Search

A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles., Author(s): Emily M. Harcourt [1]; Anna M. Kietrys [2]; Eric T. Kool (corresponding author) [2] It is understood that the sequence and structure of messenger RNA have self-regulatory effects, influencing [...]

The crystal structures of six cobalt sandwich complexes—four in the η5-cyclopentadienyl/η4-cyclobutadiene family, two from the related η5-cyclopentadienyl/η4-cyclopentadienone family—are presented and discussed alongside related structural precedents. In each of the complexes an undecorated cyclopentadienyl ligand is present whereas the partner cyclobutadiene or cyclopentadienone ligand bears four identical aromatic substituents (phenyl, p-tolyl, p-fluorophenyl, 2-thienyl or 2,2′-bithienyl). This range of substituents allows for detailed structural comparison between members of the families of sandwich complexes presented here, and with previously reported structures. Crystal structures of members of the η5-cyclopentadienyl/η4-tetraarylcyclobutadiene (left) and η5-cyclopentadienyl/η5-cyclopentadienone (right) families of sandwich complexes are presented. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) is the most abundant mRNA modification and has important links to human health. While recent studies have successfully identified thousands of mammalian RNA transcripts containing the modification, it is extremely difficult to identify the exact location of any specific m6A. Here we have identified a polymerase with reverse transcriptase activity (from Thermus thermophilus) that is selective by up to 18-fold for incorporation of thymidine opposite unmodified A over m6A. We show that the enzyme can be used to locate and quantify m6A in synthetic RNAs by analysis of pausing bands, and have used the enzyme in tandem with a nonselective polymerase to locate the presence and position of m6A in high-abundance cellular RNAs. By this approach we demonstrate that the long-undetermined position of m6A in mammalian 28S rRNA is nucleotide 4190. [ABSTRACT FROM AUTHOR]

A correction to the article "Organocatalytic removal of formaldehyde adducts from RNA and DNA bases," by Saswata Karmaker and colleagues that was published in the August 3, 2015 issue is presented.

5-Methyldeoxycytidine (5mC) is a major epigenetic marker that regulates cellular functions in mammals. Endogenous lipid peroxidation can convert 5mC into 3,N4-etheno-5-methylcytosine (ϵ5mC). ϵ5mC is structurally similar to the mutagenic analog 3,N4-ethenocytosine (ϵC), which is repaired by AlkB family enzymes in the direct reversal repair (DRR) pathway and excised by DNA glycosylases in the base excision repair (BER) pathway. However, the repair of ϵ5mC has not been reported. Here, we examined the activities against ϵ5mC by DRR and BER enzymes and TET1-3, enzymes that modify the 5-methyl group in 5mC. We found that the etheno modification of 5mC blocks oxidation by TET1-3. Conversely, three human homologs in the AlkB family, ALKBH2, 3 and FTO were able to repair ϵ5mC to 5mC, which was subsequently modified by TET1 to 5-hydroxymethylcytosine. We also demonstrated that ALKBH2 likely repairs ϵ5mC in MEF cells. Another homolog, ALKBH5, could not repair ϵ5mC. Also, ϵ5mC is not a substrate for BER glycosylases SMUG1, AAG, or TDG. These findings indicate DRR committed by ALKBH2, 3 and FTO could reduce the detrimental effects of ϵ5mC in genetics and epigenetics and may work together with TET enzymes to modulate epigenetic regulations., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The planar [maximum deviation 0.0066 (4) Å] symmetrical mol-ecule of the title compound, C(10)H(6)S(2), lies across a crystallographic inversion centre. The thio-phene rings are rotationally disordered about the acetyl-ene bond, with the two pseudo inversion-related S atoms in 0.80:0.20 occupancy sites. The C C bond distance is 1.195 (9) Å.