Caged siRNAs for Spatiotemporal Control of Gene Silencing

Photolabile Protecting Groups Based on the Excited State Meta Effect: Development and Application

This review focuses on utilization of the excited state meta effect (ESME) in the development of photolabile protecting groups (PPGs). Structurally simple ESME-based PPGs for release of various functional groups (such as carbonyl, hydroxyl, carboxyl, amino, and thiol groups) are discussed. Examples that demonstrate the appealing advantages of these new PPGs are provided, including their efficient release of "poor" leaving groups such as hydroxyl or amino group directly instead of in their respective carbonate or carbamate form. Applications of these PPGs in synthesis, release of biologically important molecules, materials science, and biomedical engineering are also described.

Targeting drug delivery with light: A highly focused approach

Light is a uniquely powerful tool for controlling molecular events in biology. No other external input (e.g., heat, ultrasound, magnetic field) can be so tightly focused or so highly regulated as a clinical laser. Drug delivery vehicles that can be photonically activated have been developed across many platforms, from the simplest "caging" of therapeutics in a prodrug form, to more complex micelles and circulating liposomes that improve drug uptake and efficacy, to large-scale hydrogel platforms that can be used to protect and deliver macromolecular agents including full-length proteins. In this Review, we discuss recent innovations in photosensitive drug delivery and highlight future opportunities to engineer and exploit such light-responsive technologies in the clinical setting.

Photoregulation of Gene Expression with Ligand-Modified Caged siRNAs through Host/Guest Interaction

Small interfering RNA (siRNA) can effectively silence target genes through Argonate 2 (Ago2)-induced RNA interference (RNAi). It is very important to control siRNA activity in both spatial and temporal modes. Among different masking strategies, photocaging can be used to regulate gene expression through light irradiation with spatiotemporal and dose-dependent resolution. Many different caging strategies and caging groups have been reported for light-activated siRNA gene silencing. Herein, we describe a novel caging strategy that increases the blocking effect of RISC complex formation/process through host/guest (including ligand/receptor) interactions, thereby enhancing the inhibition of caged siRNA activity until light activation. This strategy can be used as a general approach to design caged siRNAs for the photomodulation of gene silencing of exogenous and endogenous genes.

AT-CuAAC Synthesis of Mechanically Interlocked Oligonucleotides

We present a simple strategy for the synthesis of main chain oligonucleotide rotaxanes with precise control over the position of the macrocycle. The novel DNA-based rotaxanes were analyzed to assess the effect of the mechanical bond on their properties.

Intracellular build-up RNAi with single-strand circular RNAs as siRNA precursors

We herein report a new approach for RNA interference, so-called “build-up RNAi” approach, where single-strand circular RNAs with a photocleavable unit or disulfide moiety were used as siRNA precursors.

Light-triggered release of photocaged therapeutics - Where are we now?

The current available therapeutics face several challenges such as the development of ideal drug delivery systems towards the goal of personalized treatments for patients benefit. The application of light as an exogenous activation mechanism has shown promising outcomes, owning to the spatiotemporal confinement of the treatment in the vicinity of the diseased tissue, which offers many intriguing possibilities. Engineering therapeutics with light responsive moieties have been explored to enhance the bioavailability, and drug efficacy either in vitro or in vivo. The tailor-made character turns the so-called photocaged compounds highly desirable to reduce the side effects of drugs and, therefore, have received wide research attention. Herein, we seek to highlight the potential of photocaged compounds to obtain a clear understanding of the mechanisms behind its use in therapeutic delivery. A deep overview on the progress achieved in the design, fabrication as well as current and possible future applications in therapeutics of photocaged compounds is provided, so that novel formulations for biomedical field can be designed.

1-[3-(Diethylamino)phenyl]ethyl (DEAPE): A Photolabile Protecting Group for Hydroxyl and Carboxyl Groups

Herein we demonstrate that the photolabile protecting group (PPG), the 1-[3-(diethylamino)-phenyl]ethyl (DEAPE) group, has dramatically different photochemical properties from the parent 3-(diethylamino)benzyl (DEABn) PPG. The new PPG, derived from DEABn by adding a methyl group to the benzylic carbon, has similar reactivity as DEABn in releasing alcohol in MeCN/water; however, it is more efficient than DEABn in releasing carboxylic acid. In particular, it can release carboxylic acid efficiently in aprotic solvents and the PPG itself converts to 3-diethylaminostyrene. Photochemical removal of DEAPE can also be conveniently carried out with sunlight. The results in this work suggest that there probably exist multiple reaction pathways in cleaving the benzylic C-O bond and they can be affected by the benzylic substitution and the reaction conditions.

