Elucidation of Nucleic Acid–Drug Interactions by Tandem Mass Spectrometry

Abstract

In continuation of the long tradition of mass spectrometric research at the University of Bern, our group focuses on the characterization of nucleic acids as therapeutic agents and as drug targets. This article provides a short overview of our recent work on platinated single-stranded and higher-order nucleic acids. Nearly three decades ago the development of soft ionization techniques opened a whole new chapter in the mass spectrometric analysis of not only nucleic acids themselves, but also their interactions with potential drug candidates. In contrast to modern next generation sequencing approaches, though, the goal of the tandem mass spectrometric investigation of nucleic acids is by no means the complete sequencing of genetic DNA, but rather the characterization of short therapeutic and regulatory oligonucleotides and the elucidation of nucleic acid-drug interactions. The influence of cisplatin binding on the gas-phase dissociation of nucleic acids was studied by the means of electrospray ionization tandem mass spectrometry. Experiments on native and modified DNA and RNA oligomers confirmed guanine base pairs as the preferred platination site and laid the basis for the formulation of a gas-phase fragmentation mechanism of platinated oligonucleotides. The study was extended to double-stranded DNA and DNA quadruplexes. While duplexes are believed to be the main target of cisplatin in vivo, the recently discovered DNA quadruplexes constitute another promising target for anti-tumor drugs owing to their regulatory functions in the cell cycle.

Target-Directed Approaches for Screening Small Molecules against RNA Targets

“…Historic MS-based approaches for identifying small molecules that bind to nucleic acid focused on direct MS detection of nucleic acid–small molecule complexes. 120 -126 These include approaches such as MASS (multitarget affinity/specificity screening) 127 and DOLCE-MS (detection of oligonucleotide ligand complexes by ESI-MS). 128 Limitations due to buffer restraints (MS interferers, i.e., K + and Mg + ), RNA size, and the need for high mass resolution and accurate mass detection hinder the use of these approaches for general large-scale screening for small molecules targeting RNA.…”

Mass spectrometry of modified RNAs: recent developments

“…63, 66 Labile modified nucleosides can yield strong neutral loss pathways that dominate the MS/MS spectrum (Table 1). Figure 7 illustrates the effect of labile modifications on mass spectral data.…”

“…53 As the number of MS/MS investigations of modified RNAs has increased, modification-specific fragmentation patterns have been observed in several cases. 63,66 Labile modified nucleosides can yield strong neutral loss pathways that dominate the MS/MS spectrum (Table 1). Fig.…”

Antileishmanial Drug Miltefosine‐dsDNA Interaction in situ Evaluation with a DNA‐Electrochemical Biosensor

“…The research of the interaction between toxic drugs and DNA has enabled to elucidate the implications in DNA structural modifications, and the mechanistic and cytotoxic aspects of the drugs physiological action. Different methods, such as AFM , capillary and gel electrophoresis , fluorescence , FTIR , tandem mass , NMR , Raman , UV‐Visible spectroscopies, surface plasmon resonance , viscosimetry and electrochemistry have been applied.…”