Estimation of binding constants for complexes of polyamides and human telomeric DNA sequences by electrospray ionization mass spectrometry

Zhou, Jiang; Yuan, Gu; Tang, Feili

doi:10.1002/rcm.2597

Cited by 4 publications

(6 citation statements)

References 22 publications

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“…Previous studies have suggested that the negative ion mass spectra can effectively provide accurate pictures of the drug/DNA complexes present in solution 16–44. In our study, the alkaloids binding to the target DNA duplexes were first investigated using negative ion ESI‐MS, and relative binding affinities of the alkaloids to the duplexes were estimated.…”

Section: Resultsmentioning

confidence: 99%

“…Electrospray ionization mass spectrometry (ESI‐MS) has been proved to be a powerful tool for examining the drug/DNA complexes because of its low sample consumption and fast analysis time suitable for high throughput screening techniques 17, 18. Binding stoichiometry could be easily observed from the full scan mass spectra, while sequence selectivity19–23 and binding constants24, 25 could also be evaluated. Furthermore, the tandem mass spectra of the complexes may provide information about the binding mode 26–29.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, the tandem mass spectra of the complexes may provide information about the binding mode 26–29. To date, many well‐characterized drug/DNA complexes have been extensively studied by ESI‐MS 19–45. However, only a few recent efforts have been devoted toward the study of the binding of alkaloids to DNA by this versatile mass spectrometry technique 9–12, 16, 46…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…18,595,610,1033,1038,[1042][1043][1044][1045] ESI-MS revealed that minor groove binders form 1:1 and 2:1 complexes with DNA duplexes having a track of at least 4 A/T bases pairs (Figure 66). 12,13,489,506,521,595,609,610,622,955,1029,1034,1036,[1038][1039][1040][1041][1042][1043][1044][1045] The ratio between these stoichiometries mostly depends on the localization of ligand charges and on the sequence of the binding site. Among all the classical minor groove binders, distamycin A has the highest propensity to cooperatively form 2:1 complexes (Figure 66), 1040,955,506 with ligands arranged head-to-tail.…”

Section: Stoichiometriesmentioning

confidence: 99%

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

et al. 2021

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Nucleic acids have been among the first targets for antitumor drugs and antibiotics, and with the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to test target structure and ligand binding stoichiometry, affinity, specificity and binding modes are part of the drug development pipeline. Mass spectrometry offers unique advantages as a biophysical method due to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here we review the fundamentals of mass spectrometry and all its particularities when studying non-covalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands. 47

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“…The authors sorted the affinity of various polyamides against dsDNA by studying the effect of the molar ratio (dsDNA to polyamides) on binding or from competition studies. [43 -45] They also estimated binding constants [42] by assuming that the response of the complex was equivalent to that of the free dsDNA using an ion trap mass spectrometer. In this paper, we present a new method for the determination of the relative affinity of a ligand against various dsDNA sequences by using electrospray ionization time-of-flight mass spectrometry (ESI-QTOF) mass spectrometry.…”

Section: Introductionmentioning

confidence: 99%

A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder

Buchmann¹,

Boutorine²,

Halby³

et al. 2009

J. Mass Spectrom.

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A new method for the determination of the relative affinity of a ligand against various dsDNA sequences is presented by using electrospray ionization time-of-flight mass spectrometry (ESI-QTOF) mass spectrometry. The principle is described here through the complexation of double-stranded DNA by a polyamide ligand including twelve N-methylpyrrole rings. However this method could be applied to other ligands especially when dissociation constants (Kd) are in nanomolar range. This method does not require knowing the ligand concentration accurately. It allows determination of the relative affinity of a ligand against various dsDNA sequences for 1 : 1 complex stoichiometries in a quick manner without labeling.

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Estimation of binding constants for complexes of polyamides and human telomeric DNA sequences by electrospray ionization mass spectrometry

Cited by 4 publications

References 22 publications

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

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

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder

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