Mass Spectroscopic Study of G-Quadruplex
Mass spectrometry (MS) is an analytical tool complimentary for being sensitive, accurate, and versatile in its application, such as the identification of multistranded nucleic acid assemblies, including G-quadruplex. More specifically, electrospray ioniza
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Introduction Current mass spectrometry (MS) techniques have immense potential for characterizing the high-order structure of nucleic acids and the elucidation of their cellular interactions, primarily due to the high sensitivity of the techniques and their ability to detect non-covalent interactions [1]. Mass spectrometry has begun to incorporate new technologies to provide further support for the presence of G-quadruplex assemblies, such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) [2, 3]. In 1984, the development of electrospray ionization mass spectrometry (ESI-MS) defined a milestone in modern bioanalysis [4]. ESI is considered a “soft” ionization technique that produces ions using an electrospray in which an aerosol is generated by applying a high voltage to a liquid. Since multiple-charged ions may be formed, it is notably effective in producing ions from biological macromolecules because it reduces the amount of fragmentation that occurs when these molecules are ionized [5].
Danzhou Yang and Clement Lin (eds.), G-Quadruplex Nucleic Acids: Methods and Protocols, Methods in Molecular Biology, vol. 2035, https://doi.org/10.1007/978-1-4939-9666-7_6, © Springer Science+Business Media, LLC, part of Springer Nature 2019
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Huihui Li
In 1993, Goodlett et al. directly observed a stable four-stranded G-quadruplex DNA in the presence of monoatomic cations using negative ESI-MS [6]. Another soft ionization method is matrix assisted laser desorption ionization (MALDI), which uses a matrix absorbing a laser energy to create ions [7]. MALDI is a powerful tool for the analysis of single large biomolecules, especially proteins. Since the matrix used for MALDI-MS is usually acidic and denaturing, macrobiomolecular complexes (such as DNA-drug complex) cannot be preserved in the MALDI process. Besides, there are some separation methods used for distinguishing various G-quadruplex structures. Among them, ion mobility spectrometry (IMS) could separate ions with different shape and charge. IMS coupled with MS (IMS-MS) can provide information on collision cross section (CCS) related to the arrival time of an ion inside the mobility cell. It is still debatable whether the CCSs obtained by IMS-MS is consistent with those from in-solution measurements. However, IMS-MS has been successfully used to gain information on the similar telomeric G-quadruplex shape preserving K+ or NH4+ ions [8]. We have demonstrated that the noncovalent interactions, which stabilize the multistranded motifs in solution, can be efficiently preserved in the gas phase during the ESI process [2]. For stable G-quadruplexes, the oligonucleotides could be dissolved in a small amount of KCl (up to 1 mM) using trimethylammonium acetate (TMAA), which is a volatile bulky buffer not fit into the G-quadruplex cavity [7]. However, low stability G-quadruplexes were not easily detected and appeared with poor resolution in the ESI-MS spectra. On the other hand, the presence of K+ ions, which is usually needed to stabi
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