptors, retinoic acid receptors (RARs) and retinoic X receptors (RXRs). Although the pyridine derivatives, 6-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carbamoyl]pyri dine-3-carboxylic acid (2b) and 6-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carboxamido]py ridine-3-carboxylic acid (5b) are more potent than the corresponding benzoic acid-type retinoids, Am80 (2a) and Am580 (5a), the replacement of the benzene ring of Am580 (5a), Am555 (6a), or Am55 (7a) with a pyrimidine ring caused loss of the retinoidal activity both in HL-60 cell differentiation assay and in RAR transactivation assay using COS-1 cells. On the other hand, pyrimidine analogs (PA series, 10 and 11) of potent RXR agonists (retinoid synergists) with a diphenylamine skeleton (DA series, 8 and 9) exhibited potent retinoid synergistic activity in HL-60 cell differentiation assay and activated RXRs. Among the synthesized compounds, 2-[N-n-propyl-N-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)a mino]pyrimidine-5-carboxylic acid (PA013, 10e) is most active retinoid synergist in HL-60 assay.     

Compelling Advantages of Negative Ion Mode Detection in High-Mass MALDI-MS for Homomeric Protein Complexes

Chemical cross-linking in combination with high-mass MALDI mass spectrometry allows for the rapid identification of interactions and determination of the complex stoichiometry of noncovalent protein–protein interactions. As the molecular weight of these complexes increases, the fraction of multiply charged species typically increases. In the case of homomeric complexes, signals from multiply charged multimers overlap with singly charged subunits. Remarkably, spectra recorded in negative ion mode show lower abundances of multiply charged species, lower background, higher reproducibility, and, thus, overall cleaner spectra compared with positive ion mode spectra. In this work, a dedicated high-mass detector was applied for measuring high-mass proteins (up to 200 kDa) by negative ion mode MALDI-MS. The influences of sample preparation and instrumental parameters were carefully investigated. Relative signal integrals of multiply charged anions were relatively independent of any of the examined parameters and could thus be approximated easily for the spectra of cross-linked complexes. For example, the fraction of doubly charged anions signals overlapping with the signals of singly charged subunits could be more precisely estimated than in positive ion mode. Sinapinic acid was found to be an excellent matrix for the analysis of proteins and cross-linked protein complexes in both ion modes. Our results suggest that negative ion mode data of chemically cross-linked protein complexes are complementary to positive ion mode data and can in some cases represent the solution phase situation better than positive ion mode.     

PSORALENS CLEAVE pBR322 DNA UNDER ULTRAVIOLET RADIATION

Supercoiled (SC) pBR322 was used to probe the recent claim that 5-geranoxylpsoralen (5-GOP) did not photoreact with DNA. Contrary to expectations, 5-GOP was found to damage DNA in the presence of UV-A through two competing pathways: (a) single strand breaks, identified by the conversion of supercoiled into open circular and linear DNA, and (b) cross-linking, revealed by the fluence-dependent decrease in the extent of denaturation of the double stranded supercoiled DNA to single stranded circular DNA. In addition, a fluence-dependent modification reduced the ability of the restriction enzyme EcoR I to linearize the photosensitized DNA, and alkali-labile lesions were generated. Psoralen, 5-methoxypsoralen, and 8-methoxypsoralen, which are well-known to undergo cycloaddition to DNA, had a more pronounced effect on supercoiled DNA. Single strand breaks occurred more readily than with 5-GOP, and the surviving SC form remaining had reduced electrophoretic mobility in agarose gels. In all cases, the DNA damage was more prominent when oxygen was absent.     

Disperse red 1 end capped oligoesters. Synthesis by noncatalyzed ring opening oligomerization and structural characterization

The synthesis of novel azofunctional oligoesters through bulk ring opening of ε‐caprolactone and D ,L ‐lactide (LA) at 100 and 130 °C, respectively, mediated by N‐ethyl‐N‐(2‐hydroxyethyl)‐4‐(4‐nitrophenylazo)aniline (Disperse Red 1) (DR1) is described. The synthetic procedure allows “clean” products because no catalysts were used in the reaction. Moreover, DR1 moiety is showed for the first time to promote the ring opening of cyclic esters. The molecular structure of the obtained oligoesters was established by NMR spectroscopy, MALDI ToF MS and electrospray ionization mass spectrometry (ESI MS). ESI‐MS/MS fragmentation experiments were used to demonstrate the nature of the chain end groups (hydroxyl and DR1). Intermolecular transesterification reactions were proved by mass spectrometry studies at least in the case of LA oligomerization. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 534–547, 2009     

MALDI coupled to modified traveling wave ion mobility mass spectrometry for fast enantiomeric determination

