1887

Chapter 3 : Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap03-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap03-2.gif

Abstract:

This chapter reviews applications of electrospray ionization (ESI) to the analysis of RNA and its constituents. Some examples of modified nucleosides discovered by liquid chromatography (LC)/mass chromatography (MS) and characterized include four sugar-methylated nucleosides in tRNA from hyperthermophilic archaea, 5-methylcarboxymethyl-2’-O-methyluridine in rat liver tRNA, and two sugar-methylated nucleosides in the cap4 subunit of trypanosomal mRNA. A method has been implemented for mapping modified nucleosides in RNA, based on electrospray ionization mass spectrometry of RNase T-derived oligonucleotides. The ability to mass measure the small peaks suggests that oligonucleotides can be analyzed at levels lower than the 20 pmol of tRNA utilized in the present example. To examine levels of modified nucleosides in tRNA as a function of growth temperature in the thermophilic archaeon , it was grown at 70, 85, and 100°C. The strategies and examples of nucleic acid analysis using mass spectrometry presented in this chapter utilize ESI because of its successful implementation for the analysis of nucleic acids and their constituents from the monomer level in digests all the way up to intact tRNA and 5S rRNA.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3

Key Concept Ranking

Nucleic Acid Constituents
0.78500265
Ionization Mass Spectrometry
0.5606502
High-Performance Liquid Chromatography
0.5080458
Bacteria and Archaea
0.4653405
Nucleic Acids
0.46517107
0.78500265
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

Schematic diagram of the sample inlet and ESI for a triple quadrupole mass spectrometer.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Chromatogram (detection at 254 nm) from a directly combined high-performance LC/ESI-MS analysis of nucleosides from a total digest of mixed tRNA from MRE600. Major modified nucleosides are as follows: 1, Ψ; 2, D; 3, acpU; 4, sC; 5, Cm; 6, I; 7, mG; 8, mU; 9, sU; 10, UM; 11, oQ; 12, mG; 13, Gm; 14, tA; 15, mA; 16, mA. (Inset) ESI mass spectrum of the peak at centered at 16.8 min. Symbols are defined in Appendix 1.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Expanded UV chromatogram (A) and reconstructed ion chromatograms for the MH ion of methylguanosine (B) (/ 298) and the BH ions for methylguanine (C) (/ 166) and guanine (D) (/ 152), extracted from the analysis shown in Fig. 2 . For clarity, ion abundances have been normalized to the most abundant peak in each panel.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Product ion spectra from collision-induced dissociation of the BH ions (/ 166) characteristic for base-methylated guanosines, acquired from an LC/MS/MS analysis of a digest of wheat germ tRNA. (A) 1-Methylguanosine; (B) -methylguanosine; (C) 7-methylguanosine.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Scheme for mapping modified nucleosides in RNA by mass spectrometric analysis of RNase Τ-generated oligonucleotides.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Chromatogram from directly combined high-performance LC/ESI-MS of an RNase Tdigest of 20 pmol of tRNA .

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

ESI mass spectrum of ACUoQUAms AA4ψCUGp (peak 10 in Fig. 6 ). (Inset) Oligonucleotide masses derived from the mass spectrum.

