RESUMO
A 2-amino-1,8-naphthyridine derivative that is described to bind single guanine bulges in RNA-DNA and RNA-RNA duplexes was synthesized and its interaction with the single G bulge in the conserved CREX of the Hepatitis E Virus (HEV) genome was explored by NMR and molecular modeling. Results indicate that the ligand intercalates in the internal loop, though none of the expected hydrogen bonds with the single G in the bulge could be demonstrated.
Assuntos
Sequência Conservada , Genoma Viral/genética , Vírus da Hepatite E/genética , Sequências Repetidas Invertidas , Naftiridinas/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Pareamento de Bases , Sequência de Bases , Ligantes , Espectroscopia de Ressonância Magnética , Modelos Moleculares , RNA Viral/químicaRESUMO
Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.
