Probe Design for the Effective Fluorescence Imaging of Intracellular RNA

Over the past two decades, the spatiotemporal analysis of fluorescently labeled single RNA species has provided a broad insight into the synthesis, localization, degradation, and transport of RNA. To elucidate the dynamic behavior of functional RNAs in living cells, researchers throughout the world have proposed numerous fluorometric strategies for intracellular RNA imaging. Because, like most other biological molecules, RNA is intrinsically nonfluorescent, the development of methods for the labeling of RNAs of interest with fluorescent molecules is essential. Several artificial tag sequences have been attached onto the 3′ end of target RNAs and used as scaffolds for interacting with their fluorescent counterparts. In this Personal Account, we focus on the methods that have been developed to show how RNAs expressed in cells can be labeled and visualized by fluorescent proteins, small molecules, or nucleic acids. Each of these methods is designed to increase the sensitivity and specificity for imaging or to decrease the background fluorescence.     

Repurposing Antiviral Drugs for Orthogonal RNA‐Catalyzed Labeling of RNA

In vitro selected ribozymes are promising tools for site‐specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2′,5′‐branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA.     

Repurposing Antiviral Drugs for Orthogonal RNA-Catalyzed Labeling of RNA

In vitro selected ribozymes are promising tools for site-specific labeling of RNA. Previously known nucleic acid catalysts attached fluorescently labeled adenosine or guanosine derivatives through 2′,5′-branched phosphodiester bonds to the RNA of interest. Herein, we report new ribozymes that use orthogonal substrates, derived from the antiviral drug tenofovir, and attach bioorthogonal functional groups, as well as affinity handles and fluorescent reporter units through a hydrolytically more stable phosphonate ester linkage. The tenofovir transferase ribozymes were identified by in vitro selection and are orthogonal to nucleotide transferase ribozymes. As genetically encodable functional RNAs, these ribozymes may be developed for potential cellular applications. The orthogonal ribozymes addressed desired target sites in large RNAs in vitro, as shown by fluorescent labeling of E. coli 16S and 23S rRNAs in total cellular RNA.     

De novo sequencing of highly modified therapeutic oligonucleotides by hydrophobic tag sequencing coupled with LC–MS

Correct sequences are prerequisite for quality control of therapeutic oligonucleotides. However, there is no definitive method available for determining sequences of highly modified therapeutic RNAs, and thereby, most of the oligonucleotides have been used clinically without direct sequence determination. In this study, we developed a novel sequencing method called ‘hydrophobic tag sequencing’. Highly modified oligonucleotides are sequenced by partially digesting oligonucleotides conjugated with a 5′‐hydrophobic tag, followed by liquid chromatography–mass spectrometry analysis. 5′‐Hydrophobic tag‐printed fragments (5′‐tag degradates) can be separated in order of their molecular masses from tag‐free oligonucleotides by reversed‐phase liquid chromatography. As models for the sequencing, the anti‐VEGF aptamer (Macugen) and the highly modified 38‐mer RNA sequences were analyzed under blind conditions. Most nucleotides were identified from the molecular weight of hydrophobic 5′‐tag degradates calculated from monoisotopic mass in simple full mass data. When monoisotopic mass could not be assigned, the nucleotide was estimated using the molecular weight of the most abundant mass. The sequences of Macugen and 38‐mer RNA perfectly matched the theoretical sequences. The hydrophobic tag sequencing worked well to obtain simple full mass data, resulting in accurate and clear sequencing. The present study provides for the first time a de novo sequencing technology for highly modified RNAs and contributes to quality control of therapeutic oligonucleotides. Copyright © 2016 John Wiley & Sons, Ltd.     

Preparation of 4′-Spirocyclobutyl Nucleoside Analogues as Novel and Versatile Adenosine Scaffolds

Despite the large variety of modified nucleosides that have been reported, the preparation of constrained 4′-spirocyclic adenosine analogues has received very little attention. We discovered that the [2+2]-cycloaddition of dichloroketene on readily available 4′-exo-methylene furanose sugars efficiently results in the diastereoselective formation of novel 4′-spirocyclobutanones. The reaction mechanism was investigated via density functional theory (DFT) and found to proceed either via a non-synchronous or stepwise reaction sequence, controlled by the stereochemistry at the 3′-position of the sugar substrate. The obtained dichlorocyclobutanones were converted into nucleoside analogues, providing access to a novel class of chiral 4′-spirocyclobutyl adenosine mimetics in eight steps from commercially available sugars. Assessment of the biological activity of designed 4′-spirocyclic adenosine analogues identified potent inhibitors for protein methyltransferase target PRMT5.     

Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

The investigation of non‐coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo‐enzymatic RNA synthesis containing photoactivatable or ¹³C,¹⁵N‐labelled nucleosides. All four ribonucleotides containing ortho‐nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C‐nucleotides and ¹³C,¹⁵N‐labelled nucleotides were incorporated position‐specifically in high yields. We applied this approach for the synthesis of light‐inducible 2′dG‐sensing riboswitch variants and detected ligand‐induced structural reorganization upon irradiation by NMR spectroscopy. This chemo‐enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid‐phase synthesis.     

Oligonucleotide-Addressed Covalent 3′-Terminal Derivatization of Small RNA Strands for Enrichment and Visualization

The HEN1 RNA 2′-O-methyltransferase plays important roles in the biogenesis of small non-coding RNAs in plants and proved a valuable tool for selective transfer of functional groups from cofactor analogues onto miRNA and siRNA duplexes in vitro. Herein, we demonstrate the versatile HEN1-mediated methylation and alkylation of small RNA strands in heteroduplexes with a range of complementary synthetic DNA oligonucleotides carrying user-defined moieties such as internal or 3′-terminal extensions or chemical reporter groups. The observed DNA-guided covalent functionalization of RNA broadens our understanding of the substrate specificity of HEN1 and paves the way for the development of novel chemo-enzymatic tools with potential applications in miRNomics, synthetic biology, and nanomedicine.     

