Tandem Mass Spectrometry of Modified and Platinated Oligoribonucleotides

Abstract

Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2′-O-methyl-and methylphosphonatederivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS n ). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2′-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2′-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3′-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to w x -ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2′-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2′-O-methyl-and 2′-O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.

OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

“…The output obtained by considering all possible types of fragment ions is shown in Figure 6b. In contrast to unmodified RNA, abundant fragment ions were assigned as members of the d-and z-ion series, which is in good agreement with the dissociation mechanisms of methoxymethylphosphonate [8].…”

“…Cisplatin is one of the most widely used chemotherapeutic drugs and was found to form adducts with DNA, RNA, and proteins in vivo. The impact of cisplatin on the gas-phase dissociation of single-stranded DNA and RNA has been investigated extensively in the past few years [7,8].…”

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

“…[41][42][43][44] Because one can predict the fragment ions produced, one can also determine the sequence of an oligonucleotide based on the mass and the fragment ions generated de novo. From the precursor mass a list of potential nucleotide compositions can be generated, and depending on the enzyme used, some limitations of compositions can be incorporated into the analysis scheme.…”

Elucidation of Nucleic Acid–Drug Interactions by Tandem Mass Spectrometry

“…While methylphosphonate nucleic acids themselves are of interest for antisense applications, they represent a valuable instrument to study the role of specific phosphate groups in gas-phase recent years, a comprehensive armamentarium of dissociation mechanisms has been assembled, which can be applied to deciphering tandem mass spectrometric data obtained from DNA, RNA, and the many structurally altered oligonucleotide analogues. [6][7][8][9][10][11][12] …”

“…Comparative analysis of 2'-O-methyl oligoribonucleotides confirmed that the 2'-hydroxyl group is not involved in the formation of the high-intensity w-ion. [9] In fact, the platinated RNA dissociates in a DNA-like manner as a result of the cisplatin moiety that destabilizes the N-glycosidic bond.…”