Publications by authors named "Yusuke Nakatsuji"

We applied heteroduplex oligonucleotide (HDO) technology, which uses an oligonucleotide hybridized with a complementary strand, to efficiently deliver locked nucleic acid (LNA)-based splice-switching oligonucleotides (SSOs) to the nucleus. Using an assay involving cationic lipids, we revealed that HDO technology increased the exon-skipping activity of LNA-based SSOs. To assess the effect of heteroduplex SSOs (HDSSOs) on exon-skipping activity, we designed and evaluated various HDSSOs using a series of complementary oligonucleotides with different sugar chemistries (DNA, RNA, and LNA), linkages (phosphodiester; PO and phosphorothioate; PS linkages), and lengths.

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Our group previously developed a series of bridged nucleic acids (BNAs), including locked nucleic acids (LNAs), amido-bridged nucleic acids (AmNAs), and guanidine-bridged nucleic acids (GuNAs), to impart specific characteristics to oligonucleotides such as high-affinity binding and enhanced enzymatic resistance. In this study, we designed a series of LNA-, AmNA-, and GuNA-modified splice-switching oligonucleotides (SSOs) with different lengths and content modifications. We measured the melting temperature () of each designed SSO to investigate its binding affinity for RNA strands.

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1,3-Diaza-2-oxophenoxazine ("phenoxazine"), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π-π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex-forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9-triaza-2-oxophenoxazine (9-TAP), could improve triplex-forming abilities.

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PAGE and UV melting analysis revealed that longer LNA-based splice-switching oligonucleotides (SSOs) formed secondary structures by themselves, reducing their effective concentration. To avoid such secondary structure formation, we introduced 7-deaza-2'-deoxyguanosine or 2'-deoxyinosine into the SSOs. These modified SSOs, with fewer secondary structures, showed higher exon skipping activities.

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Metal-mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three- or more-metal-coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex.

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The 2'-O,4'-C-methylene-bridged or locked nucleic acid (2',4'-BNA/LNA), with an N-type sugar conformation, effectively improves duplex-forming ability. 2',4'-BNA/LNA is widely used to improve gene knockdown in nucleic acid based therapies and is used in gene diagnosis. Metal-mediated base pairs (MMBPs), such as thymine (T)-Hg -T and cytosine (C)-Ag -C have been developed and used as attractive tools in DNA nanotechnology studies.

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Oligonucleotide-mediated splicing modulation is a promising therapeutic approach for Duchenne muscular dystrophy (DMD). Recently, eteplirsen, a phosphorodiamidate morpholino oligomer-based splice-switching oligonucleotide (SSO) targeting DMD exon 51, was approved by the U.S.

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Batch experiments were conducted to examine mechanisms for removal of p-nitrophenol (PNP) from aqueous solution using zero-valent iron (ZVI). Removal of PNP using ZVI was mainly attributed to three mechanisms: degradation, precipitation and adsorption. A complete removal of 30 mg L(-1) PNP with ZVI dosage of 1000 mg L(-1) achieved within 30 min at pH 3.

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