In this work, the use of MALDI traveling wave ion mobility spectrometry‐mass spectrometry (MALDI‐TWIMS‐MS) for stereoselective structural analysis of direct cleavage and identification of 2‐substituted piperidines obtained through solid‐phase asymmetric synthesis by using heterogeneous 8‐phenylmenthyl‐based chiral auxiliary resins. A strategy for gas‐phase chiral and structural characterization of small molecular weight molecules by using MALDI‐IMS‐MS technique is discussed. Because both MALDI and IMS do not directly offer chiral resolution, an easy methodology by adding a chiral phase is described to carry out in situ online ion/molecule complexation with different chiral analytes inside the mass spectrometer. Piperidine enantiomers were resolved, and separation obtained shows dependence of surface areas. To corroborate this assumption and elucidate the separation mechanism to accomplish an analytical technique by which fast determination of the chirality of molecules may be determined for a wide range organic compound applications, it was performed DFT calculations to determine the cross‐sectional areas of proton‐bound dimer complexes. Drift times are affected by cross‐sectional areas, correlating bigger times with bigger molecular volumes during the ion mobility experiments of proton‐bound dimer complexes.     

Probing the limits of liquid droplet laser desorption mass spectrometry in the analysis of oligonucleotides and nucleic acids

In the present work we demonstrate the advantages of LILBID mass spectrometry (laser‐induced liquid bead ion desorption) in the analysis of nucleic acids and large oligonucleotides. For established methods like matrix‐assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), the mass analysis of oligonucleotides or of noncovalent oligonucleotide‐protein complexes, in particular of very large ones, still represents a considerable challenge either due to the lack of native solutions or nonspecific adduct formation or due to a reduced salt tolerance or a high charge state of the ions. With LILBID, oligonucleotides, solvated in micro‐droplets of aqueous buffer at certain pH and ion strength, are brought into the gas phase by laser ablation. We show that our method is able to detect single‐ and double‐stranded oligonucleotides with high softness, demonstrated by the buffer dependence of the melting of a duplex. The absolute sensitivity is in the attomole range concomitant with a total analyte consumption in the femtomole region. The upper mass limit of oligonucleotides still detected with good signal‐to‐noise ratio with LILBID is the 1.66 MDa plasmid pUC19. With DNA ladders from short duplexes with sticky ends, we show that LILBID correctly reflects the relative thermodynamic stabilities of the ladders. Moreover, as an example for a specific DNA–protein complex we show that a NF‐κB p50 homodimer binds sequence specifically to its match DNA. In summary we demonstrate that LILBID, although presently performed only with low mass resolution, due to these advantages, is an alternative mass spectrometric method for the analysis of oligonucleotides in general and of specific noncovalent nucleic acid–protein complexes in particular. Copyright © 2009 John Wiley & Sons, Ltd.     

Epitope mapping on bovine prion protein using chemical cross-linking and mass spectrometry

An analytical strategy for the analysis of antigen epitopes by chemical cross-linking and mass spectrometry is demonstrated. The information of antigen peptides involved in the binding to an antibody can be obtained by monitoring the antigen peptides modified by a partially hydrolyzed cross-linker in the absence and in the presence of an antibody. This approach was shown to be efficient for characterization of the epitope on bovine prion protein bPrP(25-241) specifically recognized by a monoclonal antibody, 3E7 (mAb3E7), with only a small amount of sample (200 picomoles) needed. After cross-linking of the specific immuno complex, a matrix-assisted laser desorption/ionization (MALDI) mass spectrometer equipped with an ion conversion dynode (ICD) high-mass detector was used to optimize the amount of cross-linked complex formed at 202 kDa before proteolytic digestion. To identify the cross-linked peptides after proteolysis without ambiguity, isotope-labeled cross-linkers, disuccinimidyl suberate (DSS-d0/d12) and disuccinimidyl glutarate (DSG-d0/d6), together with high-resolution Fourier transform ion-cyclotron resonance mass spectrometry (FTICR-MS) were used. As a result, a complete fading of the peak intensities corresponding to the peptides representing the epitope was observed when bPrP/mAb3E7 complexes were formed.     

Double cation adduction in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of electron deficient anthraquinone derivatives

Six anthraquinone derivatives were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS). Clear (pseudo) molecular ions were observed for all the compounds. Interestingly, for some derivatives, strong ions with double cation adduction were also recorded in the positive mode. It is remarkable that all these ions are singly charged. In this work, possible mechanisms for the double cation adduction were investigated and discussed. It appears that the double cation adduction was due to the electron deficient nature of the derivatives, and formed by taking up two singly charged cations and one electron. Substituents on the anthraquinone ring were found to have a significant effect on the double cation adduction. In contrast, no considerable influence of the acidity of MALDI matrix/solution was observed, even on the double proton adduction. Furthermore, it was demonstrated that double cation adduction might occur in the MALDI gas-phase plume. In addition to the anthraquinones, three more electron deficient compounds of different types, i.e. a perylene bisimide derivative (PB), 3,7-decanoylamino-4,8-dihydrobenzo[1,2-b:4,5-b']dithiophene-4,8-dione (TQ) and 6,6-phenyl C61-butyric acid methyl ester (PCBM), were also analyzed with MALDI TOF MS. The results indicate that the 'abnormal' double cation adduction might be a 'normal' phenomenon in the MALDI TOF MS analysis of many electron deficient compounds.     