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818296.chap3
1. Apffel, A.,, J. A. Chakel,, S. Fischer,, K. Lichtenwalter,, and W. S. Hancock. 1997. Analysis of oligonucleotides by HPLC-electrospray ionization mass spectrometry. Anal. Chem. 69: 1320 1325.
2. Auxilien, S.,, P. F. Crain,, R. W. Trewyn,, and H. Grosjean. 1996. Mechanism, specificity and general properties of the yeast enzyme catalyzing the formation of inosine-34 in the anticodon of transfer RNA. J. Mol. Biol. 262: 351 379.
3. Bangs, J. D.,, P. F. Crain,, T. Hashizume,, J. A. McCloskey,, and J. C. Boothroyd. 1992. Mass spectrometry of mRNA cap 4 from trypanosomatids reveals two novel nucleosides. J. Biol. Chem. 267: 9805 9815.
4. Bruenger, E.,, J. A. Kowalak,, Y. Kuchino,, J. A. McCloskey,, H. Mizushima,, K. O. Stetter,, and P. F. Crain. 1993. 5S rRNA modification in the hyperthermophilic archaea Sulfolobus solfataricus and Pyrodictium occultum. FASEB J. 7: 196 200.
5. Buck, M.,, M. Connick,, and B. N. Ames. 1983. Complete analysis of tRNA-modified nucleosides by high-performance liquid chromatography: the 29 modified nucleosides of Salmonella typhimurium and Escherichia coli tRNAs. Anal. Biochem. 129: 1 13.
6. Busch, K. L.,, G. L. Glish,, and S. A. McLuckey. 1988. Mass Spectrometry /Mass Spectrometry. Techniques and Applications of Tandem Mass Spectrometry. VCH Publishers, Inc., New York, N.Y..
7. Cheng, X.,, I. Camp,, D. G. Q., Wu,, R. Bakhtiar,, D. L. Springer,, B. J. Morris,, J. E. Bruce,, G. A. Anderson,, C. G. Edmonds,, and R. D. Smith. 1996. Molecular weight determination of plasmid DNA using electrospray ionization mass spectrometry. Nucleic Acids Res. 24: 2183 2189.
8. Cole, R. B. (ed.). 1997. Electrospray Ionization Mass Spectrometry. Fundamentals, Instrumentation, and Applications. Wiley-Interscience, New York, N.Y..
9. Crain, P. F. 1990a. Mass spectrometric techniques in nucleic acid research. Mass Spectrom. Rev. 9: 504 554.
10. Crain, P. F. 1990b. Preparation and enzymatic digestion of RNA and DNA for mass spectrometry. Methods Enzymol. 193: 782 790.
11. Crain, P. F., 1997. Nucleic acids and their constituents, p. 421 427. In R. B. Cole (ed.), Electrospray Mass Spectrometry. Fundamentals, Instrumentation, and Applications. Wiley-Interscience, New York, N.Y..
12. Crain, P. F.,, and J. A. McCloskey. Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids. Curr. Opin. Biotechnol., in press.
13. Crow, F. W.,, K. B. Tomer,, M. L. Gross,, J. A. McCloskey,, and D. E. Bergstrom. 1984. Fast atom bombardment combined with tandem mass spectrometry for the determination of nucleosides. Anal. Biochem. 139: 243 262.
14. Dalluge, J. J.,, T. Hamamoto,, K. Horikoshi,, R. Y. Morita,, K. O. Stetter,, and J. A. McCloskey. 1997. Posttranscriptional modification of transfer RNA in psychrophilic bacteria. J. Bacteriol. 179: 1918 1923.
15. Dalluge, J. J.,, T. Hashizume,, and J. A. McCloskey. 1996. Quantitative measurement of dihyrouridine in RNA using isotope dilution chromatography-mass spectrometry (LC/MS). Nucleic Acids Res. 24: 3242 3245.
16. Diamond, A.,, I. S. Choi,, P. F. Crain,, T. Hashizume,, S. C. Pomerantz,, R. Cruz,, C. Steer,, K. E. Hill,, R. F. Burk,, J. A. McCloskey,, and D. Hatfield. 1993. Dietary selenium affects methylation of the wobble nucleoside in the anticodon of selenocysteine tRNA [Ser]Sec.y. Biol. Chem. 268: 14215 14223.
17. Edmonds, C. G.,, P. F. Crain,, R. Gupta,, T. Hashizume,, C. H. Hocart,, J. A. Kowalak,, S. C. Pomerantz,, K. O. Stetter,, and J. A. McCloskey. 1991. Posttranscriptional modification of tRNA in thermophilic archaea (archaebacteria). J. Bacteriol. 173: 3138 3148.
18. Edmonds, C. G.,, P. F. Crain,, T. Hashizume,, R. Gupta,, K. O. Stetter,, and J. A. McCloskey. 1987. Structural characterization of four ribose-methylated nucleosides from transfer RNA of extremely thermophilic archaebacteria. J. Chem. Soc. Chem. Commun. 173: 909 910.
19. Edmonds, C. G.,, S. C. Pomerantz,, F. F. Hsu,, and J. A. McCloskey. 1988. Thermospray liquid chromatography/mass spectrometry in deuterium oxide. Anal. Chem. 60: 2314 2317.
20. Edmonds, C. G.,, M. L. Vestal,, and J. A. McCloskey. 1985. Thermospray liquid chromatography-mass spectrometry of nucleosides and enzymatic hydrolysates of nucleic acids. Nucleic Acids Res. 13: 8197 8206.
