401812-99-5Relevant articles and documents
An Unconventional Acid-Labile Nucleobase Protection Concept for Guanosine Phosphoramidites in RNA Solid-Phase Synthesis
Jud, Lukas,Micura, Ronald
, p. 3406 - 3413 (2017)
We present an innovative O6-tert-butyl/N2-tert-butyloxycarbonyl protection concept for guanosine (G) phosphoramidites. This concept is advantageous for 2′-modified G building blocks because of very efficient synthetic access when compared with existing routes that usually employ O6-(4-nitrophenyl)ethyl/N2-acyl protection or that start from 2-aminoadenosine involving enzymatic transformation into guanosine later on in the synthetic path. The new phosphoramidites are fully compatible with 2′-O-tBDMS or TOM phosphoramidites in standard RNA solid-phase synthesis and deprotection, and provide excellent quality of tailored RNAs for the growing range of applications in RNA biophysics, biochemistry, and biology.
Selective Enzymatic Demethylation of N2,N2-Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing
Dai, Qing,Zheng, Guanqun,Schwartz, Michael H.,Clark, Wesley C.,Pan, Tao
, p. 5017 - 5020 (2017)
The abundant Watson–Crick face methylations in biological RNAs such as N1-methyladenosine (m1A), N1-methylguanosine (m1G), N3-methylcytosine (m3C), and N2,N2-dimethylguanosine (m22G) cause significant obstacles for high-throughput RNA sequencing by impairing cDNA synthesis. One strategy to overcome this obstacle is to remove the methyl group on these modified bases prior to cDNA synthesis using enzymes. The wild-type E. coli AlkB and its D135S mutant can remove most of m1A, m1G, m3C modifications in transfer RNA (tRNA), but they work poorly on m22G. Here we report the design and evaluation of a series of AlkB mutants against m22G-containing model RNA substrates that we synthesize using an improved synthetic method. We show that the AlkB D135S/L118V mutant efficiently and selectively converts m22G modification to N2-methylguanosine (m2G). We also show that this new enzyme improves the efficiency of tRNA sequencing.
Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization
Bartee, David,Nance, Kellie D.,Meier, Jordan L.
, p. 3487 - 3496 (2022/03/03)
N4-Acetylcytidine (ac4C) is a post-transcriptional modification of RNA that is conserved across all domains of life. All characterized sites of ac4C in eukaryotic RNA occur in the central nucleotide of a 5′-CCG-3′ consensus sequence. However, the thermodynamic consequences of cytidine acetylation in this context have never been assessed due to its challenging synthesis. Here, we report the synthesis and biophysical characterization of ac4C in its endogenous eukaryotic sequence context. First, we develop a synthetic route to homogeneous RNAs containing electrophilic acetyl groups. Next, we use thermal denaturation to interrogate the biochemical effects of ac4C on duplex stability and mismatch discrimination in a native sequence found in human rRNA. Finally, we demonstrate the ability of this chemistry to incorporate ac4C into the complex modification landscape of human tRNA and use duplex melting to highlight an enforcing role for ac4C in this unique sequence context. By enabling ex vivo biophysical analyses of nucleic acid acetylation in its physiological sequence context, these studies establish a chemical foundation for understanding the function of a universally conserved nucleobase in biology and disease.
Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL)
Brillet, Karl,Delazer, Isabel,Ennifar, Eric,Gasser, Catherina,Himmelsto?, Maximilian,Klotz, Sarah,Lusser, Alexandra,Micura, Ronald,Neuner, Eva,Pascher, Katharina,Rieder, Dietmar,Trixl, Lukas
supporting information, p. 6881 - 6886 (2020/03/05)
Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH4Cl/OsO4-based conversion of 6-thioguanosine (6sG) into A′, where A′ constitutes a 6-hydraz
Synthesis of cyclic di-nucleotidic acids as potential inhibitors targeting diguanylate cyclase
Ching, Shi Min,Tan, Wan Jun,Chua, Kim Lee,Lam, Yulin
experimental part, p. 6657 - 6665 (2010/10/21)
Five analogs of cyclic di-nucleotidic acid including c-di-GMP were synthesized and evaluated for their biological activities on Slr1143, a diguanylate cyclase of Synechocystis sp. Slr1143 was overexpressed from the recombinant plasmid which contained the gene of interest and subsequently purified by affinity chromatography. A new HPLC method capable of separating the compound and product peaks with good resolution was optimized and applied to the analysis of the compounds. Results obtained show that cyclic di-inosinylic acid 1b demonstrates a stronger inhibition on Slr1143 than c-di-GMP and is a potential inhibitor for biofilm formation.
An improved method for synthesizing cyclic bis(3′-5′)diguanylic acid (c-di-GMP)
Hyodo, Mamoru,Hayakawa, Yoshihiro
, p. 2089 - 2093 (2007/10/03)
This paper describes a new method for synthesizing biologically important cyclic bis(3′-5′)diguanylic acid (c-di-GMP) in a higher yield than that previously reported to be available by our synthetic method. In the new synthesis, the following two means, i
Synthesis of 2'-O-substituted ribonucleosides.
Serebryany,Beigelman
, p. 1007 - 1009 (2007/10/03)
An efficient synthesis of 2'-O-substituted ribonucleosides, including 2'-O-TBDMS and 2'-O-TOM protected as well as 2'-O-Me and 2'-O-allyl derivatives is presented. Di-t-butylsilylene group was employed for simultaneous protection of 3'- and 5'- hydroxyl functions of nucleoside on the first step. Subsequent silylation or alkylation of free 2'-OH followed by introduction of suitable protection on the base moiety and removal of cyclic silyl protection gave target compounds in a high yield.
An efficient preparation of protected ribonucleosides for phosphoramidite RNA synthesis
Serebryany, Vladimir,Beigelman, Leonid
, p. 1983 - 1985 (2007/10/03)
An efficient synthesis of protected ribonucleosides useful for phosphoramidite RNA synthesis is described. Di-t-butylsilylene group was employed for simultaneous protection of 3′- and 5′-hydroxyl functions of nucleoside. Subsequent silylation of free 2′-O
