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Nucleic Acids Research, 1994, Vol. 22, No. 19 3895-3903
© 1994

MOLECULAR BIOLOGY

Negative electrospray ionization mass spectrometry of synthetic and chemically modified oligonucleotides

Noelle Potier, Alain Van Dorsselaer*, Yves Cordier1, Olivier Roch1 and Rainer Bischoff1

Laboratoire de Spectrométrie de Masse Bio-Organique assisté au CNRS, Université Louis Pasteur 67000 Strasbourg 1Transgène S.A. 11 rue de Molsheim, 67082 Strasbourg Cedex, France

*To whom correspondence should be addressed

Received July 29, 1994. Revised August 8, 1994. Accepted August 8, 1994.

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.


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