Sequence Confirmation

Generally, although tandem mass spectrometry (MS/MS) is used to sequence nucleic acids, collision-induced dissociation (CID), the technique typically used for conventional ion cleavage, has been problematic because of the difficulty inproducing fragments that suggest particularly internalsequences. Matrix-assisted laser desorption / ionization (MALDI) is used as a technique for ionizing various biopolymers, including nucleicacids. MALDI can softly ionize a sample without causing unwanted fragmentation. However, by using a specific MALDI matrix with increased laser irradiation, it is possible to cause ionization and fragmentation at the same time. Then the resulting in-source decay (ISD) fragment ions can be used for structural analysis. MALDI-ISD fragmentation of nucleic acids provides successive fragment ions by simple cleavages and is therefore highly useful for simple sequencing of nucleic acids. This Application News describes an example of sequencing antisense nucleic acids by ISD fragmentation using a Shimadzu MALDI-8030 bench top linear MALDI-TOF mass spectrometer.

The functions of nucleic acid medicines are various: small interfering RNA (siRNA) to control protein synthesis by coupling with mRNA, miRNA to strengthen miRNA functions, aptamers that bind to a protein to inhibit its functions, and ribozymes to directly cleave the target RNA are but a few. Their basic structure is a chain comprising a few dozen (deoxy)nucleotides including adenine, thymine, guanine, cytosine, and uracil, which are components of DNA and RNA. Such nucleic acid medicines can be chemically synthesized without the need to culture cells as in antibody medicines. The obtained molecules are medium-sized having a molecular weight ranging from several thousands to tens of thousands. This article reports an example of determining a molecular weight and base sequence of synthetic nucleic acid using MALDI-TOF mass spectrometry.