OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids

Nyakas, Adrien; Blum, Lorenz C.; Stucki, Silvan R.; Reymond, Jean-Louis; Schürch, Stefan (2013). OMA and OPA—Software-Supported Mass Spectra Analysis of Native and Modified Nucleic Acids. Journal of the American Society for Mass Spectrometry, 24(2), pp. 249-256. Springer-Verlag 10.1007/s13361-012-0529-1

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The platform-independent software package consisting of the oligonucleotide mass assembler (OMA) and the oligonucleotide peak analyzer (OPA) was created to support the analysis of oligonucleotide mass spectra. It calculates all theoretically possible fragments of a given input sequence and annotates it to an experimental spectrum, thus, saving a large amount of manual processing time. The software performs analysis of precursor and product ion spectra of oligonucleotides and their analogues comprising user-defined modifications of the backbone, the nucleobases, or the sugar moiety, as well as adducts with metal ions or drugs. The ability to expand the library of building blocks and to implement individual structural variations makes it extremely useful for supporting the analysis of therapeutically active compounds. The functionality of the software tool is demonstrated on the examples of a platinated doublestranded oligonucleotide and a modified RNA sequence. Experiments also reveal the unique dissociation behavior of platinated higher-order DNA structures.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Nyakas, Adrien; Reymond, Jean-Louis and Schürch, Stefan

Subjects:

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

ISSN:

1044-0305

Publisher:

Springer-Verlag

Funders:

[4] Swiss National Science Foundation

Language:

English

Submitter:

Stefan Schürch

Date Deposited:

12 Apr 2014 10:49

Last Modified:

23 Oct 2019 16:56

Publisher DOI:

10.1007/s13361-012-0529-1

Uncontrolled Keywords:

DNA, RNA, Oligonucleotides, Tandem mass spectrometry, Software, Fragmentation, Double-stranded DNA, Nucleic acids, Cisplatin

BORIS DOI:

10.7892/boris.42717

URI:

https://boris.unibe.ch/id/eprint/42717

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