SECTION I. Modified Nucleotides
Chapter 1: Identifying modifications in RNA by mass spectrometry.
Chapter 2: Identification of modified residues in RNAs by reverse transcription-based methods.
SECTION II. tRNA Modifications
Chapter 3: Detection of enzymatic activity of transfer RNA modification enzymes using radiolabelled tRNA substrates.
Chapter 4: In vitro detection of the enzymatic activity of folate-dependent tRNA(U54, C5)-methyltransferase.
Chapter 5: Probing the intermediacy of covalent RNA•enzyme complexes in RNA modification enzymes.
Chapter 6: Identification and characterization of modification enzymes by biochemical analysis of the proteome.
Chapter 7: Identification of genes encoding tRNA modification enzymes via comparative genomics.
Chapter 8: Identification and characterization of archaeal and fungal tRNA methyltransferases.
Chapter 9: Mass spectrometric identification and characterization of RNA-modifying enzymes.
Chapter 10: Chaplet column chromatography: isolation of a large set of individual RNAs in a single step.
SECTION III. SNO-mediated Modifications
Chapter 11: Biochemical Purification of box H/ACA RNPs involved in pseudouridylation.
Chapter 12: In Vitro Reconstitution and Affinity Purification of Catalytically Active Archaeal Box C/D sRNP Complexes.
Chapter 13: Identifying effects of snoRNA-guided modifications on the synthesis and function of the yeast ribosome.
Chapter 14: The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes.
Chapter 15: A Dedicated Computational Approach for the Identification of Archaeal H/ACA sRNAs.
Chapter 16: Reconstitution of archaeal H/ACA sRNPs and test of their activity