Mass spectrometry of RNA: linking the genome to the proteome - PubMed (original) (raw)

Review

Mass spectrometry of RNA: linking the genome to the proteome

Zhaojing Meng et al. Brief Funct Genomic Proteomic. 2006 Mar.

Abstract

Ribonucleic acids (RNAs) are continuing to attract increased attention as they are found to play pivotal roles in biological systems. Just as genomics and proteomics have been enabled by the development of effective analytical techniques and instrumentation, the large-scale analysis of non-protein coding (nc)RNAs will benefit as new analytical methodologies, such as mass spectrometry (MS), are developed for their analysis. Mass spectrometry offers a number of advantages for RNA analysis arising from its ability to provide mass and sequence information starting with limited amounts of sample. This review will highlight recent developments in the field of MS that enable the characterization of RNA modification status, RNA tertiary structures, and ncRNA expression levels. These developments will also be placed in perspective of how MS of RNAs can help elucidate the link between the genome and proteome.

PubMed Disclaimer

Figures

Figure 1

Endonuclease cleavage mechanism. The 3′-cyclic phosphate (I) is an intermediate in this reaction. Because an oxygen from water present in the buffer is incorporated at the 3′-phosphate (II), a facile means of stable isotope labeling is available.

Figure 2

Structures of uridine and pseudoridine.

Figure 3

ESI-FTICRMS direct infusion analysis of SL2 RNA probed with (a) DMS, (b) KT and (c) CMCT. The inset shows the sites were modified by DMS (star), KT (diamond) and CMCT (circle). DMS: methylation of exposed G and A; KT: modification on exposed G; CMCT: modification on exposed G. Figure reprinted with permission from J. Mol. Biol., (2003) Vol. 330, pp. 211-223.

Figure 4

General overview of the described 18O labeling and MALDI-MS approach for quantification of RNA samples.

References

1. Huttenhofer A, Schattner P, Polacek N. Non-coding RNAs: hope or hype? Trends Gen. 2005;21:289–297. - PubMed
1. Meli M, Albert-Fournier B, Maurel M-C. Recent Findings in the Modern RNA World. Int. Microbiol. 2001;4:5–11. - PubMed
1. Limbach PA. Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides. Mass Spectrom. Rev. 1996;15:297–336. - PubMed
1. Nordhoff E, Kirpekar F, Roepstorff P. Mass Spectrometry of Nucleic Acids. Mass Spectrom. Rev. 1996;15:67–138. - PubMed
1. Crain PF, McCloskey JA. Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Curr. Opin. Biotech. 1998;9:25–34. - PubMed

Mass spectrometry of RNA: linking the genome to the proteome - PubMed (original) (raw)