Efficient Synthesis of Light-Triggered Circular Antisense Oligonucleotides Targeting Cellular Protein Expression

Light-activated ("caged") antisense oligonucleotides are powerful molecules for regulating gene expression at submicron spatial resolution through the focal modulation of endogenous cellular processes. Cyclized caged oligos are particularly promising structures because of their inherent stability and similarity to naturally occurring circular DNA and RNA molecules. Here, we introduce an efficient route for cyclizing an antisense oligodeoxynucleotide incorporating a photocleavable linker. Oligo cyclization was achieved for several sequences in nearly quantitative yields through intramolecular copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). Caging stability and light activation were characterized by FRET efficiency, denaturing gel assay, and melting temperature measurements. Finally, a cyclized caged oligo was designed to target gfap, and it gave a tenfold reduction in glial fibrillary acidic protein upon photoactivation in astrocytes.

RNA Cloaking by Reversible Acylation

We describe a selective and mild chemical approach for controlling RNA hybridization, folding, and enzyme interactions. Reaction of RNAs in aqueous buffer with an azide-substituted acylating agent (100-200 mm) yields several 2'-OH acylations per RNA strand in as little as 10 min. This poly-acylated ("cloaked") RNA is strongly blocked from hybridization with complementary nucleic acids, from cleavage by RNA-processing enzymes, and from folding into active aptamer structures. Importantly, treatment with a water-soluble phosphine triggers a Staudinger reduction of the azide groups, resulting in spontaneous loss of acyl groups ("uncloaking"). This fully restores RNA folding and biochemical activity.

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

Oligonucleotides (ONs) have been envisaged for therapeutic applications for more than thirty years. However, their broad use requires overcoming several hurdles such as instability in biological fluids, low cell penetration, limited tissue distribution, and off-target effects. With this aim, many chemical modifications have been introduced into ONs definitively as a means of modifying and better improving their properties as gene silencing agents and some of them have been successful. Moreover, in the search for an alternative way to make efficient ON-based drugs, the general concept of prodrugs was applied to the oligonucleotide field. A prodrug is defined as a compound that undergoes transformations in vivo to yield the parent active drug under different stimuli. The interest in stimuli-responsive ONs for gene silencing functions has been notable in recent years. The ON prodrug strategies usually help to overcome limitations of natural ONs due to their low metabolic stability and poor delivery. Nevertheless, compared to permanent ON modifications, transient modifications in prodrugs offer the opportunity to regulate ON activity as a function of stimuli acting as switches. Generally, the ON prodrug is not active until it is triggered to release an unmodified ON. However, as it will be described in some examples, the opposite effect can be sought. This review examines ON modifications in response to various stimuli. These stimuli may be internal or external to the cell, chemical (glutathione), biochemical (enzymes), or physical (heat, light). For each stimulus, the discussion has been separated into sections corresponding to the site of the modification in the nucleotide: the internucleosidic phosphate, the nucleobase, the sugar or the extremities of ONs. Moreover, the review provides a current and detailed account of stimuli-responsive ONs with the main goal of gene silencing. However, for some stimuli-responsive ONs reported in this review, no application for controlling gene expression has been shown, but a certain potential in this field could be demonstrated. Additionally, other applications in different domains have been mentioned to extend the interest in such molecules.

Rapid Light-Driven Color Transition of Novel Photoresponsive Polydiacetylene Molecules

We developed new photoresponsive polydiacetylene (PR-PDA) molecules by incorporating a photocleavable moiety, 6-nitropiperonyl alcohol (NP) or 4,5-dimethoxy-2-nitrobenzyl alcohol (DMN), into a self-assembling diacetylene molecule. Inducing steric disordering of the assembled PDA molecules by the cleavage of the photoresponsive moiety under 365 nm UV irradiation results in color transition from blue to red and development of red fluorescence, allowing convenient photo patterning. Further writing and erasing of fluorescence patterns are demonstrated toward novel secure information communication and anticounterfeiting applications.

Caged circular siRNAs for photomodulation of gene expression in cells and mice

Caged siRNAs with a circular structure were successfully used for photoregulation of target genes in both cells and mice.

