NMR studies of organic solvent denatured yeast phenylalanyl transfer RNA at 220 MHZ a

Instrumental analysis of RNA modifications

Organisms from all domains of life invest a substantial amount of energy for the introduction of RNA modifications into nearly all transcripts studied to date. Instrumental analysis of RNA can focus on the modified residues and reveal the function of these epitranscriptomic marks. Here, we will review recent advances and breakthroughs achieved by NMR spectroscopy, sequencing, and mass spectrometry of the epitranscriptome.

Accurate Quantification of Nucleic Acids Using Hypochromicity Measurements in Conjunction with UV Spectrophotometry

UV absorbance spectrophotometry is widely used for the quantification of nucleic acids. For accurate quantification, it is important to determine the hypochromicity of the oligonucleotide or complex nucleic acid structure. The use of thermal denaturation studies in conjunction with UV spectrophotometry to determine hypochromicity requires prolonged, elevated temperatures, which may cause partial hydrolysis of RNA. In addition, dsRNA is difficult to denature even at elevated temperature, and the extinction coefficients of nucleic acids are also affected by temperature, which makes it difficult to accurately determine the nucleic acid concentration. To overcome these caveats, we have utilized the chemical denaturant dimethyl sulfoxide which, in conjunction with a short thermal denaturation, prevents renaturation of the duplex nucleic acids (dsDNA/RNA). Using this approach, we have measured the absorbance of both the unstructured and structured nucleic acids to accurately measure their hypochromicity and determine their extinction coefficients. For a range of different dsRNA, we have for the first time determined values of 46.18-47.29 μg/mL/A₂₆₀ for the quantification of dsRNA using UV spectrophotometry. Moreover, this approach enables the accurate determination of the relative proportion of duplex nucleic acids in mixed ds/ss nucleic acid solutions, demonstrating significant advantages over current methods.

Influence of dimethylsulfoxide on RNA structure and ligand binding

Dimethyl sulfoxide (DMSO) is widely used as a cosolvent to solubilize hydrophobic compounds in RNA-ligand binding assays. Although it is known that high concentrations of DMSO (>75%) can significantly affect RNA structure and folding energetics, a thorough analysis of how lower concentrations (<10%) of DMSO typically used in binding assays affects RNA structure and ligand binding has not been undertaken. Here, we use NMR and 2-aminopurine fluorescence spectroscopy to examine how DMSO affects the structure, dynamics, and ligand binding properties of two flexible hairpin RNAs: the transactivation response element from HIV-1 and bacterial ribosomal A-site. In both cases, 5-10% DMSO decreased stacking interactions and increased local disorder in noncanonical residues within bulges and loops and resulted in 0.3-4-fold reduction in the measured binding affinities for different small molecules, with the greatest reduction observed for an intercalating compound that binds RNA nonspecifically. Our results suggest that, by competing for hydrophobic interactions, DMSO can have a small but significant effect on RNA structure and ligand binding. These effects should be considered when developing ligand binding assays and high throughput screens.

The effects of cryopreservation on early development and chromosome constitution in Chinese hamster embryos

The effects of cryopreservation on early embryonic development were investigated in Chinese hamster embryos. Embryos were randomly divided into 3 groups, as follows: the control group, embryos which were simply cultured; the DMSO group, embryos which were exposed to dimethyl sulfoxide (DMSO) and then cultured; the cryopreservation group, embryos which were cryopreserved and then cultured. The percentages of embryos which developed into blastocysts after 40 hours of cultivation were high in all groups. However, there were significant differences in the mean number of blastomeres with lower values after an exposure to DMSO and cryopreservation (73.2 in the control group, 62.0 in the DMSO group, and 40.2 in the cryopreservation group). No significant differences in chromosome abnormality rate were evident and there was no distinct tendency for variation in karyotype among the 3 groups. These results indicate that DMSO adversely affects the division of blastomeres, and that cryopreservation with DMSO as a cryoprotectant might aggravate these adverse effects.

Proton magnetic resonance studies on the conformation of the hexanucleotide, GmpApApYpApsiP, and Related fragments from the anticodong loop of baker's yeast phenylalanine transfer ribonucleic acid

A hexanucleotide, GmpApApYpAppsiP, and 11 related compounds from the anticodon loop of Baker's yeast tRNA-Phe were studied by proton magnetic resonance from 100 to 250 MHz. Totally 19 resonance lines from all the base protons (H8, H6, and H2), H1', and methyl proton resonances of the hexamer have been assigned by a systematic "incremental procedure" in comparing all the related shorter fragments. Emphasis is given to the Y base and its stacking conformation with respect to its nearest neighboring bases. The results reveal a strong tendency of the purine bases to have a maximal extent of base-base overlap with their neighbors in the sequence. This tendency is manifested in a zigzag (or balcony-like) mode of base-stacking pattern of the -ApYpA-sequence in the hexamer in which the -pA-residue tends to stack toward the adduct ring (C10, C11, and N12) of Y. This tendency is also shown in the formation of a stack of GmAAA closing the gap left behind by the excision of Y in the hexamer GmpApAp--pApp. The implication of these findings to the structure and function of tRNA is discussed.