21. Fenn, J. B.,, M. Mann,, C. K. Meng,, S. F. Wong,, and C. M. Whitehouse. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64 71.
22. Fitzgerald, M. C.,, and L. M. Smith. 1995. Mass spectrometry of nucleic acids: the promise of matrix-assisted laser desorption-ionization (MALDI) mass spectrometry. Annu. Rev. Biophys. Biomol. Struct. 24: 117 140.
23. Gehrke, C. W.,, and K. C. Kuo,. 1990. Ribonucleoside analysis by reversed-phase high performance liquid chromatography, p. A3 A64. In C. W. Gehrke, and K. C. Kuo (ed.), Chromatography and Identification of Nucleosides, Part A. Journal of Chromatography Library, vol. 45A. Elsevier, New York, N.Y..
24. Gite, S.,, and U. L. RajBhandary. 1997. Lysine 207 as the site of cross-linking between the 3'-end of Escherichia coli initiator tRNA and methionyl-tRNA formyltransferase. J. Biol. Chem. 272: 5305 5312.
25. Gregson, J. M.,, P. F. Crain,, C. G. Edmonds,, R. Gupta,, T. Hashizume,, D. W. Phillipson,, and J. A. McCloskey. 1993. Structure of the archaeal transfer RNA nucleoside G*-15: 2-amino-4,7-dihydro-4-oxo-7- β-D-ribofuranosyl-1 H-pyrrolo[2,3-iflpyrimi-dine-5-carboximidamide (archaeosine). J. Biol. Chem. 268: 10076 10086.
26. Gregson, J. M.,, and J. A. McCloskey. 1997. Collision-induced dissociation of protonated guanine. Int. J. Mass Spectrom. Ion Processes 165/166: 475 485.
27. Gruic-Sovulj, I.,, H.-C. Ludemann,, F. Hillenkamp,, I. Weygand-Durasevic,, Z. Kucan,, and J. Peter-Katalinic. 1997. Matrix-assisted laser desorption/ionisation mass spectrometry of transfer ribonucleic acids isolated from yeast. Nucleic Acids Res. 25: 1859 1861.
28. Hahner, S.,, H.-C. Lüdemann,, F. Kirpekar,, E. Nordhoff,, P. Roep-storff,, H.-J. Galla,, and F. Hillenkamp. 1997. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) of endonuclease digests of RNA. Nucleic Acids Res. 25: 1957 1964.
29. Jensen, O. N.,, S. Kulkarni,, J. V. Aldrich,, and D. F. Barofsky. 1996. Characterization of peptide oligonucleotide heteroconjugates by mass spectrometry. Nucleic Acids Res. 24: 3866 3872.
30. Karas, M.,, and F. Hillenkamp. 1988. Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60: 2299 2301.
31. Kawai, G.,, T. Hashizume,, M. Yasuda,, T. Miyazawa,, J. A. McCloskey,, and S. Yokoyama. 1992. Conformational rigidity of N 4-acetyl-2'- O-methylcytidine found in tRNA of extremely thermophilic archaebacteria (Archaea). Nucleosides Nucleotides 11: 759 771.
32. Keith, G., 1990. Nucleic acid chromatographic isolation and sequence methods, p. A103 A140. In C. W. Gehrke, and K. C. Kuo (ed.), Chromatography and Identification of Nucleosides, Part A. Journal of Chromatography Library, vol. 45A. Elsevier, New York, N.Y..
33. Koster, H.,, K. Tang,, D.-J. Fu,, A. Braun,, D. van den Boom,, C. L. Smith,, R. J. Cotter,, and C. R. Cantor. 1996. A strategy for rapid and efficient DNA sequencing by mass spectrometry. Nat. Biotechnol. 14: 1123 1128.
34. Kowalak, J. A.,, E. Bruenger,, T. Hashizume,, J. M. Peltier,, J. Ofen-gand,, and J. A. McCloskey. 1996. Structural characterization of U*-1915 in domain IV from E. coli 23S ribosomal RNA as 3-methylpseudouridine. Nucleic Acids Res. 24: 688 693.
35. Kowalak, J. A.,, E. Bruenger,, and J. A. McCloskey. 1995. Post-transcriptionai modification of the central loop of domain V in E. coli 23S ribosomal RNA. J. Biol. Chem. 270: 17758 17764.
36. Kowalak, J. A.,, J. J. Dalluge,, J. A. McCloskey,, and K. O. Stetter. 1994. The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry 33: 7869 7876.
37. Kowalak, J. A.,, S. C. Pomerantz,, P. F. Crain,, and J. A. McCloskey. 1993. A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry. Nucleic Acids Res. 21: 4577 4585.
38. Kuchino, Y.,, N. Hanyu,, and S. Nishimura. 1987. Analysis of modified nucleosides and nucleotide sequences of tRNA. Methods Enzymol. 155: 379 396.
39. Limbach, P. A. 1996. Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides. Mass Spectrom. Rev. 15: 297 336.
40. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1994. Enzymatic sequencing of oligonucleotides with electrospray mass spectrometry. Nucleic Acids Res. Symp. Ser. 31: 127 128.
41. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1995. Molecular mass measurement of intact ribonucleic acids using electrospray ionization quadrupole mass spectrometry. J. Am. Soc. Mass Spectrom. 6: 27 39.
