RESUMEN
The interactions between a novel enediyne [1-methyl-2-(phenylethynyl)-3-(3-phenylprop-2-ynyl)-3H-benzimidazolium] (1) and various cytosine-containing oligonucleotides were studied using electrospray ionization mass spectrometry (ESI-MS) in a flow injection analysis mode useful for small volumes. This enediyne ligand, developed as a potential alternative to the highly cytotoxic natural enediynes, some of which have been successfully used as anti-tumor agents, has previously been shown to interact with DNA through frank strand scission as well as via the formation of adducts that lead to 2'-deoxycytidine-specific cleavage. Through ESI-MS, the structures of these adducts were examined and a sequence dependence of the 2'-deoxycytidine-specific cleavage was noted. Collisionally activated dissociation of the observed adducts confirmed the strength of the interactions between the enediyne and DNA and supports a direct linkage between the enediyne and the cytosine nucleobase, likely the result of a nucleophilic attack of the phenylethynyl group by the cytosine amine.
Asunto(s)
Alquinos/química , Bencimidazoles/química , Aductos de ADN/análisis , Electroforesis en Gel de Poliacrilamida , Indicadores y Reactivos , Oligonucleótidos/análisis , Piperidinas/química , Espectrometría de Masa por Ionización de Electrospray , Espectrometría de Masas en TándemRESUMEN
[reaction: see text] Synthesis and assembly studies of a guanosine-cytidine dinucleoside 1 that self-assembles into a trimeric supramolecule (I) are presented. Dinucleoside 1 was obtained by utilizing two consecutive palladium-catalyzed cross-coupling reactions. Ensemble I was analyzed by ESI-MS, NMR spectroscopies, size exclusion chromatography (SEC), and vapor pressure osmometry (VPO).
Asunto(s)
Citidina/química , Guanosina/química , Cromatografía en Gel , Citidina/análogos & derivados , Guanosina/análogos & derivados , Espectroscopía de Resonancia Magnética , Peso Molecular , Paladio/química , Presión , Espectrometría de Masa por Ionización de Electrospray , VolatilizaciónRESUMEN
Based on binding studies undertaken by electrospray ionization-mass spectrometry, a synthetic pyrrole-inosine nucleoside, 1, capable of forming an extended three-point Hoogsteen-type hydrogen-bonding interaction with guanine, is shown to form specific complexes with two different quadruplex DNA structures [dTG(4)T](4) and d(T(2)G(4))(4) as well as guanine-rich duplex DNA. The binding interactions of two other analogs were evaluated in order to unravel the structural features that contribute to specific DNA recognition. The importance of the Hoogsteen interactions was confirmed through the absence of specific binding when the pyrrole NH hydrogen-bonding site was blocked or removed. While 2, with a large blocking group, was not found to interact with virtually any form of DNA, 3, with the pyrrole functionality missing, was found to interact non-specifically with several types of DNA. The specific binding of 1 to guanine-rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition.
Asunto(s)
Guanina/metabolismo , Inosina/química , Nucleósidos/química , Nucleósidos/metabolismo , Pirroles/química , Composición de Base , Secuencia de Bases , ADN de Cadena Simple/química , ADN de Cadena Simple/genética , ADN de Cadena Simple/metabolismo , G-Cuádruplex , Guanina/química , Enlace de Hidrógeno , Ligandos , Nucleósidos/síntesis química , Oligonucleótidos/química , Oligonucleótidos/genética , Oligonucleótidos/metabolismo , Espectrometría de Masa por Ionización de Electrospray , Especificidad por SustratoRESUMEN
Mathematical models based on equilibrium partitioning theory were developed to relate ion abundances produced by electrospray ionization mass spectrometry with solution concentrations of complexes resulting from competitive host-guest binding. Through modeling the possible equilibria in the electrospray droplets, including the partitioning between the droplet surface and interior that dictate what ions are generated by an electrospray, the factors responsible for distorting the distribution of ions from their solution concentrations were evaluated. Experiments with crown ether-alkali metal complexes confirm the validity of the models and yield a greater understanding of the behavior of host-guest complexes in ESI-MS, allowing for more accurate and less trouble-prone measurements of solution binding interactions.
RESUMEN
While electrospray ionization mass spectrometry (ESI-MS) has become a powerful technique for analyzing many types of host-guest complexation, questions remain as to just how accurately ion abundances generated by ESI reflect the true distribution of species at equilibrium in solution. To better understand this relationship, an equilibrium partitioning model was developed to explain the various interactions that dictate how much of a particular host-guest complex is transferred from solution into the gas phase in the ESI process. By evaluating the simultaneous equilibria of the complexation reaction and the partitioning of species between the surface and interior of the ESI droplets, one can estimate the ion abundances generated. The predictions of this new model were evaluated and experimentally confirmed through the analysis of the complexes of 18-crown-6 with alkali metal cations in an ESI quadrupole ion trap mass spectrometer, and it was determined that binding constants alone may not give accurate predictions about the observed ESI-MS response to different host-guest complexes.
RESUMEN
A pyrrole-appended purine nucleoside 1 is described that can form an "extended" three-point Hoogsteen-type interaction due to the stabilization of the donor-acceptor-acceptor (DAA) motif. Nucleoside 1 is shown to bind guanosine 10 (a classic ADD motif) to form ensemble I. This interaction competes effectively with guanosine self-assembly and, as such, is capable of disrupting guanosine quadruplex formation.