Dr. Ute Bahr, Goethe University Frankfurt, Institute of Pharmaceutical Chemistry

A novel, patented method for sequence analysis of RNA oligonucleotides based on acid hydrolysis has been published recently¹. Treatment of RNA oligonucleotides with strong acids at pH 1-2 rapidly leads to hydrolysis of the phosphodiester bonds at 5’-position of ribose. Analysis of the resulting degradation products by MALDI coupled to a high resolution mass spectrometer shows mass ladders from both sides of the nucleotides without interfering fragments from base losses or internal fragments. From the mass differences between adjacent peaks of a mass ladder the complete sequence can be determined (see Figure 1). This simple and fast method can be applied for controlling sequences of synthetic oligomers including double strands as well as for de-novo sequencing. Moreover, the method is applicable for localization and identification most RNA modifications.

¹ Ute Bahr, Hüseyin Aygün, Michael Karas
Sequencing of siRNA Single and Double Strands by Acid Hydrolysis and MALDI Mass Spectrometry.
Anal. Chem. 2009, 81, 3173-3179

Figure 1 | MALDI mass spectrum of a synthetic oligonucleotide after acid hydrolysis from a MALDI Orbitrap in the negative ion mode.

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