42. Little, D. P.,, A. Braun,, M. J. O'Donnell,, and H. Koster. 1998. Mass spectrometry from miniaturized arrays for full comparative DNA analysis. Nat. Med. 3: 1415 1416.
43. Mangroo, D.,, P. A. Limbach,, J. A. McCloskey,, and U. L. RajBhandary. 1995. An anticodon mutant of Escherichia coli initiator tRNA: importance of a newly acquired base modification next to the anticodon on its activity in initiation. J. Bacteriol. 177: 2858 2862.
44. McCloskey, J. A. 1990. Constituents of nucleic acids: overview and strategy. Methods Enzymol. 193: 771 781.
45. McCloskey, J. A.,, and P. F. Crain. 1998. The RNA modification database—1998. Nucleic Acids Res. 26: 198 200.
46. McLuckey, S. A.,, G. J. Van Berkel,, and G. L. Glish. 1992. Tandem mass spectrometry of small, multiply charged oligonucleotides. J. Am. Soc. Mass Spectrom. 3: 60 70.
47. Millard, B. J. 1979. Quantitative Mass Spectrometry. Heyden & Son, Ltd., London, United Kingdom.
48. Ni, J.,, S. C. Pomerantz,, J. Rozenski,, Y. Zhang,, and J. A. McCloskey. 1996. Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry. Anal. Chem. 68: 1989 1999.
49. Nordhoff, E.,, F. Kirpekar,, and P. Roepstorff. 1996. Mass spectrometry of nucleic acids. Mass Spectrom. Rev. 15: 67 138.
50. Poison, A. G.,, P. F. Crain,, S. C. Pomerantz,, J. A. McCloskey,, and B. Bass. 1991. The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifyingactivity: a high performance liquid chromatography-mass spectrometry analysis. Biochemistry 30: 11507 11514.
51. Pomerantz, S. C.,, J. A. Kowalak,, and J. A. McCloskey. 1993. Determination of oligonucleotide composition from mass spectrometrically measured molecular weight. J. Am. Soc. Mass Spectrom. 4: 204 209.
52. Pomerantz, S. C.,, and J. A. McCloskey. 1990. Analysis of RNA hydrolyzates by LC/MS. Methods Enzymol. 193: 796 824.
53. Pomerantz, S. C.,, J. A. McCloskey,, T. Tarasow,, and B. E. Eaton. 1997. Deconvolution of combinatorial oligonucleotide libraries by electrospray ionization tandem mass spectrometry. J. Am. Chem. Soc. 119: 3861 3867.
54. Reddy, D. M.,, P. F. Crain,, C. G. Edmonds,, R. Gupta,, T. Hashizume,, K. O. Stetter,, F. Widdel,, and J. A. McCloskey. 1992. Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea. Nucleic Acids Res. 20: 5607 5615.
55. Severs, J. C.,, and R. D. Smith,. 1997. Capillary electrophoresis-electrospray ionization mass spectrometry, p. 343 382. In R. B. Cole (ed.), Electrospray Ionization Mass Spectrometry. Fundamentals, Instrumentation, and Applications. Wiley-Interscience, New York, N.Y..
56. Sprinzl, M.,, C. Horn,, M. Brown,, A. Ioudovitch,, and S. Steinberg. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26: 148 153.
57. Takeda, N.,, S. C. Pomerantz,, and J. A. McCloskey. 1991. Detection of ribose-methylated nucleotides in enzymatic hydrolysates of RNA by thermospray liquid chromatography-mass spectrometry. J. Chromatogr. 562: 225 235.
58. Urlaub, H.,, B. Thiede,, E.-C. Miiller,, R. Brimacombe,, and B. Wittmann-Liebold. 1997a. Identification and sequence analysis of contact sites between ribosomal proteins and rRNA in Escherichia coli 30 S subunits by a new approach using matrix-assisted laser desorption/ionization-mass spectrometry combined with N-terminal microsequencing. J. Biol. Chem. 272: 14547 14555.
59. Urlaub, H.,, B. Thiede,, E.-C. Miiller,, and B. Wittmann-Liebold. 1997b. Contact sites of peptide-oligoribonucleotide cross-links identified by a combination of peptide and nucleotide sequencing with MALDI MS. J. Protein Chem. 16: 375 383.
60. Ushida, C.,, T. Muramatsu,, H. Mizushima,, T. Ueda,, K. Watanabe,, K. O. Stetter,, P. F. Crain,, and J. A. McCloskey. 1996. Structural feature of the initiator tRNA gene from Pyrodictium occultum and the thermal stability of its gene product, tRNA Met. Biochemie 768: 847 855.
61. Voyksner, R. D., 1997. Combining liquid chromatography with electrospray mass spectrometry, p. 323-341. In R. B. Cole (ed.), Electrospray Ionization Mass Spectrometry. Fundamentals, Instrumentation, and Applications. Wiley-Interscience, New York, N.Y..

Tables

Generic image for table
Table 1

Assignments of oligonucleotides from RNase T digestion of tRNA

Citation: Crain P. 1998. Detection and Structure Analysis of Modified Nucleosides in RNA by Mass Spectrometry, p 47-57. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch3

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error