Development of a matrix-assisted laser desorption ionization mass spectrometric method for rapid process-monitoring of phthalocyanine compounds

Phthalocyanines (PCs), an important class of chemicals widely used in many industrial sectors, are macrocyclic compounds possessing a heteroaromatic π-electron system with optical properties influenced by chemical structures and impurities or by-products introduced during the synthesis process. Analytical tools allowing for rapid monitoring of the synthesis processes are of significance for the development of new PCs with improved performance in many application areas. In this work, we report a matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOFMS) method for rapid and convenient monitoring of PC synthesis reactions. For this class of compounds, intact molecular ions could be detected by MALDI using retinoic acid as matrix. It was shown that relative quantification results of two PC compounds could be generated by MALDI MS. This method was applied to monitor the bromination reactions of nickel- and copper-containing PCs. It was demonstrated that, compared to the traditional UV–visible method, the MALDI MS method offers the advantage of higher sensitivity while providing chemical species and relative quantification information on the reactants and products, which are crucial to process monitoring.     

Synthesis and photophysical evaluation of a pyridinium 4-amino-1,8-naphthalimide derivative that upon intercalation displays preference for AT-rich double-stranded DNA

The synthesis, characterisation and solid state crystal structure of a cationic 4-amino-1,8-naphthalimide derivative (1) are described. The photophysical properties of 1 are shown to vary with the solvent polarity and H-bonding ability. The fluorescence of 1 is enhanced and blue-shifted in its 1:1 complex with 5'-adenosine-monophosphate while it is partially quenched and red-shifted in its complex with 5'-guanosine-monophosphate. Linear and circular dichroism measurements show that 1 binds to double-stranded DNA by intercalation. Comparative UV-visible and fluorescence studies with double stranded synthetic polynucleotides poly(dA-dT)(2) and poly(dG-dC)(2) show that 1 binds much more strongly to the AT polymer; 1 also has a strong preference for A-T rich sequences in natural DNA. Thermal denaturation measurements also reveal a much greater stabilisation of the double-stranded poly(dA-dT)(2) than of natural DNA.     

Detection of Radical Adducts with Small Molecular Weights by Matrix-Assisted Laser Desorption/Ionization with Fourier Transform Mass Spectrometry

As an alternative method, matrix-assisted laser desorption/ionization with Fourier transform mass spectrometry （MALDI-FTMS） has been successfully used to detect and identify free radical adducts with small molecular weights of hydroxyl and 2-cyano-2-propyl radicals trapped with 5,5-dimethylpyrroline N-oxide （DMPO）. The detection and identification by MS/MS experiments using sustained offresonance irradiation collision-induced dissociation （SORI-CID） of [（DMPO＋·OH-·H）＋H^＋] （m/z 130.0868） and [DMPO＋2 ·CH（CH3）2CN＋H^＋] （m/z 250.1917） have demonstrated that MALDI-FTMS could be an effective method for detection and identification of free radical adducts. Other radical adducts have been also detected and identified. The approach of MALDI-FTMS is simple, fast, and sensitive which has potential for high-throughput analysis.     

Effect of sample preparation methods on the analysis of dispersed polysaccharides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Effect of sample preparation methods on the matrix-assisted laser desorption/ionization (MALDI) analysis of dispersed polysaccharides is reported. By using the conventional drop-drying method, the measured number-averaged molecular weights were found to differ significantly from the values obtained from gel-permeation chromatography (GPC). These discrepancies were found to increase as the average masses of the polysaccharides increased. To understand the impact of the sample preparation method on the MALDI measurement, a dispersed dextran sample was separated into ten narrow-distribution fractions. Mixtures of different mass fractions were prepared and analyzed by using different mixing and preparation methods. By using the ratio of the signal intensity for the low-mass fraction to that of the high-mass fraction as an indicator, the impact of sample preparation conditions on the enhancement of low-mass components (or suppression of high-mass components) was determined. From the results obtained, it is postulated that the difference in solubilities between the low-mass and high-mass components for dispersed polymers might be large enough to induce an enhancement of low-mass components (or suppression of high-mass components) at the surface of the crystals during sample crystallization in the drop-drying method.