Influence of oligonucleotides structures for separation of diastereomers by capillary electrophoresis method using polyvinylpyrrolidone 1,300,000.

In the field of oligonucleotides drug discovery, phosphorothioate (PS) modification has been recognized as an effective tool to overcome the nuclease digestion, and generates 2n of possible diastereomers, where n equals the number of PS linkages. However, it is also well known that differences in drug efficacy and toxicity are caused by differences in stereochemistry of oligonucleotides. Therefore, the development of a high-resolution analytical method that enables stereo discrimination of oligonucleotides is desired. Under this circumstance, capillary electrophoresis (CE) using polyvinylpyrrolidone (PVP) is considered as one of the useful tools for the separation analysis of diastereomers. In this study, we evaluated the several oligonucleotides with the structural diversities in order to understand the separation mechanism of the diastereomers by CE. Especially, five kinds of 2'-moieties were deeply examined by CE with PVP 1,300,000 polymer solution. We found that different trend of the peak shapes and the peak resolution were observed among these oligonucleotides. For example, the better peak resolution was observed in 6 mer PS3-DNA compared to the rigid structure of 6 mer PS3-LNA. As for this reason, the computational simulation revealed that difference of accessible surface area caused by the steric structure of thiophosphate in each oligonucleotide is one of the key attributes to explain the separation of the diastereomers. In addition, we achieved the separation of sixteen peak tops of the diastereomers in 6 mer PS4-DNA, and the complete separation of fifteen diastereomers in 6 mer PS4-RNA. These knowledge for the separation of the diastereomers by CE will be expected to the quality control of the oligonucleotide drugs.

A new strategy to exploit maximum rate performance for aqueous batteries through a judicious selection of MOF-type electrodes.

A metal-organic framework (MOF) having a redox active 1,4,5,8-naphthalenetetracarboxdiimide (NDI) derivative in its organic linker shows excellent rate performance as an electrode material for aqueous batteries thanks to its large pores. Among aqueous electrolytes examined, K+-based ones exhibit the highest rate performance, which is caused by the highest mobility of the smallest hydrated K+ ion not only in the aqueous electrolyte but also in the electrode. Since the use of a counter electrode with insufficiently small pores for the full-cell configuration offsets this merit, our study may lead to a conclusion that the maximum rate performance for aqueous batteries will be accomplished only through further elaboration of both electrode materials with sufficiently large pores, in which hydrated ions can travel equally fast as those in the electrolyte.

Selective Inhibition of L-type Amino Acid Transporter 1 Suppresses Cell Proliferation in Ovarian Clear Cell Carcinoma.

BACKGROUND/AIM: Ovarian clear cell carcinoma (OCCC) is a histological type of ovarian cancer that is refractory to chemotherapy and has poor prognosis, which necessitates the development of novel treatment therapies. In this study, we focused on L-type amino acid transporter 1 (LAT1), which is involved in cancer growth, and investigated the effect of its selective inhibition on cell proliferation in OCCC. MATERIALS AND METHODS: The inhibitory effect of nanvuranlat (JPH203), a LAT1 selective inhibitor, on the cellular uptake of [3H] leucine was evaluated using the OCCC cell line JHOC9, which expresses the LAT1 protein. In addition, the kinetics of cell proliferation and changes in phosphorylation of the mTOR pathway were analyzed. The correlation between LAT1 expression and progression-free survival (PFS) was evaluated using clinical specimens of OCCC. RESULTS: Nanvuranlat inhibited [3H] leucine intracellular uptake and cell proliferation in a dose-dependent manner in JHOC9 cells. In addition, it suppressed the activity of the mTOR signaling pathway, which is thought to inhibit cancer cell proliferation. LAT1 expression was most frequent in OCCC among clinical specimens of epithelial ovarian cancer. A correlation between LAT1 expression and PFS was observed in OCCC. CONCLUSION: LAT1 selective inhibition suppresses cell proliferation via the mTOR pathway by inhibiting leucine uptake in OCCC. This study illustrates the potential of using LAT1 selective inhibition as a treatment strategy for OCCC.

Creation of single molecular conjugates of metal-organic cages and DNA.

Here we report the development of an equimolar conjugate of a metal-organic cage (MOC) and DNA (MOC-DNA). Several MOC-DNA conjugates were assembled into a programmed structure by coordinating with a template DNA having a complementary base sequence. Moreover, conjugation with the MOC drastically enhanced the permeability of DNA through the lipid bilayer, presenting great potential as a drug delivery system.

Enhanced electrochemical performance of Li2.72Na0.31MnPO4CO3 as a cathode material in "water-in-salt" electrolytes.

A carbonophosphate compound of Li2.72Na0.31MnPO4CO3 was synthesized via ion exchange. The initial discharge capacity of Li2.72Na0.31MnPO4CO3 in 15 molal (or 15 m) LiTFSI was 110 mA h g-1 at 2 mA cm-2 (∼0.5C). Due to the decomposition of Li2.72Na0.31MnPO4CO3, the capacity retention degraded to 64% after 100 cycles.

Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization.

