Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

Transcription is tightly regulated by epigenetic modifications that control the expression of specific genes. One such modification is 5-methylcytosine (5mC) that is formed by cytosine methylation via DNA methyltransferases and functions as a transcriptional silencer of gene promoters. Dynamically regulated subsequent modifications by ten-eleven translocation (TET) enzymes catalyze the sequential oxidation of 5mC for generating 5-hydroxymethylcytosine, 5-formylcytosine (5fC), and 5-carboxylcytosine. Recently, these oxidized cytosine derivatives were indicated as not merely intermediates in the demethylation process; however, each derivative plays a unique biologically relevant role. A photo-crosslinkable oligonucleotide probe for detecting these cytosine modifications could support the spatiotemporal functional analysis of cytosine derivatives via a light stimulus. Herein, we designed novel photoreactive nucleosides by conjugating a psoralen (Ps) derivative, trioxsalen, to the C2' position of guanosine (GPs and GPs2) and developed photo-crosslinkable oligonucleotides (GPs-Oligo and GPs2-Oligo). In particular, GPs-Oligo demonstrated an intriguing and unique ability of photo-crosslinking with 5fC. GPs-Oligo was employed to detect 5fC using a DNA chip glass plate, which demonstrated the potential of GPs-Oligo for future investigation of the function of 5fC inside cells.

DOI： 10.1021/jacs.5c11463

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Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

A triplex-forming oligonucleotide (TFO) can form a sequence-specific triple helix via Hoogsteen hydrogen bonding to polypurine tracts within a major groove side of a DNA duplex. Triplex formation can induce a double-strand break, and this phenomenon at the amplified gene loci can selectively induce the cell death of cancer cells with specific gene amplification. However, the relationship between the binding affinity of TFO for target gene loci and the cell death response remains unclear. In this study, we aimed to develop DNA intercalator-conjugated TFOs with higher affinity for the human epidermal growth factor receptor type2 (HER2) gene, which is often amplified in breast cancer cells, than the unmodified TFO. The binding affinity of the TFOs for the target DNA duplex was analyzed using nondenaturing polyacrylamide gel electrophoresis, and one of the DNA intercalator-conjugated TFOs showed a higher binding affinity for the target duplex than the unmodified TFO. We also evaluated the cell death responses induced by these TFOs using the WST-8 assay, suggesting that the higher binding affinity of the TFO for amplified gene loci can lead to a stronger cell death response of cancer cells with specific gene amplification.

DOI： 10.1002/cmdc.202500325

PubMed

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) have been employed for the photodynamic regulation of gene expression by the photo-cross-linking of psoralen with the target DNA. However, stable triplex formation requires a consecutive purine base sequence in one strand of the target DNA duplexes. The pyrimidine-base interruption in the consecutive purine base sequence drastically decreases the thermodynamic stability of the corresponding triplex, which hampers the TFO application. Here, we propose a design of the Ps-TFO for stable triplex formation with target DNA sequences containing pyrimidine-base interruptions under physiological conditions. This Ps-TFO, named 1'(one)-psoralen-conjugated triplex-forming oligonucleotide (OPTO), incorporates a synthesized nucleoside mimic 1'-psoralen-conjugated deoxyribose to increase the thermodynamic stability of the corresponding triplex by the intercalation of psoralen. The triplex-forming abilities of the OPTO were successfully demonstrated in combination with LNA and 5-methylcytosine, indicating that the use of OPTO will expand the range of the target sequences of TFO for photodynamic gene regulation.

DOI： 10.1038/s42004-025-01416-2

PubMed

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Georg Thieme Verlag KG  

Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) have been used to induce DNA mutations or suppress gene expression via the formation of crosslinked products with DNA in a sequence-specific manner. Psoralen can crosslink with DNA at its furan ring and/or pyrone ring side, yielding either a monoadduct or diadduct (interstrand crosslinking) product. The differences in the crosslinked structures of Ps-TFOs with the target DNAs are closely related to the changes in the biological outcomes induced by the Ps-TFOs. However, only few reports have discussed the photo-crosslinking properties of Ps-TFOs. The photo-crosslinking properties of Ps-TFOs with structurally diverse psoralen derivatives remain elusive. Herein, we report the modular synthesis of methyl-substituted novel psoralen N-hydroxysuccinimide (NHS) esters. Using these esters, the effect of the methyl substituent of psoralen on the photo-crosslinking of the corresponding Ps-TFOs was examined. Results revealed that the amount of the diadduct product was significantly reduced in the presence of the methyl substituents at C-3 and C-4 position while maintaining the total amount of photo-crosslinking product. This work demonstrates the possibility to control the crosslinked product of Ps-TFOs by introducing methyl groups into psoralen—this ability to manipulate the product is an important factor in the biological applications of Ps-TFOs.

DOI： 10.1055/a-2229-7441

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Language：English   Publishing type：Research paper (scientific journal)  

Exosomes are a type of extracellular vesicles that contain diverse molecules and are present in our body fluids. They play a crucial role in transporting materials and transmitting signals between cells. Currently, there have been numerous reports on the use of exosomes in drug delivery systems (DDS). However, most existing methods for utilizing exosomes in DDS require the isolation and purification of exosomes, which raises concerns about yield and potential damage to the exosomes. Recently, we have developed a novel DDS called "ExomiR-Tracker" that harnesses exosomes without the need for isolation and purification. This system aims to deliver nucleic acid drugs effectively. ExomiR-Tracker consists of an anti-exosome antibody equipped with nona-D-arginines (9 mer) and nucleic acid drugs which have complementary sequence of target microRNA (anti-miR). In this study, we modified ExomiR-Tracker by incorporating branched nona-D-arginines (9 + 9 mer) molecules (referred to as Branch ExomiR-Tracker) and evaluated its efficacy in lung adenocarcinoma cells (A549 cells). The improved complex formation ability and enhanced cellular uptake of anti-miR, demonstrated by our findings, highlight the advantages of incorporating branched oligoarginine peptides into the ExomiR-Tracker platform. These results represent significant progress in revealing the effectiveness of Branch ExomiR-Tracker against adhesive cancer cells, which has not been shown to be effective with the conventional Linear ExomiR-Tracker.

DOI： 10.1248/cpb.c23-00430

PubMed

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

J-GLOBAL

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Authorship：Lead author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

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Authorship：Lead author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (scientific journal)  

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Event date： 2025.9

Language：Japanese  

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Event date： 2025.3

Language：Japanese   Presentation type：Oral presentation (invited, special)  

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Event date： 2024.9

Language：English   Presentation type：Poster presentation  

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Event date： 2024.3

Language：Japanese   Presentation type：Oral presentation (general)  

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Event date： 2024.3

Language：Japanese   Presentation type：Oral presentation (general)  

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Applicant：長崎大学

Application no：特願2022-206081  Date applied：2022.12

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Type：Competition, symposium, etc. 

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Type：Academic society, research group, etc. 

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Type：Competition, symposium, etc. 

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Type：Academic society, research group, etc. 

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Type：Academic society, research group, etc. 

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