The RNA modification database, RNAMDB: 2011 update

Since its inception in 1994, The RNA Modification Database (RNAMDB, http://rna-mdb.cas.albany.edu/RNAmods/) has served as a focal point for information pertaining to naturally occurring RNA modifications. In its current state, the database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species in which it is found, and references to the first reported structure determination and synthesis. Though newly transferred in its entirety to The RNA Institute, the RNAMDB continues to grow with two notable additions, agmatidine and 8-methyladenosine, appended in the last year. The RNA Modification Database is staying up-to-date with significant improvements being prepared for inclusion within the next year and the following year. The expanded future role of The RNA Modification Database will be to serve as a primary information portal for researchers across the entire spectrum of RNA-related research.

[1]  M. Sekine,et al.  Alkylation of 6-N-acylated adenosine derivatives by the use of phase transfer catalysis , 1995 .

[2]  K. Stetter,et al.  Posttranscriptional modification of transfer RNA in the submarine hyperthermophile Pyrolobus fumarii. , 2000, Nucleic acids symposium series.

[3]  D. Bergstrom.  Unnatural Nucleosides with Unusual Base Pairing Properties , 2001, Current protocols in nucleic acid chemistry.

[4]  T. Sugimoto,et al.  Structure of wye (Yt base) and wyosine (Yt) from Torulopsis utilis phenylalanine transfer ribonucleic acid. , 1976, Biochemistry.

[5]  J. F. Curran.  Modified Nucleosides in Translation , 1998 .

[6]  M. Robins,et al.  Nucleic acid related compounds. 13 , 1974 .

[7]  L. H. Hansen,et al.  Identification of 8-methyladenosine as the modification catalyzed by the radical SAM methyltransferase Cfr that confers antibiotic resistance in bacteria. , 2009, RNA.

[8]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[9]  S. Douthwaite,et al.  Identifying modifications in RNA by MALDI mass spectrometry. , 2007, Methods in enzymology.

[10]  M. Maccoss,et al.  Nucleic acid related compounds. 20. Sugar, base doubly modified nucleosides at the 5'-terminal "cap" of mRNAs and in nuclear RNA. , 1976, Biochemical and biophysical research communications.

[11]  K. Raviprakash,et al.  2'-O-methyl-1-methyl adenosine: a new modified nucleoside in ragi (Eleusine coracana) tRNA. , 1984, Biochemical and biophysical research communications.

[12]  Dieter Söll,et al.  Trna: Structure, Biosynthesis, and Function , 1995 .

[13]  D. Söll,et al.  Agmatidine, a modified cytidine in the anticodon of archaeal tRNAIle, base pairs with adenosine but not with guanosine , 2010, Proceedings of the National Academy of Sciences.

[14]  Razvan Nutiu,et al.  Aptamers with fluorescence-signaling properties. , 2005, Methods.

[15]  K. Yamauchi,et al.  Selective Methylation of Nucleosides1 , 1980 .

[16]  Paul F Agris,et al.  tRNA's modifications bring order to gene expression. , 2008, Current opinion in microbiology.

[17]  J. Poehlsgaard,et al.  The Cfr rRNA Methyltransferase Confers Resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A Antibiotics , 2006, Antimicrobial Agents and Chemotherapy.

[18]  Henri Grosjean,et al.  Modification And Editing Of Rna , 1998 .

[19]  Takeo Suzuki,et al.  Novel taurine-containing uridine derivatives and mitochondrial human diseases. , 2001, Nucleic acids research. Supplement.

[20]  D. Fabris,et al.  Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA , 2005, Journal of the American Society for Mass Spectrometry.

[21]  Yoshiyuki Kuchino,et al.  Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification , 1988, Nature.

[22]  Jef Rozenski,et al.  The Small Subunit rRNA Modification Database , 2004, Nucleic Acids Res..

[23]  Peter F. Stadler,et al.  tRNAdb 2009: compilation of tRNA sequences and tRNA genes , 2008, Nucleic Acids Res..

[24]  Paul F Agris,et al.  tRNA's wobble decoding of the genome: 40 years of modification. , 2007, Journal of molecular biology.

[25]  Xuemei Chen,et al.  Methylation as a Crucial Step in Plant microRNA Biogenesis , 2005, Science.

[26]  Irwin D Kuntz,et al.  The collaboratory for MS3D: a new cyberinfrastructure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches. , 2008, Journal of proteome research.

[27]  Franck A. P. Vendeix,et al.  Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. , 2009, RNA.

[28]  Marcin Feder,et al.  MODOMICS: a database of RNA modification pathways , 2005, Nucleic Acids Res..

[29]  A. Mankin,et al.  The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. , 2007, RNA.

[30]  John SantaLucia,et al.  AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA. , 2007, Journal of chemical theory and computation.

[31]  Jef Rozenski,et al.  The RNA Modification Database: 1999 update , 1999, Nucleic Acids Res..

[32]  D. Söll,et al.  N 6‐Acetyladenosine: A new modified nucleoside from Methanopyrus kandleri tRNA , 2005, FEBS letters.

[33]  Jian-Kang Zhu,et al.  Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana , 2009, BMC Genomics.

[34]  James A. McCloskey,et al.  The RNA modification database , 1997, Nucleic Acids Res..

[35]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[36]  D. Fabris,et al.  Untying the FIV frameshifting pseudoknot structure by MS3D. , 2005, Journal of molecular biology.

[37]  D. Fabris,et al.  Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D. , 2010, Journal of mass spectrometry : JMS.

[38]  Chuanzheng Zhou,et al.  The synthesis of therapeutic locked nucleos(t)ides. , 2009, Current opinion in drug discovery & development.

[39]  Kathleen R. Noon,et al.  Structures of two new "minimalist" modified nucleosides from archaeal tRNA. , 2004, Bioorganic chemistry.

[40]  S. Yokoyama,et al.  Modified Nucleosides and Codon Recognition , 1995 .

[41]  Paul F Agris,et al.  Bringing order to translation: the contributions of transfer RNA anticodon‐domain modifications , 2008, EMBO reports.

[42]  P. Limbach,et al.  Summary: the modified nucleosides of RNA. , 1994, Nucleic acids research.

[43]  E. De Clercq,et al.  Antiviral activity of C-alkylated purine nucleosides obtained by cross-coupling with tetraalkyltin reagents. , 1993, Journal of medicinal chemistry.

[44]  J. Chattopadhyaya,et al.  Synthesis of O2'-methyluridine, O2'-methylcytidine, N4,O2'-dimethylcytidine and N4,N4,O2'-trimethylcytidine from a common intermediate. , 1986, Acta chemica Scandinavica. Series B: Organic chemistry and biochemistry.

[45]  J. Kowalak,et al.  Posttranscriptional Modification of the Central Loop of Domain V in Escherichia coli 23 S Ribosomal RNA (*) , 1995, The Journal of Biological Chemistry.