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

Abstract

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.

DNA Interaction Studies of an Anticancer Plant Alkaloid, Vincristine, Using Fourier Transform Infrared Spectroscopy

“…Spectral changes observed for guanine and cytosine base vibrations may be attributed to vincristine interaction with DNA via G-C base pairs. These results are in corroboration of the behavior of reserpine, another indole alkaloid, which showed binding preference to G-C-rich DNA duplex (Wang et al, 2008). The absorption band at 1607 cm À1 due to adenine remains unchanged in terms of shifting and intensity upon vincristine complexation with DNA.…”

Evaluation of flavonoids binding to DNA duplexes by electrospray ionization mass spectrometry

“…This fragmentation pattern is the same as that obtained for the well-known anthrapyrazole intercalators [43], suggesting that these flavonoid aglycones are likely to bind to the DNA duplexes via intercalation. Moreover, the low abundances of product ions resulted from base loss are indicative of weaker DNA-binding affinities of the flavonoid aglycones than those conventional intercalators previously studied [5,29,39]. The intercalative binding mode and weak binding affinities of the flavonoid aglycones toward DNA deduced from the tandem mass spectrometry are in fairly good agreements with the results obtained using solution-phase techniques [20,22,24].…”

“…The purpose of the present study is to evaluate the binding of flavonoids to DNA duplexes for the first time using ESI-MS. Five DNA sequences were involved (Table 2): two critical Sp-1 binding sites in human surviving promoter (duplexes 1 and 2) were selected as in our previous study [5]; the other three sequences with different GC and AT content (duplexes 3, 4, and 5) were also selected to further investigate possible sequence selectivities of the flavonoids. Binding sto- However, for duplex 2, the volume ratio of ss2a to ss2b was adjusted to 2:1 to ensure that the duplex ion was predominant in the spectrum.…”

Berberine Inhibits Fluphenazine-Induced Up-Regulation of <i>CDR1</i> in <i>Candida albicans</i>

“…tool to measure small molecules binding to specific dsDNA sequences. 32) We divided the DRE sequence found in the promoter of CDR1 into two parts: dsDNA1 of a 14 bp sequence containing CGG triplets in direct repeats and dsDNA2 consisting of 12 bp sequence rich in AT bases. Both dsDNAs were used to monitor binding of BBR to the DRE by negative ion ESI-MS.…”