Analysis of noncovalent complexes between human telomeric DNA and polyamides containing N-methylpyrrole and N-methylimidazole by using electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to investigate noncovalent complexes formed between four novel polyamides containing N-methylpyrrole (Py) and N-methylimidazole (Im), and human telomeric DNA. Of the four polyamides investigated, PyPyPygammaImImImbetaDp (3) had the highest binding affinity towards the duplex d(TTAGGGTTAGGG/CCCTAACCCTAA) (D1). Results of competition analysis showed that the polyamides had binding affinities with D1 in the order PyPyPygammaImImImbetaDp (3)>PyPyPyPygammaPyImImPybetaDp (4)>PyPyPybetaImImImbetaDp (2)>ImImImbetaDp (1). MS/MS spectra confirmed that binding between D1 and the hairpin polyamides is more stable than that with the three-ring polyamides. By contrast, in the case of single-stranded d(TTAGGGTTAGGG)(D2), the binding order changes to ImImImbetaDp (1)>PyPyPygammaImImImbetaDp (3)>PyPyPybetaImImImbetaDp (2).     

Amino-catalyzed fragmentation characteristics of polyamides containing N-methylpyrrole and N-methylimidazole by electrospray negative ionization mass spectrometry

Different negative fragmentations of synthesized polyamides containing N-methylpyrrole and N-methylimidazole were analyzed by electrospray ionization tandem mass spectrometry with low-energy collision-induced dissociation. An interesting rearrangement derived from amino catalysis of N-methylimidazole was observed. The observation is useful for the study of the correlations between the sequences of polyamides and their mass fragmentation pathways.     

Studies on electrochemical oxidation mechanisms of polyamides containing N-methylpyrrole and N-methylimidazole by electrospray ionization tandem mass spectrometry

Electrochemical oxidization mechanism of polyamides containing N-methylpyrrole and N-methylimidazole was investigated by electrospray ionization tandem mass spectrometry (ESI-MS(n)). The spectra of the oxidization products unambiguously revealed that one or two oxygen atoms are added to the polyamide after the bulk electrolysis. It was found that electrochemical oxidation preferably takes place on the imidazole ring of the polyamide with both imidazole and pyrrole to produce a carbonyl group on the rings. ESI tandem mass spectrometry has proven to be an excellent method for the structural identification of electrochemical oxidation products of DNA-recognizing polyamides.     

Investigation of non-covalent complexes of HIV-1 promoter DNA and polyamides containing N-methylpyrrole by electrospray ionization mass spectrometry

Eight novel polyamides containing N-methylpyrrole were designed to target the sequence (5'-CTGCATATAAGCAG-3'/5'-CTGCTTATATGCAG-3') of the TATA box element of the HIV-1 promoter DNA. The non-covalent complexes of the promoter DNA and the polyamides were investigated by electrospray ionization (ESI) mass spectrometry, which provided strong evidence for the binding of the novel polyamides to the sequence of the TATA box element. It also revealed that polyamide 2 (PyPyPyPybetaDp), a potent binder of HIV-1 promoter DNA and a lead molecule for the design of new anti-HIV-1 drugs, had the highest binding affinity with the TATA box element DNA among these polyamides by examining the stoichiometry and the selectivity.     

Electrospray ionization mass spectrometric study of purine base-cisplatin complexes

By mixing cisplatin (cis-diamminedichloroplatinum(II)) with purine base the following ions have been obtained under electrospray ionization conditions: [A+Pt(NH3)2 Cl]+, [A+PtNH3Cl]+, [G+Pt(NH3)2 Cl]+ and [G+PtNH3)Cl]+. Their collision-induced dissociation led to the loss of NH3 and HCl and formation of the protonated base. The last process is strongly favoured for adenine over guanine. It confirms that, analogously as for DNA, formation of the guanine-cisplatin complex is favoured over that of the adenine complex and, as a consequence, it suggests that the mass spectrometric study of nucleic base complexes with platinum may provide some information on the interactions of DNA with other platinum drugs. The loss of NH3 accompanied by that of CO from the guanine ring has experimentally confirmed the presence of a strong hydrogen bond between the NH3 molecule and the O=C6 moiety of guanine found by theoretical calculations.     

Electrospray ionization mass spectrometric analysis of complexes between peptide‐derived Amadori products and borate ions

Hexose‐modified peptides, products of the enzymatic hydrolysis of glycated proteins, could be used as markers of diabetes mellitus, the aging process and other diseases. The main difficulty in this approach is the detection of glycated peptides in the complex mixtures of compounds. In this study we investigated the formation of borate complexes of the peptide‐derived Amadori products by high‐resolution mass spectrometry (HRMS) and tandem mass spectrometry (MS/MS) experiments. It was found that the formation of a complex with the borate ion stabilizes the sugar moiety, resulting in the simplification of the fragmentation patterns of peptide‐derived Amadori products. The level of dehydration, as well as the elimination of formaldehyde from the precursor ions of borate complexes, was lower as compared to the free peptide. On the other hand the intensity of the b‐ and y‐type ions for borate complexes is significantly higher in comparison to the free peptide‐derived Amadori product. Moreover, the elimination of a whole hexose moiety was not detected in the examined peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Electrospray ionization mass spectrometric study of 1,3,4-oxadiazole–copper complexes

