Mass Spectrometry Sequencing of Oligonucleotides

Mass spectrometry sequencing of oligonucleotides is not as common a practice as it is for proteins and peptides. However, the following mass spectrometry-based sequence determination strategies have gained acceptance  

---

R. P. Glover, G. M. A. Sweetman, P. B. Frama-, and G. C. K. Roberts, Sequencing of oligonucleotides using high performance Uquid chromatography and electrospray mass spectrometry. Rapid Commun. Mass Spectrom. 9, 97-102 (1995). 

McLafferty, F.W. Rapid Sequencing of Oligonucleotides by High-Resolution Mass Spectrometry. J. Am. Chem. Soc. 1994,116,4893-4897. 

Peptide and protein sequencing and its importance in the proteomics field were discussed in Section 2.2.3. The following gives a brief description of the mass spectrometry methods used to achieve sequencing. First, to produce protein or oligonucleotide structural/sequence information by mass spectro-metric techniques, one needs to use tandem mass spectrometry (MS-MS). In this technique, a sample is first fragmented and analyzed in one mass spec-... 

Mass spectrometry not only allows precise determination of the molecular weight of oligonucleotides, but also in a direct or indirect way the determination of their sequences. 

Negative mode FAB spectrum of an oligonucleotide with sequence UGUU. Reproduced (modified) from Grotjahn L., in Mass Spectrometry in Biomedical Research edited by Gaskell S.J., Wiley, New York, 1986, pp. 215-234, with permission. 

Oligonucleotides can undergo covalent modifications. [202] These can be natural ones such as those present in tRNA and rRNA but they can also result from reactions with exogenous substances and are the markers indicating possible degradations of the cells. They also can be modified chemically to create new drugs. Almost all these modifications are accompanied by variations in mass, and mass spectrometry is thus useful to identify their nature and position in the sequence. [203-205]... 

Smirnov, I.P., Roskey, M.T., Juhasz, P. et al. (1996) Sequencing oligonucleotides by exonuclease digestion and delayed extraction matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Anal. Biochem., 238 (1), 19-25. 

Ni, J.S., Pomerantz, S.C., Rozenski, J. et al. (1996) Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem., 68 (13), 1989-99. 

Xiong, W. et al. Separation and sequencing of isomeric oligonucleotide adducts using monohthic columns by ion-pair reversed phase nano HPLC coupled to ion trap mass spectrometry. AwaZ. Chem. 2007, 79, 5312-5321. 

Narayanaswamy, M. et al. An assay combining high-performance liquid chromatography and mass spectrometry to measure DNA interstrand cross-linking efficiency in oligonucleotides of varying sequences. Ana/. Biochem. 2008, 374,173-181. 

---