phosphoramidite and azobenzene

This article presents the detailed synthesis and characterization protocols for an ortho-functionalized tetrafluorinated azobenzene containing siRNA, which has photoswitchable properties. To design this tetrafluorinated azobenzene scaffold, several synthetic steps are performed to generate a symmetrical tetrafluorinated azobenzene diol. This diol is treated with dimethoxytrityl chloride (DMT-Cl) to protect one of the alcohols. Next, the DMT-protected tetrafluorinated monoalcohol is phosphitylated to afford the DMT-phosphoramidite building block used for solid-phase synthesis. This paper also contains the detailed biophysical characterization, biological testing, and photo-switching protocols of an ortho-functionalized fluorinated azobenzene containing siRNA (F-siRNA), which has photoswitchable properties that can be controlled with visible light. First, the F-siRNA was characterized by annealing the sense and antisense strands together and then measuring the circular dichroism (CD) profile and melting temperature (T

Topics: Azo Compounds; Gene Silencing; RNA, Small Interfering

This paper contains the detailed synthesis and characterization protocols of ortho-functionalized tetrachlorinated azobenzene-containing small interfering RNAs (siRNAs), which have photoswitchable properties effectively controlled with visible light. To design this tetrachlorinated azobenzene scaffold, a late-stage chlorination with N-chlorosuccinimide and palladium is used. Next, a single hydroxyl group from the tetrachlorinated azobenzene is protected with a 4,4'-dimethoxytrityl (DMT) group, followed by phosphitylation with 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite. These phosphoramidite monomers are compatible with automated solid-phase oligonucleotide synthesis to generate tetrachlorinated azobenzene-containing oligonucleotides. This paper also contains the detailed biophysical characterization, biological testing, and photo-switching protocols of ortho-functionalized chlorinated azobenzene-containing siRNAs (Cl-siRNAzos), which have photoswitchable properties that can be controlled with visible light. First, the Cl-siRNAzos are characterized by annealing the sense and antisense strands together and then measuring the circular dichroism (CD) profile, and the melting temperatures (T

Topics: Azo Compounds; Gene Silencing; Oligonucleotides; Organophosphorus Compounds; RNA, Small Interfering

This article contains the detailed synthesis and characterization protocols of azobenzene containing siRNAs, which have photoswitchable properties effectively controlled with light. First, the azobenzene scaffolds are synthesized via reduction of nitrophenyl alcohols in the presence of zinc. Next, the hydroxyl group of azobenzene derivatives are protected with a dimethoxytrityl (DMT) group, followed by phosphitylation with 2-cyanoethyl-N,N-diisopropylchlorophosphoramidite. These phosphoramidite monomers are compatible with automated solid-phase oligonucleotide synthesis to generate azobenzene-containing oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 4,4'-bis(hydroxymethyl)-azobenzene phosphoramidite Basic Protocol 2: Synthesis of 4,4'-bis(hydroxyethyl)-azobenzene phosphoramidite Basic Protocol 3: Synthesis, purification and characterization of oligonucleotides containing azobenzene derivatives.

Topics: Azo Compounds; Oligonucleotides; Organophosphorus Compounds; Spectrum Analysis

Plasmonic near-field coupling can induce the enhancement of photoresponsive processes by metal nanoparticles. Advances in nanostructured metal synthesis and theoretical modeling have kept surface plasmons in the spotlight. Previous efforts have resulted in significant intensity enhancement of organic dyes and quantum dots and increased absorption efficiency of optical materials used in solar cells. Here, we report that silver nanostructures can enhance the conversion efficiency of an interesting type of photosensitive DNA nanomotor through coupling with incorporated azobenzene moieties. Spectral overlap between the azobenzene absorption band and plasmonic resonances of silver nanowires increases light absorption of photon-sensitive DNA motor molecules, leading to 85% close-open conversion efficiency. The experimental results are consistent with our theoretical calculations of the electric field distribution. This enhanced conversion of DNA nanomotors holds promise for the development of new types of molecular nanodevices for light manipulative processes and solar energy harvesting.

Topics: Azo Compounds; Base Sequence; DNA; Metal Nanoparticles; Microscopy, Electron, Transmission; Models, Chemical; Molecular Structure; Nanostructures; Nanotechnology; Nanowires; Organic Chemicals; Organophosphorus Compounds; Silver; Spectrometry, Fluorescence