Interactions of cationic porphyrins with double‐stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry

Ramos, Catarina I. V.; Barros, Cristina; Fernandes, Ana M.; Santana-Marques, M. Graça; Correia, António; Tomé, João P. C.; Carrilho, Maria do Carmo T.; Faustino, Maria A. F.; Tomé, Augusto C.; Neves, Maria G. P. M. S.; Cavaleiro, José A. S.

doi:10.1002/jms.936

Cited by 21 publications

(22 citation statements)

References 51 publications

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“…Neither fragment ions generated by the loss of neutral bases from the intact dsDNA ions nor fragments from ssDNA were observed in the laser spray mass spectra, which is the same as the previous results of laser spray experiments in negative mode 34. This is an advantage of laser spray because considerable fragmentation of DNA moieties has been observed in ESI‐low energy CID mass spectra of dsDNA oligomers 11, 17, 22–24…”

Section: Resultssupporting

confidence: 84%

“…These results indicate that laser spray faithfully provides information on the thermal stabilities of the drug–DNA complexes. In contrast, in tandem mass spectra on ion‐trap16 and quadrupole22–24 instruments, fragment ions were observed in addition to those caused by the dissociation of the noncovalent complex, making it difficult to evaluate the complex stability by mass spectrometry.…”

Section: Resultsmentioning

confidence: 99%

“…Recently, a number of electrospray ionization mass spectrometry (ESI‐MS) studies have been carried out on dsDNA oligomers and their noncovalent complexes with drugs 7–24. This is because gas‐phase ions of nonvolatile and thermally labile molecules are readily formed by ESI 25–27.…”

Section: Introductionmentioning

confidence: 99%

“…If the binding of the drug molecules multiply to a dsDNA oligomer, as is often seen in the case of intercalators, it will be too complicated to analyze the binding affinities of these drugs. It has been demonstrated that ESI‐MS/MS experiments with ion‐trap16 or quadrupole mass spectrometers22–24 can give information on the relative binding affinities of various drugs to dsDNA oligomers. Unfortunately, however, considerable fragmentation of covalent bonds in DNA oligomers was observed as well as the dissociation of dsDNA into the corresponding two single strands.…”

Section: Introductionmentioning

confidence: 99%

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Stability analysis for double‐stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

et al. 2006

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Laser spray, which is a newly developed ionization technique, can characterize the stability of noncovalent complexes in the solution phase. By using this advantage, laser spray has been applied to probe the intrinsic stability of double-stranded DNA (dsDNA) sequences and their binding affinities with various drugs in the solution phase. Systematic experiments were carried out using six 16-mer and three 22-mer dsDNA oligomers, together with the complexes of the 16-mer dsDNA with minor groove binders: berenil, Hoechst 33342, DAPI, and netropsin. Dissociation curves for each dsDNA or each complex were plotted as a function of laser power. The laser power (E50%), where 50% of each dsDNA or each complex was dissociated, was compared with its melting temperature (Tm) determined by UV spectroscopy. Linear correlations between E50% and Tm were obtained not only for the dsDNA oligomers (correlation factor r = 0.9835) but also for the 16-mer dsDNA complexes with minor groove binders (r = 0.9966). In addition, laser spray has successfully clarified the binding affinities of a 16-mer dsDNA with two intercalators: daunomycin and nogalamycin. In the case of the dsDNA-daunomycin complex, by changing the molar ratio of dsDNA : drug from 1 : 1 to 1 : 5, the concentration-dependent stability of the complex was confirmed by laser spray. The present results demonstrate that laser spray mass spectrometry can be a powerful and convenient method to investigate the relative binding affinities of dsDNA-ligand complexes in the solution phase, which could be applied to the early stage of high-throughput screening of drugs targeting for dsDNA.

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Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Stability analysis for double‐stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

et al. 2006

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“…Overall, the DNA-binding affinities of the APs obtained by ESI-MS screening correlated with their inhibitory activities. ESI-MS has also been used to evaluate the complexation of other types of novel ligands (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40), including acridines (31), cationic porphyrins (36), cryptolepine alkaloids (37), protoberbine alkaloids (38), benzopyridoindole and benzopyridoquinoxaline compounds (32), and acridine-and naphthalene-derived macrocyclic bis-intercalators (33), with DNA duplexes.…”

Section: Figurementioning

confidence: 99%

Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry

Brodbelt

2010

Annual Rev. Anal. Chem.

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Electrospray ionization mass spectrometry (ESI-MS) has enabled the detection and characterization of DNA/ligand complexes, including evaluation of both relative binding affinities and selectivities of DNA-interactive ligands. The noncovalent complexes that are transferred from the solution to the gas phase retain the signature of the native species, thus allowing the use of MS to screen DNA/ligand complexes, reveal the stoichiometries of the complexes, and provide insight into the nature of the interactions. Ligands that bind to DNA via metal-mediated modes and those that bind to unusual DNA structures, such as quadruplexes, are amenable to ESI. Chemical probe methods applied to DNA/ligand complexes with ESI-MS detection afford information about ligand-binding sites and conformational changes of DNA that occur upon ligand binding.

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Studies on alkaloids binding to GC‐rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry

et al. 2007

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Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (including berberine, jatrorrhizine, palmatine, reserpine, berbamine, and tetrandrine) show complexation with the target DNA sequences. Relative binding affinities were estimated from the negative ion ESI data, and the alkaloids show a binding preference to the duplex with higher GC content. Positive ion ESI mass spectra of the complexes were also recorded and compared with those obtained in negative ion mode. Only the 1 : 1 complex with berbamine was observed with lower abundance in the positive ion mass spectrum while complexes with the other alkaloids were absolutely absent. Collision-induced dissociation (CID) experiments indicate that the complexes with the protoberberine alkaloids (berberine, jatrorrhizine, and palmatine) dissociate via base loss and covalent cleavage. In contrast, product ion spectra of the complexes with the alkaloids reserpine, berbamine, and tetrandrine show the predominant loss of a neutral alkaloid molecule, accompanied by base loss and covalent cleavage to a lesser extent. A comparison of the gas-phase behaviors of complexes with the alkaloids to those with the traditional DNA binders has suggested an intercalative binding mode of these alkaloids to the target DNA duplexes.

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Interactions of cationic porphyrins with double‐stranded oligodeoxynucleotides: a study by electrospray ionisation mass spectrometry

Cited by 21 publications

References 51 publications

Stability analysis for double‐stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

Stability analysis for double‐stranded DNA oligomers and their noncovalent complexes with drugs by laser spray

Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry

Studies on alkaloids binding to GC‐rich human survivin promoter DNA using positive and negative ion electrospray ionization mass spectrometry

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