Enhancing Binding Affinity to CGG/CGG Triad: Optimizing Naphthyridine Carbamate Dimer Derivatives with Varied Linker Lengths.

This study examines the binding properties of six naphthyridine carbamate dimer (NCD) derivatives with varying linker lengths to the CGG/CGG triad, a non-canonical DNA structure linked to repeat expansion disorders. By altering the linker length from 2 to 4 methylene groups, we found changes in thermal stability of the ligand-bound complexes while maintaining a consistent 2:1 binding stoichiometry. Among the derivatives, CC23 showed superior binding affinity compared to the parent molecule CC33 (NCD). Spectroscopic analyses revealed that linker length influences the conformational equilibrium of NCD derivatives. Thermal melting temperature measurements demonstrated CC23's enhanced thermal stability over CC33. These findings underscore the potential of optimized NCD derivatives, like CC23, as tools to modulate CGG repeat structures, offering insights for therapeutic strategies targeting repeat expansion disorders.

Intracerebral Distribution of CAG Repeat-Binding Small Molecule Visualized by Whole-Brain Imaging.

Understanding the pharmacokinetics of drug candidates of interest in the brain and evaluating drug delivery to the brain are important for developing drugs targeting the brain. Previously, we demonstrated that a CAG repeat-binding small molecule, naphthyridine-azaquinolone (NA), resulted in repeat contraction in mouse models of dentatorubral-pallidoluysian atrophy and Huntington's disease caused by aberrant expansion of CAG repeats. However, the intracerebral distribution and drug deliverability of NA remain unclear. Here, we report three-dimensional whole-brain imaging of an externally administered small molecule using tissue clearing and light sheet fluorescence microscopy (LSFM). We designed and synthesized an Alexa594-labeled NA derivative with a primary amine for whole-brain imaging (NA-Alexa594-NH2), revealing the intracerebral distribution of NA-Alexa594-NH2 after intraparenchymal and intracerebroventricular administrations by whole-brain imaging combined with tissue clearing and LSFM. We also clarified that intranasally administered NA-Alexa594-NH2 was delivered into the brain via multiple nose-to-brain pathways by tracking the time-dependent change in the intracerebral distribution. Whole-brain imaging of small molecules by tissue clearing and LSFM is useful for elucidating not only the intracerebral distribution but also the drug delivery pathways into the brain.

Fluorescent indicator displacement assay for the discovery of UGGAA repeat-targeted small molecules.

We report that a selective fluorescent indicator NBD-NCD for UGGAA repeats resulted in fluorescence quenching upon binding to RNA and recovered the fluorescence by displacing NBD-NCD with UGGAA repeat-targeted small molecules. The fluorescent indicator displacement assay using NBD-NCD can detect the interaction of small molecules with UGGAA repeats.

A small molecule binding to TGGAA pentanucleotide repeats that cause spinocerebellar ataxia type 31.

Spinocerebellar ataxia type 31 is an autosomal dominant neurodegenerative disease caused by aberrant insertion of d(TGGAA)n into the intron shared by brain expressed, associated with Nedd4 and thymidine kinase 2 genes in chromosome 16. We reported that a naphthyridine dimer derivative with amidated linker structure (ND-amide) bound to GGA/GGA motifs in hairpin structures of d(TGGAA)n. The binding of naphthyridine dimer derivatives to the GGA/GGA motif was sensitive to the linker structures. The amidation of the linker in naphthyridine dimer improved the binding property to the GGA/GGA motif as compared with non-amidated naphthyridine dimer.

Folding RNA-Protein Complex into Designed Nanostructures.

RNA-protein (RNP) complexes are promising biomaterials for the fields of nanotechnology and synthetic biology. Protein-responsive RNA sequences (RNP motifs) can be integrated into various RNAs, such as messenger RNA, short-hairpin RNA, and synthetic RNA nanoobjects for a variety of purposes. Direct observation of RNP interaction in solution at high resolution is important in the design and construction of RNP-mediated nanostructures. Here we describe a method to construct and visualize RNP nanostructures that precisely arrange a target protein on the RNA scaffold with nanometer scale. High-speed AFM (HS-AFM) images of RNP nanostructures show that the folding of RNP complexes of defined sizes can be directly visualized at single RNP resolution in solution.

Small molecule targeting r(UGGAA)n disrupts RNA foci and alleviates disease phenotype in Drosophila model.

Synthetic small molecules modulating RNA structure and function have therapeutic potential for RNA diseases. Here we report our discovery that naphthyridine carbamate dimer (NCD) targets disease-causing r(UGGAA)n repeat RNAs in spinocerebellar ataxia type 31 (SCA31). Structural analysis of the NCD-UGGAA/UGGAA complex by nuclear magnetic resonance (NMR) spectroscopy clarifies the mode of binding that recognizes four guanines in the UGGAA/UGGAA pentad by hydrogen bonding with four naphthyridine moieties of two NCD molecules. Biological studies show that NCD disrupts naturally occurring RNA foci built on r(UGGAA)n repeat RNA known as nuclear stress bodies (nSBs) by interfering with RNA-protein interactions resulting in the suppression of nSB-mediated splicing events. Feeding NCD to larvae of the Drosophila model of SCA31 alleviates the disease phenotype induced by toxic r(UGGAA)n repeat RNA. These studies demonstrate that small molecules targeting toxic repeat RNAs are a promising chemical tool for studies on repeat expansion diseases.

