3-methyluridine and 5-methylcytidine

3-methyluridine has been researched along with 5-methylcytidine* in 2 studies

Other Studies

2 other study(ies) available for 3-methyluridine and 5-methylcytidine

Article	Year
Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. Nucleic acids research, 2017, Jul-27, Volume: 45, Issue:13 Nucleobase methylations are ubiquitous posttranscriptional modifications of ribonucleic acids (RNA) that can substantially increase the structural diversity of RNA in a highly dynamic fashion with implications for gene expression and human disease. However, high throughput, deep sequencing does not generally provide information on posttranscriptional modifications (PTMs). A promising alternative approach for the characterization of PTMs, i.e. their identification, localization, and relative quantitation, is top-down mass spectrometry (MS). In this study, we have investigated how specific nucleobase methylations affect RNA ionization in electrospray ionization (ESI), and backbone cleavage in collisionally activated dissociation (CAD) and electron detachment dissociation (EDD). For this purpose, we have developed two new approaches for the characterization of RNA methylations in mixtures of either isomers of RNA or nonisomeric RNA forms. Fragment ions from dissociation experiments were analyzed to identify the modification type, to localize the modification sites, and to reveal the site-specific, relative extent of modification for each site. Topics: Adenosine; Base Sequence; Cytidine; Ions; Methylation; Molecular Structure; RNA; Spectrometry, Mass, Electrospray Ionization; Spectroscopy, Fourier Transform Infrared; Uridine	2017
Probing the stabilizing effects of modified nucleotides in the bacterial decoding region of 16S ribosomal RNA. Bioorganic & medicinal chemistry, 2013, May-15, Volume: 21, Issue:10 The bacterial decoding region of 16S ribosomal RNA has multiple modified nucleotides. In order to study the role of N(4),2'-O-dimethylcytidine (m(4)Cm), the corresponding phosphoramidite was synthesized utilizing 5'-silyl-2'-ACE chemistry. Using solid-phase synthesis, m(4)Cm, 5-methylcytidine (m(5)C), 3-methyluridine (m(3)U), and 2'-O-methylcytidine (Cm) were site-specifically incorporated into small RNAs representing the decoding regions of different bacterial species. Biophysical studies were then used to provide insight into the stabilizing roles of the modified nucleotides. These studies reveal that methylation of cytidine and uridine has different effects. The same modifications at different positions or sequence contexts within similar RNA constructs also have contrasting roles, such as stabilizing or destabilizing the RNA helix. Topics: Circular Dichroism; Cytidine; Nucleotides; Organophosphorus Compounds; RNA, Bacterial; RNA, Ribosomal, 16S; Uridine	2013

Article

Year

Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry.

Nucleic acids research, 2017, Jul-27, Volume: 45, Issue:13

Nucleobase methylations are ubiquitous posttranscriptional modifications of ribonucleic acids (RNA) that can substantially increase the structural diversity of RNA in a highly dynamic fashion with implications for gene expression and human disease. However, high throughput, deep sequencing does not generally provide information on posttranscriptional modifications (PTMs). A promising alternative approach for the characterization of PTMs, i.e. their identification, localization, and relative quantitation, is top-down mass spectrometry (MS). In this study, we have investigated how specific nucleobase methylations affect RNA ionization in electrospray ionization (ESI), and backbone cleavage in collisionally activated dissociation (CAD) and electron detachment dissociation (EDD). For this purpose, we have developed two new approaches for the characterization of RNA methylations in mixtures of either isomers of RNA or nonisomeric RNA forms. Fragment ions from dissociation experiments were analyzed to identify the modification type, to localize the modification sites, and to reveal the site-specific, relative extent of modification for each site.

Topics: Adenosine; Base Sequence; Cytidine; Ions; Methylation; Molecular Structure; RNA; Spectrometry, Mass, Electrospray Ionization; Spectroscopy, Fourier Transform Infrared; Uridine

2017

Probing the stabilizing effects of modified nucleotides in the bacterial decoding region of 16S ribosomal RNA.

Bioorganic & medicinal chemistry, 2013, May-15, Volume: 21, Issue:10

The bacterial decoding region of 16S ribosomal RNA has multiple modified nucleotides. In order to study the role of N(4),2'-O-dimethylcytidine (m(4)Cm), the corresponding phosphoramidite was synthesized utilizing 5'-silyl-2'-ACE chemistry. Using solid-phase synthesis, m(4)Cm, 5-methylcytidine (m(5)C), 3-methyluridine (m(3)U), and 2'-O-methylcytidine (Cm) were site-specifically incorporated into small RNAs representing the decoding regions of different bacterial species. Biophysical studies were then used to provide insight into the stabilizing roles of the modified nucleotides. These studies reveal that methylation of cytidine and uridine has different effects. The same modifications at different positions or sequence contexts within similar RNA constructs also have contrasting roles, such as stabilizing or destabilizing the RNA helix.

Topics: Circular Dichroism; Cytidine; Nucleotides; Organophosphorus Compounds; RNA, Bacterial; RNA, Ribosomal, 16S; Uridine

2013