Covalent Chemical 5′‐Functionalization of RNA with Diazo Reagents

Functionalization of RNA at the 5′‐terminus is important for analytical and therapeutic purposes. Currently, these RNAs are synthesized de novo starting with a chemically functionalized 5′‐nucleotide, which is incorporated into RNA using chemical synthesis or biochemical techniques. Methods for direct chemical modification of native RNA would provide an attractive alternative but are currently underexplored. Herein, we report that diazo compounds can be used to selectively alkylate the 5′‐phosphate of ribo(oligo)nucleotides to give RNA labelled through a native phosphate ester bond. We applied this method to functionalize oligonucleotides with biotin and an orthosteric inhibitor of the eukaryotic initiation factor 4E (eIF4E), an enzyme involved in mRNA recognition. The modified RNA binds to eIF4E, demonstrating the utility of this labelling technique to modulate biological activity of RNA. This method complements existing techniques and may be used to chemically introduce a broad range of functional handles at the 5′‐end of RNA.     

RNA Ligation for Mono and Dually Labeled RNAs

Labeled RNAs are invaluable probes for investigation of RNA function and localization. However, mRNA labeling remains challenging. Here, we developed an improved method for 3′-end labeling of in vitro transcribed RNAs. We synthesized novel adenosine 3′,5′-bisphosphate analogues modified at the N6 or C2 position of adenosine with an azide-containing linker, fluorescent label, or biotin and assessed these constructs as substrates for RNA labeling directly by T4 ligase or via postenzymatic strain-promoted alkyne-azide cycloaddition (SPAAC). All analogues were substrates for T4 RNA ligase. Analogues containing bulky fluorescent labels or biotin showed better overall labeling yields than postenzymatic SPAAC. We successfully labeled uncapped RNAs, NAD-capped RNAs, and 5′-fluorescently labeled m⁷Gp₃A_m-capped mRNAs. The obtained highly homogenous dually labeled mRNA was translationally active and enabled fluorescence-based monitoring of decapping. This method will facilitate the use of various functionalized mRNA-based probes.     

New approaches towards the synthesis and characterization of alkoxy substituted spirobifluorenes and spirosilabifluorenes for organic optoelectronics

Alkoxy substituted spirobifluorene derivatives namely 2,2′,7,7′-tetrabromo-3,6-bis(methoxy)-9,9′spirobifluorene (MSBF), 2,2′,7,7′-tetrabromo-3,6-bis(ethoxy)-9,9′spirobifluorene (ESBF), 2,2′,7,7′-tetrabromo-3,6-bis(butoxy)-9,9′spirobifluorene (BSBF), 2,2′,7,7′-tetrabromo-3,3′,6,6′-tetra(methoxy)-9,9′-spiro-9-silabifluorene (MSSiBF) and their key intermediates have been synthesised successfully. All compounds have been fully characterised by ¹H and ¹³C NMR, FTIR, UV-visible spectroscopy, MS spectrometry. TGA analysis revealed good thermal stability. The systematic investigation on the solubility, thermostability and photophysical property of synthesized compound showed that alkoxy substituted spirobifluorene were unique in rigidity and have wide range of applications in molecular electronics and can be used as building units for optoelectronics material.     

Cu(I)‐Catalyzed Efficient Synthesis of 2′‐Triazolo‐nucleoside Conjugates

A small library of thirty‐two 2′‐triazolyl uridine and 2′‐triazolyl‐5‐methyluridine has been synthesized by Cu(I)‐catalyzed condensation of 2′‐azido‐2′‐deoxyuridine and 2′‐azido‐2′‐deoxy‐5‐methyluridine with different alkynes and aryl propargyl ethers in almost quantitative yields. Triazolo‐nucleoside conjugates, which can be evaluated for different biological activity for suitable drug development, were unambiguously identified on the basis of ¹H NMR, ¹³C NMR, IR, and HRMS data analysis. These compounds have been synthesized for the first time and have not been reported in the literature earlier.     

Synthesis and characterization of alkyl-, alkenyl-, acyl- and nitrogen-substituted derivatives of the potent phototoxin α-terthiophene

Some alkyl-, alkenyl-, acyl- and nitrogen- derivatives of α-terthienyl 1 have been synthesized in an effort to expand the potential insecticidal activity profile of this compound. The introduction of substituents was carried out directly on the α-terthienyl molecule. Three compounds were isolated in the nitration reaction and the compounds have been identified as 5-nitro-2,2′:5′,2″-terthiophene 5 , 3′-nitro-2,2′:5′,2″-terthiophene 6 and 3-nitro-2,2′:5′,2″-terthiophene 7 respectively. Preliminary results of biological acitivity are reported.     

Quantum chemical analysis of ATP, GTP and related compounds in gas phase

Adenosine 5′-triphosphate (ATP) and Guanine 5′-triphosphate (GTP), which are highly significant species for biological system as sources of energy, along with two other compounds, ribose 5′-triphosphate (RTP) and triposphate (TP), have been investigated theoretically. The capability of releasing terminal phosphoric acid and existent intramolecular bonds in their structure have been studied in gas phase. Due to the presence of hydrogen bonds in the above molecules, several inner and stable rings have been formed by atoms in molecules. The Quantum Theory of Atoms in Molecules (QTAIM) has been used in order to discover the intramolecular interactions properties in terms of charge densities. We have also demonstrated that the release of terminal phosphoric acid in ATP and GTP are both facilitated in the presence of ribose and base in comparison with TP and RTP. Our calculations have been done using density functional procedure.