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Self reporting RNA probes as an alternative to cleavable small molecule mass tags

Self reporting RNA probes as an alternative to cleavable small molecule mass tags
Self reporting RNA probes as an alternative to cleavable small molecule mass tags
The large size of biological molecules such as proteins and oligonucleotides makes them inherently problematic to analyse and quantify directly by mass spectrometry. For these molecules, electrospray ionisation produces multiply charged species and associated alkali metal adducts which can reduce sensitivity and complicate quantification. Whereas time-of-flight mass analysers, often coupled to matrix-assisted laser desorption/ionisation, can have insufficient mass resolution to resolve these large molecules in the higher m/z range. This has led to the development of cleavable small molecule mass tag approaches for the indirect analysis of biomolecules such as proteins and oligonucleotides. Existing methodologies require the design and synthesis of a cleavable linker to join the biomolecule and the mass tag. Here, an alternative approach to small molecule mass tags is presented, which exploits the properties of the RNA molecule to afford self-reporting probes which can be easily synthesised using automated phosphoramidite chemistry. The sugar-phosphate backbone of RNA was used as a built-in enzyme cleavable linker and through the use of RNase digestion of bromine labelled oligonucleotides the observation of a range of small molecule mass tags by mass spectrometry is demonstrated. This study provides a proof-of-concept that RNase digestion can be used to produce labelled small molecule mass tags from oligonucleotide probes, thus eliminating the need for custom design and synthesis of a cleavable linker.
0003-2654
5817-5822
Riley, Jo-Anne
a4cc980c-b007-466f-93d0-4dfc3ed4f738
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Gale, Nittaya
eead6253-2431-407b-ab6b-92e35d41c3ef
Herniman, Julie
530b1a36-1386-4602-8df7-defa6eb3512b
Langley, G. John
7ac80d61-b91d-4261-ad17-255f94ea21ea
Riley, Jo-Anne
a4cc980c-b007-466f-93d0-4dfc3ed4f738
Brown, Tom
a64aae36-bb30-42df-88a2-11be394e8c89
Gale, Nittaya
eead6253-2431-407b-ab6b-92e35d41c3ef
Herniman, Julie
530b1a36-1386-4602-8df7-defa6eb3512b
Langley, G. John
7ac80d61-b91d-4261-ad17-255f94ea21ea

Riley, Jo-Anne, Brown, Tom, Gale, Nittaya, Herniman, Julie and Langley, G. John (2012) Self reporting RNA probes as an alternative to cleavable small molecule mass tags. Analyst, 137 (24), 5817-5822. (doi:10.1039/C2AN36086A). (PMID:23096125)

Record type: Article

Abstract

The large size of biological molecules such as proteins and oligonucleotides makes them inherently problematic to analyse and quantify directly by mass spectrometry. For these molecules, electrospray ionisation produces multiply charged species and associated alkali metal adducts which can reduce sensitivity and complicate quantification. Whereas time-of-flight mass analysers, often coupled to matrix-assisted laser desorption/ionisation, can have insufficient mass resolution to resolve these large molecules in the higher m/z range. This has led to the development of cleavable small molecule mass tag approaches for the indirect analysis of biomolecules such as proteins and oligonucleotides. Existing methodologies require the design and synthesis of a cleavable linker to join the biomolecule and the mass tag. Here, an alternative approach to small molecule mass tags is presented, which exploits the properties of the RNA molecule to afford self-reporting probes which can be easily synthesised using automated phosphoramidite chemistry. The sugar-phosphate backbone of RNA was used as a built-in enzyme cleavable linker and through the use of RNase digestion of bromine labelled oligonucleotides the observation of a range of small molecule mass tags by mass spectrometry is demonstrated. This study provides a proof-of-concept that RNase digestion can be used to produce labelled small molecule mass tags from oligonucleotide probes, thus eliminating the need for custom design and synthesis of a cleavable linker.

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e-pub ahead of print date: 16 October 2012
Published date: 12 November 2012
Organisations: Chemistry

Identifiers

Local EPrints ID: 345618
URI: http://eprints.soton.ac.uk/id/eprint/345618
ISSN: 0003-2654
PURE UUID: b31a9d2e-46c5-4243-88b8-02dfdbc75b94
ORCID for Julie Herniman: ORCID iD orcid.org/0000-0003-4834-1093
ORCID for G. John Langley: ORCID iD orcid.org/0000-0002-8323-7235

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Date deposited: 27 Nov 2012 15:04
Last modified: 20 Jul 2019 01:23

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Contributors

Author: Jo-Anne Riley
Author: Tom Brown
Author: Nittaya Gale
Author: Julie Herniman ORCID iD
Author: G. John Langley ORCID iD

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