Incorporation and Utility of a Responsive Ribonucleoside Analogue in Probing the Conformation of a Viral RNA Motif by Fluorescence and 19 F NMR Spectroscopy

Development of versatile probes that can enable the study of different conformations and recognition properties of therapeutic nucleic acid motifs by complementing biophysical techniques can greatly aid nucleic acid analysis and therapy. Here, we report the design, synthesis and incorporation of an environment-sensitive ribonucleoside analogue, which serves as a two-channel biophysical platform to investigate RNA structure and recognition by fluorescence and ¹⁹ F NMR spectroscopy techniques. The nucleoside analogue is based on a 5-fluorobenzofuran-uracil core and its fluorescence and ¹⁹ F NMR chemical shifts are highly sensitive to changes in solvent polarity and viscosity. Notably, the modified ribonucleotide and phosphoramidite substrates can be efficiently incorporated into RNA oligonucleotides (ONs) by in vitro transcription and standard solid-phase ON synthesis protocol, respectively. Fluorescence and ¹⁹ F readouts of the nucleoside incorporated into model RNA ONs are sensitive to the neighbouring base environment. The responsiveness of the probe was aptly utilized in detecting and quantifying the metal ion-induced conformational change in an internal ribosome entry site RNA motif of hepatitis C virus, which is an important therapeutic target. Taken together, our probe is a good addition to the nucleic acid analysis toolbox with the advantage that it can be used to study nucleic acid conformation and recognition simultaneously by two biophysical techniques.

Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules

A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.

Simultaneous Amino Acid Analysis Based on 19F NMR Using a Modified OPA-Derivatization Method

To provide alternative methods of analyzing amino acids without liquid chromatography, ¹⁹F NMR-based simultaneous and individual detection methods for amino acids using o-phthalaldehyde (OPA)-based ¹⁹F labeling have been developed. Since the chemical shifts of almost all ¹⁹F-labeled amino acids differ from each other, and they can be discriminated on the ¹⁹F NMR spectrum, simultaneous detection of amino acids has been successfully demonstrated. The discrimination pattern of the peak identical to that of the ¹⁹F-labeled amino acids was largely dependent on the chemical structure of the thiols having ¹⁹F nuclei, strongly suggesting that there is a large potential for clearer discrimination of amino acids by optimizing the thiol structure and/or combined use of thiols.

Disassembly-driven signal turn-on probes for bimodal detection of DNA with 19F NMR and fluorescence

Self-assembling molecular probes that can detect DNA in a ¹⁹F NMR and fluorescence signal turn-on manner were successfully developed.