Synthesis of scpBNA‑^mC, -A, and -G Monomers and Evaluation of the Binding Affinities of scpBNA-Modified Oligonucleotides toward Complementary ssRNA and ssDNA

We previously reported the synthesis and evaluation of 2′-<i>O</i>,4′-<i>C</i>-spirocyclopropylene-bridged nucleic acid (scpBNA) bearing a thymine (T) nucleobase. Oligonucleotides (ONs) modified with scpBNA-T exhibited strong binding affinity to complementary single-stranded RNA (ssRNA) and high enzymatic stability. These biophysical properties suggest that scpBNAs are well suited for use in antisense strategies. Herein, we describe the synthesis of scpBNA monomers bearing 5-methylcytosine (^mC), adenine (A), and guanine (G) nucleobases for use in a variety of sequences. The prepared scpBNA monomers were incorporated into ONs at various positions. The scpBNA-modified ONs exhibited excellent duplex-forming ability with the complementary ssRNA comparable to ONs modified with 2′-<i>O</i>,4′-<i>C</i>-methylene-bridged nucleic acid (2′,4′-BNA/LNA). Moreover, ON modified with scpBNA-^mC, -A, and -G showed higher enzymatic stability than the corresponding 2′,4′-BNA/LNA-modified ON. These results demonstrated a promising role for the incorporation of scpBNA monomers into therapeutic antisense ONs

Synthesis and Properties of Nucleobase-Sugar Dual Modified Nucleic Acids: 2<b>′</b>‑OMe-RNA and scpBNA Bearing a 5‑Hydroxycytosine Nucleobase

Naturally occurring 5-hydroxycytosine (5‑OHCyt), which is associated with DNA damage, was recently found to reduce the hepatotoxicity of antisense oligonucleotides (ASOs) without compromising its antisense activity when used as a replacement for cytosine (Cyt). Additionally, sugar-modified nucleic acids, such as 2′-O-methylribonucleic acid (2′-OMe-RNA) and 2′-O,4′-C-spirocyclopropylene-bridged nucleic acid (scpBNA), have emerged as useful antisense materials. Herein, we aimed to combine these two advantages by designing dual modified nucleic acids 2′-OMe-RNA-5‑OHCyt and scpBNA-5‑OHCyt bearing the 5‑OHCyt nucleobase to develop efficient and safe ASOs. We describe the synthesis of 2′-OMe-RNA-5‑OHCyt and scpBNA-5‑OHCyt phosphoramidites and their incorporation into oligonucleotides (ONs). The duplex-forming ability and base discrimination properties of 2′-OMe-RNA-5‑OHCyt- and scpBNA-5‑OHCyt-modified ONs were similar to those of 2′-OMe-RNA-Cyt- and scpBNA-mCyt-modified ONs, respectively. We also synthesized two 2′-OMe-RNA-5‑OHCyt-modified ASOs, and one of the two was found to exhibit reduced hepatotoxicity while retaining target mRNA knockdown activity in in vivo experiments

Design and Concise Synthesis of a Novel Type of Green Fluorescent Protein Chromophore Analogue

A small molecular model compound for the green fluorescent protein chromophore was readily synthesized by a novel condensation reaction of (thio)imidate with imino-ester via an aziridine intermediate. This compound showed fluorescence in the solid and frozen solution states but not in the solution state. Its fluorescent property was successfully applied in the detection of dsDNA

Design and Concise Synthesis of a Novel Type of Green Fluorescent Protein Chromophore Analogue

A small molecular model compound for the green fluorescent protein chromophore was readily synthesized by a novel condensation reaction of (thio)imidate with imino-ester via an aziridine intermediate. This compound showed fluorescence in the solid and frozen solution states but not in the solution state. Its fluorescent property was successfully applied in the detection of dsDNA

Inhibitors for Bacterial Cell-Wall Recycling

Gram-negative bacteria have evolved an elaborate process for the recycling of their cell wall, which is initiated in the periplasmic space by the action of lytic transglycosylases. The product of this reaction, β-d-<i>N-</i>acetylglucosamine-(1→4)-1,6-anhydro-β-d-<i>N-</i>acetylmuramyl-l-Ala-γ-d-Glu-<i>meso</i>-DAP-d-Ala-d-Ala (compound <b>1</b>), is internalized to begin the recycling events within the cytoplasm. The first step in the cytoplasmic recycling is catalyzed by the NagZ glycosylase, which cleaves in a hydrolytic reaction the <i>N</i>-acetylglucosamine glycosidic bond of metabolite <b>1</b>. The reactions catalyzed by both the lytic glycosylases and NagZ are believed to involve oxocarbenium transition species. We describe herein the synthesis and evaluation of four iminosaccharides as possible mimetics of the oxocarbenium species, and we disclose one as a potent (compound <b>3</b>, <i>K</i>_i = 300 ± 15 nM) competitive inhibitor of NagZ