The complexes of 2,5-disubstituted-1,3,4-oxadiazoles, namely 2,5-diphenyl-1,3,4-oxadiazole (1), 2,5-bis(2-pyridyl)-1,3,4-oxadiazole (2) and 2,5-bis(4-pyridyl)-1,3,4-oxadiazole (3), with copper cation were studied by electrospray ionization mass spectrometry (ESI-MS). The ability of the compounds studied to form complexes with copper (under the ESI conditions) can be ordered as 2 > 1 > 3. The compounds studied tend to form both 1 : 1 and 2 : 1 chelate complexes with both copper(II) and copper(I). The complexes with copper(I) are formed in the ESI process. The influence of solvent polarity, solution flow-rate, counter ions (Cl⁻, NO₃⁻, CH₃COO⁻, SO₄²⁻, acetylacetonates) on the type of the ions observed was studied. Copyright © 2004 John Wiley & Sons, Ltd.     

Electrospray ionization mass spectrometric analysis of highly reactive glycosyl halides

Highly reactive glycosyl chlorides and bromides have been analysed by a routine mass spectrometric method using electrospray ionization and lithium salt adduct-forming agents in anhydrous acetonitrile solution, providing salient lithiated molecular ions [M+Li]?, [2M+Li]? etc. The role of other adduct-forming salts has also been evaluated. The lithium salt method is useful for accurate mass determination of these highly sensitive compounds.     

Electrospray ionization tandem mass spectrometric characterization of DNA adducts formed by bromobenzoquinones

Bromobenzoquinones (BBQs) represent a class of reactive metabolites of various aromatic contaminants with bromine-containing substituents, including bromobenzene, bromophenols, polybrominated diphenyl ethers (PBDEs). Recently, 2,6-dibromobenzoquinone also has been detected directly from drinking water. The alternation of the genome caused by covalent binding of chemicals or their metabolites to DNA provides a viable mechanism for carcinogenicity. In the present study, electrospray ionization coupled with ion trap mass spectrometry (ITMS), triple quadrupole MS or quadrupole time-of-flight MS was applied for the analysis of DNA adducts formed by BBQs. The study demonstrated 2-monobromobenzoquinone and 2,6-dibromobenzoquinone could covalently bind to deoxyguanosine (dG) and DNA in vitro. The chemical structures of the DNA adducts were confirmed by accurate mass values, collision-induced fragmentation tandem mass spectra as well as isotopic patterns. Generally, the reaction mechanism for the DNA adduction involved Michael addition between the electron-deficient carbon from the quinone and the nucleophilic exocyclic nitrogen from the dG followed by reductive cyclization with loss of a small molecule such as H(2)O, or HBrO. It was of particular interest to note that some adducts were generated from the reaction of one dG molecule with two BBQ molecules. The obtained results provided new information for assessing the potential cancer risk associated with bromobenzene, bromophenols, PBDEs and BBQs.     

Electrospray ionization mass spectrometric fragmentation of hydroquinone derivatives

The fragmentation patterns of nine di-, tri- and tetracyclic hydroquinones with potential antitumor activity were rationalized by invoking competing mechanisms that included sterically accelerated homolytic cleavage, Meerwein-type rearrangements and dehydrations through elimination or intramolecular nucleophilic substitution.     

Electrospray ionization mass spectrometric analysis of self-assembled 1,1′-ferrocenedicarboxylic acid

Self-assembly of 1,1′-ferrocenedicarboxylic acid in solution was detected by electrospray mass spectrometry (ESI-MS). The ESI mass spectra showed the acid was self-assembled as a cyclic tetramer in methanol and acetonitrile, and the tetramer was found to complex more strongly with the sodium ion than with any other alkali metal ion. The result was supported by semiempirical molecular orbital calculations, which indicate that the tetramer possesses a cyclic structure like a pseudo-crown ether, and its internal diameter is consistent with the diameter of a sodium ion.     

Electrospray ionization mass spectrometric analysis of nucleic acids using high-throughput on-line desalting

A rapid on-line desalting method utilizing ion-pair reversed-phase high-performance liquid chromatography (IP-RP-HPLC) was employed in tandem with negative electrospray ionization mass spectrometry (ESI-MS) for the routine analysis of nucleic acids. Desalting was performed on a short 10 x 2.1 mm guard column packed with 3.5 microm C(18) sorbent. The HPLC system was connected in-line to an orthogonal ESI-TOF mass spectrometer via a six-port, two-position switching valve, allowing desalting followed by mass analysis of nucleic acids. Duty cycle times for the method were as low as 1.5 min per sample. This allowed for the analysis of approximately 950 samples per 24-h time period, which is suitable for medium- to high-throughput applications. Average mass accuracy was determined to be 80 ppm for oligonucleotides up to 110 mer in length with external calibration. The method was utilized for synthetic oligonucleotide quality control and analysis of DNA genotyping fragments.