Solution structure of a modified 2′,5′-linked RNA hairpin involved in an equilibrium with duplex

The isomerization of phosphodiester functionality of nucleic acids from 3′,5′- to a less common 2′,5′-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2′,5′-linked RNA analogue, 3′-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3′-MOE-2′,5′-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3′-MOE-2′,5′-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3′-MOE-2′,5′-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson–Crick A5·*U8 base pair and by n → π* stacking interactions of O4′ lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3′-MOE-2′,5′-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids

Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs

RNA G-quadruplex (RG4) structures are involved in multiple biological processes. Recent genome-wide analyses of human mRNA transcriptome identified thousands of putative intramolecular RG4s that readily assemble in vitro but shown to be unfolded in vivo. Previously, we have shown that mature cytoplasmic tRNAs are cleaved during stress response to produce tRNA fragments that function to repress translation in vivo. Here we report that these bioactive tRNA fragments assemble into intermolecular RG4s. We provide evidence for the formation of uniquely stable tetramolecular RG4 structures consisting of five tetrad layers formed by 5ʹ-terminal oligoguanine motifs of an individual tRNA fragment. RG4 is required for functions of tRNA fragments in the regulation of mRNA translation, a critical component of cellular stress response. RG4 disruption abrogates tRNA fragments ability to trigger the formation of Stress Granules in vivo. Collectively, our data rationalize the existence of naturally occurring RG4-assembling tRNA fragments and emphasize their regulatory roles

Fusion of the 1H NMR data of serum, urine and exhaled breath condensate in order to discriminate chronic obstructive pulmonary disease and obstructive sleep apnea syndrome

Chronic obstructive pulmonary disease, COPD, affects the condition of the entire human organism and causes multiple comorbidities. Pathological lung changes lead to quantitative changes in the composition of the metabolites in different body fluids. The obstructive sleep apnea syndrome, OSAS, occurs in conjunction with chronic obstructive pulmonary disease in about 10–20 % of individuals who have COPD. Both conditions share the same comorbidities and this makes differentiating them difficult. The aim of this study was to investigate whether it is possible to diagnose a patient with either COPD or the OSA syndrome using a set of selected metabolites and to determine whether the metabolites that are present in one type of biofluid (serum, exhaled breath condensate or urine) or whether a combination of metabolites that are present in two biofluids or whether a set of metabolites that are present in all three biofluids are necessary to correctly diagnose a patient. A quantitative analysis of the metabolites in all three biofluid samples was performed using 1H NMR spectroscopy. A multivariate bootstrap approach that combines partial least squares regression with the variable importance in projection score (VIP-score) and selectivity ratio (SR) was adopted in order to construct discriminant diagnostic models for the groups of individuals with COPD and OSAS. A comparison study of all of the discriminant models that were constructed and validated showed that the discriminant partial least squares model using only ten urine metabolites (selected with the SR approach) has a specificity of 100 % and a sensitivity of 86.67 %. This model (AUCtest = 0.95) presented the best prediction performance. The main conclusion of this study is that urine metabolites, among the others, present the highest probability for correctly identifying patents with COPD and the lowest probability for an incorrect identification of the OSA syndrome as developed COPD. Another important conclusion is that the changes in the metabolite levels of exhaled breath condensates do not appear to be specific enough to differentiate between patients with COPD and OSA

Effect of Neighbors on the Conformational Preferences of Glycosidic Linkages in Glycyrrhizic Acid and Its Mono- and Dideprotonated Forms: X‑ray, NMR, and Computational Studies

Three-dimensional structure of glycyrrhizic acid is determined by the conformation of the disaccharide unit and its relative orientation to a virtually rigid aglycone. X-ray crystallography, NMR spectroscopy, and density functional theory (DFT) calculations were used to study the conformational preferences of the glycosidic linkages in solid state, solution and vacuo, respectively. Experimental data have revealed that conformation of glycosidic bonds, that is adopted in the solid state, is also favored in solution. The molecular geometry optimizations have shown that a strongly twisted orientation of the two glucopyranose units, characteristic of the solid state, is stabilized by the bridging interaction of water molecules and/or cations with disaccharide COOH/COO¯ groups. Our results illustrate the impact of environment on the preferred conformation of disaccharide unit in the studied glycoside and point to a possible reason for the observed rigid conformation of the glycosidic bonds in solution and in the solid state

Effect of Neighbors on the Conformational Preferences of Glycosidic Linkages in Glycyrrhizic Acid and Its Mono- and Dideprotonated Forms: X‑ray, NMR, and Computational Studies

Three-dimensional structure of glycyrrhizic acid is determined by the conformation of the disaccharide unit and its relative orientation to a virtually rigid aglycone. X-ray crystallography, NMR spectroscopy, and density functional theory (DFT) calculations were used to study the conformational preferences of the glycosidic linkages in solid state, solution and vacuo, respectively. Experimental data have revealed that conformation of glycosidic bonds, that is adopted in the solid state, is also favored in solution. The molecular geometry optimizations have shown that a strongly twisted orientation of the two glucopyranose units, characteristic of the solid state, is stabilized by the bridging interaction of water molecules and/or cations with disaccharide COOH/COO¯ groups. Our results illustrate the impact of environment on the preferred conformation of disaccharide unit in the studied glycoside and point to a possible reason for the observed rigid conformation of the glycosidic bonds in solution and in the solid state