Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides

Abstract

We report here on the analysis of synthetic oligonucleotides by electrospray ionization mass spectrometry (ESI-MS). After intensive removal of salt ions (especially sodium cations), negative ion mass spectra, allowing mass measurement with an accuracy of 0.01%, were obtained on several oligonucleotides up to 80 nucleotides. In most cases, the resolution was sufficient to observe n-1 and n-2 forms due to internal deletions during automated synthesis, and to identify the missing nucleotides. A 132-mer, whose size is close to the limit of automated chemical synthesis, was also successfully mass measured. A quantitative study showed that ESI-MS can provide quantitative data on oligonucleotides of similar size and structure. The described methodology is used to characterize oligonucleotide analogues such as phosphorothioate oligonucleotides designed for antisense applications. Finally, analyses in the positive ion mode on a trimer TpTpT in the presence of different amine bases were performed and allowed a better understanding of the influence of these bases on the ions formation.

Analysis of short tandem repeat polymorphisms by electrospray ion trap mass spectrometry

“…In the past, several strategies were developed to obtain sufficiently pure DNA samples. Most involved either ethanol precipitation (16,21,22,33,(38)(39)(40)(41) or centrifugation through appropriate filter systems/spin columns (30)(31)(32)34,41) followed by microdialysis (42)(43)(44) or incubation with cation exchange particles (17) for final desalting.…”

Electrospray ionisation mass spectrometry of ruthenium and palladium complexes with oligonucleotides

“…During the last decade the development of electrospray ionisation mass spectrometry (ESI-MS) has allowed accurate mass measurements to be performed on relatively large oligonucleotides including plasmid DNA. [15][16][17][18][19] ESI-MS has also been used for the characterisation of covalent [20][21][22][23][24] and non-covalent [25][26][27][28] drug-DNA complexes. For example, ESI-MS studies on DNA bound to the antibiotic hedamycin revealed that the drug selectively binds to specific DNA sequences and significantly increased the stability of duplex DNA in the gas phase.…”

RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template

“…Photo-crosslinked peptide conjugates containing RNA mono-and dinucleotides were not detected in the tryptic peptide mixtures. The low ionization efficiency of nucleic acids by electrospray in positive ion mode often causes signal suppression of crosslinked peptide-RNA entities (Potier et al 1994;Sannes-Lowery et al 1997). Also, unknown photoreaction mechanism of nucleotides, adverse reactions caused by long UV irradiation (Kubasek et al 1993), hampers prediction of the final products.…”