RNA Sequence Analysis using the Acid-Hydrolysis Method

Introduction

Oligonucleotides with various types of sequences, with antisense effect as well as RNA interference effects, have been synthesized in the course of nucleic acid drug development. Although quality control of synthetic oligonucleotides is essential, no standard method has been established for base sequencing of oligonucleotides with relatively few bases, in the order of 20-30 bases. Thus, there is need for a simple, yet highly reliable sequence analysis method. Here we investigated RNA sequencing analysis using the acid-hydrolysis method. We conducted investigation of acid-hydrolysis of a 21- base synthetic siRNA and 2'-O-methylated siRNA. A mixed solution of a low molecular weight matrix (3-hydroxypicolininc acid: 3HPA) and acid (trifluoroacetic acid: TFA) was added to the sample solution, and the mass spectrum was acquired by MALDI-TOF-MS. As a result, we were able to identify the entire 19-mer sequence except for 2 bases at the 3'-terminal, and were also able to verify that this is also effective for the 2'-O-methylation modified RNA.

December 3, 2010 GMT