Topological capture of mRNA for silencing gene expression

We describe herein topological mRNA capture using branched oligodeoxynucleotides (ODNs) with multiple reactive functional groups. These fragmented ODNs efficiently formed topological complexes on template mRNA in vitro. In cell-based experiments targeting AcGFP mRNA, the bifurcated reactive ODNs showed a much larger gene silencing effect than the corresponding natural antisense ODN.

Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids

The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.

Peptide Nucleic Acid Conjugates of Quinone Methide Precursors Alkylate Ribonucleic Acid after Activation with Light

Quinone methide precursors 2 and 3 were protected with a photoreactive 2-nitrobenzyl group and conjugated to peptide nucleic acids (PNA) using a Huisgen click reaction. After brief irradiation at 365 nm, cross-linking with complementary RNA strands started and was analyzed with an ALFexpress sequencer. When this method was used, the gel temperature had a major influence on apparent rates. Quinone methides are known to form transient as well as stable bonds with nucleotides. Although both were detected at 25 °C, analysis at 57 °C only recorded the stable types of cross-links, suggesting much slower alkylation kinetics. Linker 11 allowed us to attach quinone methides to internal positions of the PNA/RNA duplex and to capture a model of miR-20a with good efficiency.

Controlled Delivery of Extracellular ROS Based on Hematoporphyrin-Incorporated Polyurethane Film for Enhanced Proliferation of Endothelial Cells

The principle of photodynamic treatment (PDT) involves the administration of photosensitizer (PS) at diseased tissues, followed by light irradiation to produce reactive oxygen species (ROS). In cells, a moderate increase in ROS plays an important role as signaling molecule to promote cell proliferation, whereas a severe increase of ROS causes cell damage. Previous studies have shown that low levels of ROS stimulate cell growth through PS drugs-treating PDT and nonthermal plasma treatment. However, these methods have side effects which are associated with low tissue selectivity and remaining of PS residues. To overcome such shortcomings, we designed hematoporphyrin-incorporated polyurethane (PU) film induced generation of extracellular ROS with singlet oxygen and free radicals. The film can easily control ROS production rate by regulating several parameters including light dose, PS dose. Also, its use facilitates targeted delivery of ROS to the specific lesion. Our study demonstrated that extracellular ROS could induce the formation of intracellular ROS. In vascular endothelial cells, a moderated increase in intracellular ROS also stimulated cell proliferation and cell cycle progression by accurate control of optimum levels of ROS with hematoporphyrin-incorporated polymer films. This modulation of cellular growth is expected to be an effective strategy for the design of next-generation PDT.

Interstrand cross-link and bioconjugate formation in RNA from a modified nucleotide

RNA oligonucleotides containing a phenyl selenide derivative of 5-methyluridine were chemically synthesized by solid-phase synthesis. The phenyl selenide is rapidly converted to an electrophilic, allylic phenyl seleneate under mild oxidative conditions. The phenyl seleneate yields interstrand cross-links when part of a duplex and is useful for synthesizing oligonucleotide conjugates. Formation of the latter is illustrated by reaction of an oligonucleotide containing the phenyl selenide with amino acids in the presence of mild oxidant. The products formed are analogous to those observed in tRNA that are believed to be formed posttranslationally via a biosynthetic intermediate that is chemically homologous to the phenyl seleneate.