Oligonucleotide analysis

Molecular weight measurement of an intact oligonucleotide, up to at least 75-mers in size, can be performed using MALDI-TOF MS, in order to determine its intact mass and provide information on the degree of purity of the sample.

Oligonucleotide sequencing is used for the composition/sequence confirmation of deoxyribonucleotides up to 55-mers. Two methods can be applied, MALDI-TOF MS or ES-MS/MS.

Using MALDI-TOF MS - sequential nucleotide digestion of either end, using multiple concentrations of specific exonucleases, gives a distribution of fragments which can be analysed by MALDI-TOF MS.

Using ES-MS/MS - the technique of MSMS may be applied to the sequencing of oligonucleotides and relies upon assignment of fragment ions between each of the nucleotides. The methodology can be used for both DNA and RNA (or mixed) oligomers and requires no pre-treatment of phosphothioate linkages. Modified nucleotides may also be successfully analyzed and the technique can be applied to mixtures with no necessity to separate the individual species.