Clustering of nucleobases with alkali metals studied by electrospray ionization tandem mass spectrometry: implications for mechanisms of multistrand DNA stabilization

Abstract

Self-clustering of the five common nucleobases was investigated by electrospray ionization tandem mass spectrometry and shown to provide insight into the non-covalent interactions between identical bases. Alkali and ammonium cations significantly increase self-aggregation of the nucleobases and lead to the formation of uniquely stable magic number clusters. Sodium adducts of guanine, thymine and uracil preferentially take the form of tetrameric (quartet) clusters. This gas-phase result correlates with previously reported solution-phase data on sodium cation stabilized guanosine, thymine and uracil quartet structures believed to be responsible for telomere stabilization. In the presence of potassium, cesium or ammonium cations, pentameric magic number clusters are formed from thymine and uracil, while in solution the nucleoside isoguanosine yields clusters of this favored size. The formation of magic number metaclusters occurs for thymine and uracil in the presence of ammonium cations. These doubly charged 10- and 15-mers are tentatively attributed to the formation of pentamer/ammonium cation/ pentamer sandwich structures.

Thymine quintets and their higher order assemblies studied by electrospray ionization mass spectrometry and theoretical calculation

“…The observation of [T 15 + 2M] 2+ was reported before by Koch et al for M = K + , Cs + , and NH 4 + , and such a metacluster was very briefly proposed to consist of three pentamers held by two cations simply based on its CID results. [26] Surprisingly, unlike our results described in the above section, [T 10 + M] + was not observed in their experiments except for uracil in the presence of NH 4 + . [26] In comparison with [T 15 + 2M] 2+ , [26] CID experiments on [T 15 …”

“…[4,12 -14] G-quartets have been investigated by several techniques including gel electrophoresis, [15,16] NMR, [17,18] circular dichroism, [19] scanning probe microscopy, [20] X-ray diffraction, [21,22] density functional theory (DFT) calculations [23,24] and electrospray ionization (ESI) mass spectrometry. [25,26] Recently, we reported that [G 4 + Na] + and [T 4 + Na] + can be directly produced as magic number clusters from ambient solid guanine and thymine samples mixed with NaCl by desorption electrospray ionization (DESI) mass spectrometry. [27] Very interestingly, however, when thymine was mixed with KCl, [T 5 + K] + appeared as the most dominant cluster ion.…”

Temperature-dependent IR spectroscopic and structural study of 18-crown-6 chelating ligand in the complexation with sodium surfactant salts and potassium picrate

“…Their selective cation binding makes them applicable for different environmental usage [5,6], drug delivery [7,8], recovery or removal of specific species, models for biological receptors [9], reaction catalysts as well as active sites in ion selective electrodes [10] or chromatographic agents [11]. Alkali metal elements have indispensable role in many biological processes, primarily to be as bulk electrolytes that stabilize surface charges on proteins and nucleic acids [12], and also play unique structural roles in biological systems [13,14]. Their complexes with crown ligands are coordination compounds based on electrostatic interaction through ion-dipole attractions [15], with the usage for simulations of natural substances, their properties and behavior.…”

Self-Assembling of cytosine nucleoside into triply-bound dimers in acid Media. A comprehensive evaluation of proton-bound pyrimidine nucleosides by electrospray tandem mass spectrometry, X-rays diffractometry, and theoretical calculations

“…Accordingly, the observation that a good correlation is shown by ESI and solutionphase data has, very recently, prompted the investigation of nucleoside self-clustering in the gas phase [20].…”