We have found that antisense oligonucleotides and siRNA molecules modified with repeat structures of disulfide units can be directly introduced into the cytoplasm and exhibit a suppressive effect on gene expression. In this study, we analyzed the mechanism of cellular uptake of these membrane-permeable oligonucleotides (MPONs). Time-course analysis by confocal microscopy showed that the uptake of MPONs from the plasma membrane to the cytoplasm reached 50 % of the total uptake in about 5 min. In addition, analysis of the plasma membrane proteins to which MPONs bind, identified several proteins, including voltage-dependent anion channel. Next, we analyzed the behavior of MPONs in the cell and found them to be abundant in the nucleus as early as 24 h after addition with the amount increasing further after 48 and 72 h. The amount of MPONs was 2.5-fold higher than that of unmodified oligonucleotides in the nucleus after 72 h. We also designed antisense oligonucleotides and evaluated the effect of MPONs on mRNA exon skipping using DMD model cells; MPONs caused exon skipping with 69 % efficiency after 72 h, which was three times higher than the rate of the control. In summary, the high capacity for intracytoplasmic and nuclear translocation of MPONs is expected to be useful for therapeutic strategies targeting exon skipping.

Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells.

Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.

Correction: Local structure of a highly concentrated NaClO4 aqueous solution-type electrolyte for sodium ion batteries.

Correction for 'Local structure of a highly concentrated NaClO4 aqueous solution-type electrolyte for sodium ion batteries' by Ryo Sakamoto et al., Phys. Chem. Chem. Phys., 2020, 22, 26452-26458, DOI: 10.1039/D0CP04376A.

Chemical Synthesis of Circular RNAs with Phosphoramidate Linkages for Rolling-Circle Translation.

Recently, many types of circular RNAs have been reported in human cells. One interesting aspect of circular RNAs is their translation into proteins. We previously discovered that circular RNA without a stop codon can be translated into long repeating peptides via rolling-circle translation in both prokaryotic and eukaryotic systems. Because the rate-limiting step of translation-ribosome binding-occurs only once in rolling-circle translation, the translation efficacy is very efficient compared to translation of linear mRNAs. However, preparation of circular RNAs involves costly and time-consuming enzymatic methods, and there was no practical non-enzymatic method. We recently reported a chemical synthesis strategy using short RNA fragments and one or two phosphoramidate linkages. In this article, we describe the chemical synthesis and purification methods for preparation of circular RNAs for rolling-circle translation. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of 3'-amino-modified guanosine controlled-pore glass Basic Protocol 2: Solid-phase synthesis of linear RNA fragments Basic Protocol 3: Chemical synthesis of circular RNAs.

Local structure of a highly concentrated NaClO4 aqueous solution-type electrolyte for sodium ion batteries.

Aqueous Na-ion batteries with highly concentrated NaClO4 aq. electrolytes are drawing attention as candidates for large-scale rechargeable batteries with a high safety level. However, the detailed mechanism by which the potential window in 17 m NaClO4 aq. electrolyte was expanded remains unclear. Therefore, we investigated the local structure around a Na+ ion or a ClO4- ion using X-ray diffraction combined with empirical potential structure refinement (EPSR) modelling and Raman spectroscopy. The results showed that in 17 m NaClO4 aq. electrolyte, most of the water molecules were coordinated to Na+ ions and few free water molecules were present. The 17 m NaClO4 aq. electrolyte could be interpreted as widening the potential window because almost all water molecules participated in hydration of the Na+ ions.

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis.

Messenger RNAs (mRNAs) with phosphorothioate modification (PS-mRNA) to the phosphate site of A, G, C, and U with all 16 possible combinations were prepared, and the translation reaction was evaluated using an E. coli cell-free translation system. Protein synthesis from PS-mRNA increased in 12 of 15 patterns when compared with that of unmodified mRNA. The protein yield increased 22-fold when the phosphorothioate modification at A/C sites was introduced into the region from the 5'-end to the initiation codon. Single-turnover analysis of PS-mRNA translation showed that phosphorothioate modification increases the number of translating ribosomes, thus suggesting that the rate of translation initiation (rate of ribosome complex formation) is positively affected by the modification. The method provides a new strategy for improving translation by using non-natural mRNA.

Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation.

Circular RNA without a stop codon enables rolling circle translation. To produce circular RNAs, we carried out one-pot chemical synthesis of circular RNA from RNA fragments with the use of an EDC/HOBt-based chemical ligation reaction. The synthesized circular RNAs acted as translation templates, despite the presence of unnatural phosphoramidate linkages.

Cathode Properties of Na3FePO4CO3 Prepared by the Mechanical Ball Milling Method for Na-ion Batteries.

The carbonophosphate Na3FePO4CO3 was synthesized by the mechanical ball milling method for the first time. The composition of the obtained sample with a higher amount of Fe2+ was Na2.66Fe2+0.66Fe3+0.34PO4CO3 as confirmed by Mössbauer analysis, owing to the good airtight properties of this method. The obtained samples in an organic electrolyte delivered an initial discharge capacity of 124 mAh/g at room temperature, and a larger discharge capacity of 159 mAh/g (1.66 Na+/mole) at 60 °C. With 17 m NaClO4 aqueous electrolyte, a discharge capacity of 161 mAh/g (1.69 Na+/mole) was delivered because of the high ionic conductivity of the concentrated aqueous electrolyte. During the charge-discharge process, the formation of Fe4+ after charging up to 4.5 V and the return of Fe2+ after discharging down to 1.5 V were detected by ex-situ X-ray absorption near edge structure (XANES) analysis.