By means of RNA interference (RNAi), small interfering RNAs (siRNAs) play important roles in gene function study and drug development. Recently, photolabile siRNAs were developed to elucidate the process of gene silencing in terms of space, time and degree through chemical modification of siRNAs. We report herein a novel type of photolabile siRNA that was synthesized through cyclizing two ends of a single stranded RNA with a photocleavable linker. These circular siRNAs became more resistant to serum degradation. Using reporter assays of firefly/Renilla luciferase and GFP/RFP, the gene silencing activities of caged circular siRNAs for both genes were evaluated in HEK293 cells. The results indicated that the target genes were successfully photomodulated using these caged circular siRNAs that were formed by caged circular antisense guide RNAs and their linear complementary sense RNAs. Using the caged circular siRNA targeting GFP, we also successfully achieved photomodulation of GFP expression in mice. Upon further optimization, this new type of caged circular siRNA is expected to be a promising tool for studying gene therapy.

A Two-Photon-Photocleavable Linker for Triggering Light-Induced Strand Breaks in Oligonucleotides

We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal. In cell culture we were able to show the regulation of NF-κB-controlled transcription of green fluorescent protein.

Chemical synthesis of long RNAs with terminal 5'-phosphate groups

Long structured RNAs are useful biochemical and biological tools. They are usually prepared enzymatically, but this precludes their site-specific modification with functional groups for chemical biology studies. One solution is to perform solid-phase synthesis of multiple RNAs loaded with 5'-terminal phosphate groups, so that RNAs can be concatenated using template ligation reactions. However, there are currently no readily available reagents suitable for the incorporation of the phosphate group into long RNAs by solid-phase synthesis. Here we describe an easy-to-prepare phosphoramidite reagent suitable for the chemical introduction of 5'-terminal phosphate groups into long RNAs. The phosphate is protected by a dinitrobenzhydryl group that serves as an essential lipophilic group for the separation of oligonucleotide by-products. The phosphate is unmasked quantitatively by brief UV irradiation. We demonstrate the value of this reagent in the preparation of a library of long structured RNAs that are site-specifically modified with functional groups.

Phototriggered protein syntheses by using (7-diethylaminocoumarin-4-yl)methoxycarbonyl-caged aminoacyl tRNAs

The possibility of spatiotemporally photocontrolling translation holds considerable promise for studies on the biological roles of local translation in cells and tissues. Here we report caged aminoacyl-tRNAs (aa-tRNAs) synthesized using a (7-diethylaminocoumarin-4-yl)methoxycarbonyl (DEACM)-cage compound. DEACM-caged aa-tRNA does not spontaneously deacylate for at least 4 h in neutral aqueous solution, and does not bind to the elongation factor Tu. On irradiation at ∼405 nm at 125 mW cm⁻², DEACM-aa-tRNA is converted into active aa-tRNA with a half-life of 19 s. Notably, this rapid uncaging induced by visible light does not impair the translation system. Translation is photoinduced when DEACM-aa-tRNA carrying a CCCG or a CUA anticodon is uncaged in the presence of mRNAs harbouring a CGGG four-base codon or a UAG amber codon, respectively. Protein synthesis is phototriggered in several model systems, including an in vitro translation system, an agarose gel, in liposomes and in mammalian cells.

Spatiotemporal regulation of protein synthesis would advance studies into the consequences of localised protein translation in cells and tissues. Here, Ohtsuki et al. improve on an earlier caged-tRNA design to provide caged aminoacyl-tRNAs that are rapidly uncaged by visible light.

NIR-Remote Selected Activation Gene Expression in Living Cells by Upconverting Microrods

An NIR-controlled gene expression system based on upconverting rods (UCRs) is demonstrated. The UCRs can harvest the "biocompatible" NIR light and convert it into local UV light, resulting in cleavage of the photosensitive molecule (4-(hydroxymethyl)-3-nitrobenzoic acid, ONA) and on-demand release of gene carriers, thus realizing target gene expression at high spatial and temporal resolutions.

On-demand drug delivery from local depots

Stimuli-responsive polymeric depots capable of on-demand release of therapeutics promise a substantial improvement in the treatment of many local diseases. These systems have the advantage of controlling local dosing so that payload is released at a time and with a dose chosen by a physician or patient, and the dose can be varied as disease progresses or healing occurs. Macroscale drug depot can be induced to release therapeutics through the action of physical stimuli such as ultrasound, electric and magnetic fields and light as well as through the addition of pharmacological stimuli such as nucleic acids and small molecules. In this review, we highlight recent advances in the development of polymeric systems engineered for releasing therapeutic molecules through physical and pharmacological stimulation.