1,3-Di(quinolin-2-yl)guanidine binds to GGCCCC hexanucleotide repeat DNA in C9ORF72.

Aberrant expansion of GGGGCC (G4C2) hexanucleotide repeat (HNR) in the first intron of C9ORF72 has been found in frontotemporal dementia and amyotrophic lateral sclerosis (FTD/ALD). The non-canonical DNA structures of the expanded repeats are causative to repeat instability leading to contraction and expansion. We demonstrate that 1,3-di(quinolin-2-yl)guanidine (DQG) binds to GGCCCC/GGCCCC (G2C4/G2C4) motif in double stranded DNA and also antisense G2C4 HNR DNA in C9ORF72. Large increase in the melting temperature of dsDNA containing the G2C4/G2C4 motif was confirmed by the binding of DQG. The marked CD spectral changes indicated structural transition of d(G2C4)9 from i-motifs and/or hairpins to DQG-stabilized d(G2C4)9 structures.

Bicyclic and tricyclic C-C mismatch-binding ligands bind to CCG trinucleotide repeat DNAs.

We have reported bicyclic and tricyclic C-C mismatch-binding ligands that selectively bind to CCG trinucleotide repeat (TNR) DNAs. Bivalent interaction and enlarging the aromatic ring system of the cytosine-recognition unit led to the ligand binding to CCG TNRs accompanied by the formation of stable ligand-CCG TNR complexes and a large conformational change.

Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate.

Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA-protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA-protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA-protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour.Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.

Fluorescence Probe for Detecting CCG Trinucleotide Repeat DNA Expansion and Slip-Out.

Trinucleotide repeat expansion in genomic DNA causes severe neurodegenerative diseases. Fluorescence probes that bind to trinucleotide repeats have potential as diagnostic tools of trinucleotide repeat disorders. Here, we report a novel tricyclic ligand that binds to CCG trinucleotide repeat DNA. The expansion of the aromatic ring system of the 2-amino-1,8-naphthyridine chromophore from the bicyclic to the tricyclic improved the binding ability to the CCG/CCG motif without losing the selectivity and emissive character. The fluorescence sensitively decreased in response to binding to the CCG trinucleotide repeat. The degree of quenching depended on the number of CCG repeats. In addition, the fluorescence detection was applicable to CCG slip-out DNA.

Folding RNA-Protein Complex into Designed Nanostructures.

RNA-protein (RNP) complexes are promising biomaterials for the fields of nanotechnology and synthetic biology. Protein-responsive RNA sequences (RNP motifs) can be integrated into various RNAs, such as messenger RNA, short-hairpin RNA, and synthetic RNA nano-objects for a variety of purposes. Direct observation of RNP interaction in solution at high resolution is important in the design and construction of RNP-mediated nanostructures. Here we describe a method to construct and visualize RNP nanostructures that precisely arrange a target protein on the RNA scaffold with nanometer scale. High-speed AFM (HS-AFM) images of RNP nanostructures show that the folding of RNP complexes of defined sizes can be directly visualized at single RNP resolution in solution.

Modulation of binding properties of amphiphilic DNA containing multiple dodecyl phosphotriester linkages to lipid bilayer membrane.

DNA is a promising functional molecule to modify and design lipid membrane functions. In order to use DNA in a hydrophilic-hydrophobic interface including lipid membrane, we have developed an amphiphilic DNA having dodecyl phosphotriester linkages (dod-DNA). Herein, we report the binding of a series of amphiphilic dod-DNAs to the lipid bilayer membrane. Surface plasmon resonance (SPR) assay and fluorescent microscopy showed that dod-DNA having three dodecyl groups at each end strongly bound to lipid membrane due to the slow dissociation rate and the dod-DNA can be used as a linear template for molecular arrangement on the membrane surface.

G-quadruplex formation of entirely hydrophobic DNA in organic solvents.

We report herein a novel hydrophobic G-quadruplex DNA consisting of dodecyl phosphotriester linkages. The 6-mer hydrophobic DNA having a TG4T sequence binds to monovalent cations to form a tetramolecular G-quadruplex in low polarity organic solvents.

Characterization of skin inflammation induced by repeated exposure of toluene, xylene, and formaldehyde in mice.