Intracellular Delivery of Antisense DNA and siRNA with Amino Groups Masked with Disulfide Units.

Efficient methods for delivery of antisense DNA or small interfering RNA (siRNA) are highly needed. Cationic materials, which are conventionally used for anionic oligonucleotide delivery, have several drawbacks, including aggregate formation, cytotoxicity and a low endosome escape efficiency. In this report a bio-reactive mask (i.e., disulfide unit) for cationic amino groups was introduced, and the mask was designed such that it was removed at the target cell surface. Insolubility and severe cellular toxicity caused by exposed cationic groups are avoided when using the mask. Moreover, the disulfide unit used to mask the cationic group enabled direct delivery of oligonucleotides to the cell cytosol. The molecular design reported is a promising approach for therapeutic applications.

Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors.

We herein report a new approach for RNA interference, so-called "build-up RNAi" approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors. The advantages of using these circular RNA formats for RNAi were presented in aspects of immunogenicity and cellular uptake.

N6-methyl adenosine in siRNA evades immune response without reducing RNAi activity.

siRNA is a powerful method to suppress specific gene expression and has recently been utilized for molecular biology as well as medicine. However, introduction of dsRNA stimulates immune-responses as side-effects. In the present study, we utilized N6-methyl adenosine, one of the natural modified nucleosides, instead of adenosine in siRNA. When adenosine in the passenger or guide strand of siRNA was completely replaced with N6-methyl adenosine, the immune response against siRNA was evaded without any reduction in RNAi activity. This knowledge will promote the medical application of siRNA and enhance our understanding on cellular discrimination of non-self and self dsRNA.

Disulfide-Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA.

Development of intracellular delivery methods for antisense DNA and siRNA is important. Previously reported methods using liposomes or receptor-ligands take several hours or more to deliver oligonucleotides to the cytoplasm due to their retention in endosomes. Oligonucleotides modified with low molecular weight disulfide units at a terminus reach the cytoplasm 10 minutes after administration to cultured cells. This rapid cytoplasmic internalization of disulfide-modified oligonucleotides suggests the existence of an uptake pathway other than endocytosis. Mechanistic analysis revealed that the modified oligonucleotides are efficiently internalized into the cytoplasm through disulfide exchange reactions with the thiol groups on the cellular surface. This approach solves several critical problems with the currently available methods for enhancing cellular uptake of oligonucleotides and may be an effective approach in the medicinal application of antisense DNA and siRNA.

Enhanced Intercellular Delivery of cRGD-siRNA Conjugates by an Additional Oligospermine Modification.

Small interfering RNA (siRNA), consisting a 21-mer duplex molecule, is often modified by conjugation with specific ligands to enhance its capacity for tissue-specific delivery. However, these attempts are hampered by the low permeability of negatively charged RNA molecules to enter the cell membrane. In this study, we designed and synthesized siRNA conjugates modified with cationic oligospermine and cyclic RGD (cRGD) to overcome the low-membrane permeability of siRNA. The siRNA conjugate, which contains 15 spermines and a cRGD peptide, showed sufficient gene-silencing activity at 250 nM final concentration without a transfection reagent. Under these conditions, the cationic oligospermine and cRGD-siRNA conjugate did not show any cytotoxicity.

Diazirine-containing tag-free RNA probes for efficient RISC-loading and photoaffinity labeling of microRNA targets.

We designed and synthesized a photo-reactive and tag-free RNA probe for the identification of microRNA (miRNA) targets. To synthesize the RNA probe, we designed a novel nucleoside analog 1-O-[3-ethynyl-5-(3-trifluoromethyl-3H-diazirine-3-yl)]benzyl-ß-d-ribofuranose containing aryl trifluoromethyl diazirine and ethynyl moieties. The RNA probe containing this analog was observed to form crosslinks with complementary RNA by UV irradiation and was rapidly tagged by Cu-catalyzed azide alkyne cycloaddition (CuAAC). In addition, the tag-free and photo-reactive miRNA-145 probe showed comparable gene silencing activity to that of unmodified miRNA-145. Therefore, miRNA probes containing the nucleoside analog are promising candidates for the identification of target mRNAs of miRNAs.

Design and synthesis of novel photoinduced electron transfer-based hybridization probes.

Photoinduced electron transfer (PeT)-based hybridization probe is a linear and quencher-free oligonucleotide (ON) probe for DNA or RNA detection. In this report, we designed and synthesized novel adenosine analogues for PeT-based hybridization probe. In particular, the analogue containing a piperazinomethyl moiety showed effective quenching property under physiological conditions. When the probe containing the analogue was hybridized with a complementary DNA or RNA, the fluorescence increased 3- or 4-fold, respectively, compared to the single-stranded state.