RNA Sequence Analysis using the Acid-Hydrolysis Method

Oligonucleotides with various types of sequences,with antisense effect as well as RNA interferenceeffects, have been synthesized in the course ofnucleic acid drug development. Although qualitycontrol of synthetic oligonucleotides is essential, nostandard method has been established for basesequencing of oligonucleotides with relatively fewbases, in the order of 20-30 bases. Thus, there isneed for a simple, yet highly reliable sequenceanalysis method.Here we investigated RNA sequencing analysis usingthe acid-hydrolysis method.We conducted investigation of acid-hydrolysis of a 21-base synthetic siRNA and 2'-O-methylated siRNA. Amixed solution of a low molecular weight matrix(3-hydroxypicolininc acid: 3HPA) and acid(trifluoroacetic acid: TFA) was added to the samplesolution, and the mass spectrum was acquired byMALDI-TOF-MS. As a result, we were able to identifythe entire 19-mer sequence except for 2 bases at the3'-terminal, and were also able to verify thatthis is also effective for the 2'-O-methylation modifiedRNA.

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Life Science Lab Instruments, Mass Spectrometry, MALDI-TOF Mass Spectrometry
Pharmaceutical, Life Science, Genomics, AXIMA Assurance
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