Volatile organic compounds (VOCs) are considered the main cause of sick building syndrome and they are likely to irritate the skin, eyes, and mucous membrane; however, the toxic threshold and the mechanisms of cutaneous reaction induced by long-time VOC exposure have not been clarified. In the present study, we investigated the effect of repeated painting of VOCs onto mouse skin. Various concentrations of toluene, xylene, and formaldehyde (FA) were applied once a week for 5 weeks. While FA solution (2-10%) induced remarkable ear swelling and caused evident infiltration of inflammatory cells, high concentrations of toluene and xylene (50 or 100%) evoked mild ear swelling and marginal inflammatory cell invasion. In addition, FA exposure markedly increased the expression of interleukin-4 (IL-4), brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3), and transient receptor potential vanilloid-1 (TRPV-1) mRNAs in the ears and IL-4 and NT-3 mRNAs in the cervical lymph nodes. Furthermore, capsazepine, a TRPV-1 antagonist, significantly suppressed ear swelling caused by repeated painting of 5% FA. These findings demonstrate that FA has more potent irritancy against skin than toluene or xylene and suggest that the Th2 response, neurotrophins and TRPV-1 play important roles in FA-induced skin inflammation.

Discrimination of N6-methyl adenine in a specific DNA sequence.

We have developed a novel chemistry-based method to detect adenine methylation. A DNA probe functionalized with a formyl group discriminates between adenine and N6-methyl adenine by the formation of a selective interstrand cross-link.

DNA cross-link generated by a novel modified DNA containing a formyl group.

We here report the synthesis of novel modified nucleic acid containing a formyl group and the evaluation of interstrand cross-linking between the modified DNA and the complementary strand. The synthesis of the formyl-containing oligodeoxynucleotide (ODN) was achieved by a post synthetic modification of corresponding ODN containing a 1,2-diol. The ODN containing the diol moiety was successfully synthesized by a standard phosphoramidite method, and was quantitatively converted to the desired formyl-containing ODN by sodium periodate oxidation. Hybridizaiton of the formyl ODN and the complementary ODN produced the interstrand cross-link between the formyl group and N(6)-exocyclic amino group of adenine.

Inhibition of IgE-dependent mouse triphasic cutaneous reaction by a boiling water fraction separated from mycelium of Phellinus linteus.

Phellinus linteus, a mushroom, contains constituents that exhibit potent antitumor effects through activating immune cells. Recently, anti-inflammatory and anti-allergic properties of P. linteus extracts have also been implicated. In the present study, therefore, we separated the constituents of mycelium of P. linteus into five fractions-chloroform-soluble (CF), ethyl acetate-soluble (EA), methanol-soluble (AE), water-soluble (WA) and boiling water-soluble (BW) fractions-and examined their suppressive effects on the IgE-dependent mouse triphasic cutaneous reaction. The triphasic reaction was induced in the ear of BALB/c mice passively sensitized with anti-dinitrophenol IgE by painting with 2,4-dinitrofluorobenzene 24 h later. Ear swelling appeared triphasically with peak responses at 1 h, 24 h and 8 days after the challenge. ME, WA and BW given orally at a dose of 100 mg kg significantly inhibited the first and second phase ear swelling, and BW also inhibited the third phase response. CF only inhibited the second phase. The inhibition by BW was the most potent and almost dose-dependent at doses of 30-300 mg kg. BW also inhibited vascular permeability increase caused by passive cutaneous anaphylaxis and histamine, and ear swelling caused by tumor necrosis factor-alpha. In contrast, BW apparently potentiated the production of interleukin-4 and interferon-gamma from anti-CD3-stimulated mouse splenocytes. These results indicate that BW derived from mycelium of P. linteus contains some constituents with anti-allergic as well as immunopotentiating properties.

Kampo Medicines for Mite Antigen-Induced Allergic Dermatitis in NC/Nga Mice.

We have established an allergic dermatitis model in NC/Nga mice by repeated local exposure of mite antigen for analyzing atopic dermatitis. We examined how four Kampo medicines, Juzen-taiho-to, Hochu-ekki-to, Shofu-san and Oren-gedoku-to, on the dermatitis model to obtain basic information on their usefulness for treating atopic dermatitis. Mite antigen (Dermatophagoides farinae crude extract) solution at a concentration of 10 mg/ml was painted on the ear of NC/Nga mice after tape stripping. The procedure was repeated five times, at 7 day intervals. An apparent biphasic ear swelling was caused after the fourth and fifth antigen exposures with elevated serum IgE levels and accumulation of inflammatory cells. In the cervical lymph nodes and ear lobes, the five procedures of antigen exposure induced interleukin-4 mRNA expression but reduced interferon-gamma mRNA expression. Oral administration of all four Kampo medicines inhibited the formation of ear swelling and inflammatory cell accumulation. Juzen-taiho-to and Hochu-ekki-to apparently prevented the elevation of serum IgE level. Furthermore, the four Kampo medicines showed a tendency to prevent not only the increase in interleukin-4 mRNA expression but also the decrease in interferon-gamma mRNA expression. The present results indicate that Juzen-taiho-to, Hochu-ekki-to, Shofu-san and Oren-gedoku-to may correct the Th1/Th2 balance skewed to Th2, and this activity helps inhibit dermatitis in NC/Nga mice. The ability of the Kampo medicines to correct the Th1/Th2 balance seems to underlie their effectiveness in treating of atopic dermatitis.