Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

Schürch, Stefan; Bernal-Mendez, E.; Leumann, Christian (2002). Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides. Journal of the American Society for Mass Spectrometry, 13(8), pp. 936-945. Springer 10.1016/s1044-0305(02)00413-0

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The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions. (C) 2002 American Society for Mass Spectrometry.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Schürch, Stefan, Leumann, Christian


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Christian Leumann

Date Deposited:

19 May 2015 12:52

Last Modified:

05 Dec 2022 14:46

Publisher DOI:


Web of Science ID:


Additional Information:

Notes: ISI Document Delivery No.: 588ME
Times Cited: 50
Cited Reference Count: 32
Schurch, S Bernal-Mendez, E Leumann, CJ
Elsevier science inc
New york
Date: Aug
Type of Work: Article

Uncontrolled Keywords:

multiply-charged oligonucleotides collision-induced dissociation post-source-decay fragmentation mechanisms metastable decay nucleic-acids dna oligodeoxynucleotides ionization cleavage





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