Construction of a Near-Infrared-Activatable Enzyme Platform To Remotely Trigger Intracellular Signal Transduction Using an Upconversion Nanoparticle

Photoactivatable (caged) bioeffectors provide a way to remotely trigger or disable biochemical pathways in living organisms at a desired time and location with a pulse of light (uncaging), but the phototoxicity of ultraviolet (UV) often limits its application. In this study, we have demonstrated the near-infrared (NIR) photoactivatable enzyme platform using protein kinase A (PKA), an important enzyme in cell biology. We successfully photoactivated PKA using NIR to phosphorylate its substrate, and this induced a downstream cellular response in living cells with high spatiotemporal resolution. In addition, this system allows NIR to selectively activate the caged enzyme immobilized on the nanoparticle surface without activating other caged proteins in the cytosol. This NIR-responsive enzyme-nanoparticle system provides an innovative approach to remote-control proteins and enzymes, which can be used by researchers who need to avoid direct UV irradiation or use UV as a secondary channel to turn on a bioeffector.

Strategies for siRNA navigation to desired cells

Whilst small interfering (si) RNAs have emerged as a promising therapeutic modality for treating a diversity of human diseases, delivery constitutes the most serious obstacle to siRNA drug development. As the most used delivery agents can enter all cell types, specificity must be built into the delivery agents or directly attached to the siRNA molecules. The use of antibodies, peptides, Peptide-Fc fusions, aptamers, and other targeting ligands has now enabled efficient gene silencing in the desired cell populations/tissues in vitro and in vivo. The present review summarizes these current innovations, which are important for the design of safe therapeutic siRNAs.

Photoregulating RNA digestion using azobenzene linked dumbbell antisense oligodeoxynucleotides

Introduction of 4,4'-bis(hydroxymethyl)-azobenzene (azo) to dumbbell hairpin oligonucleotides at the loop position was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation. Here, we designed and synthesized a series of azobenzene linked dumbbell antisense oligodeoxynucleotides (asODNs) containing two terminal hairpins that are composed of an asODN and a short inhibitory sense strand. Thermal melting studies of these azobenzene linked dumbbell asODNs indicated that efficient trans to cis photoisomerization of azobenzene moieties induced large difference in thermal stability (ΔTm = 12.1-21.3 °C). In addition, photomodulation of their RNA binding abilities and RNA digestion by RNase H was investigated. The trans-azobenzene linked asODNs with the optimized base pairs between asODN strands and inhibitory sense strands could only bind few percentage of the target RNA, while it was able to recover their binding to the target RNA and degrade it by RNase H after light irradiation. Upon optimization, it is promising to use these azobenzene linked asODNs for reversible spatial and temporal regulation of antisense activities based on both steric binding and RNA digestion by RNase H.

Synthesis of 2'-O-photocaged ribonucleoside phosphoramidites

The chemical synthesis and incorporation of the phosphoramidite derivatives of 2 '-O-photocaged ribonucleosides (A, C, G and U) with o-nitrobenzyl, α-methyl-o-nitrobenzyl or 4,5-dimethoxy-2-nitrobenzyl group into oligoribonucleotides are described. The efficiency of UV irradiated uncaging of these 2'-O-photocaged oligoribonucleotides was found in the order of α-methyl-o-nitrobenzyl < 4,5-dimethoxy-2-nitrobenzyl < 2'-O-o-nitrobenzyl.

Inhibition of murine bladder cancer cell growth in vitro by photocontrollable siRNA based on upconversion fluorescent nanoparticles

This study provides a unique approach to activate caged small interfering RNAs (siRNAs) using indirect UV light emitted by the near-infrared (NIR)-to-UV upconversion process to achieve high spatial and temporal gene interference patterns. siRNA molecules against the anti-apoptotic gene survivin was caged by light-sensitive molecules (4,5-dimethoxy-2-nitroacetophenone, DMNPE), which rendered them temporarily non-functional. NIR-to-UV NaYF4:Yb,Tm upconversion nanoparticles (UCPs) served as delivery vehicles and activators of the caged siRNA molecules in murine bladder cancer cells (MB49 cell line). Upconverted UV light at 355 nm was emitted from the NIR-irradiated UCPs, which well coincided with the wavelength needed to uncage DMNPE. Consequently, UV light acted as a switch to uncage the delivered siRNA molecule, thereby rendering fully functional for exerting its therapeutic effect in the bladder cancer cells. To achieve the highest RNA interference efficiency, conditions such as time after cellular uptake, excitation time, UCPs concentration and laser power were optimized. Results showed that 200 µg/mL nanoparticle concentration combined with 12 h incubation with MB49 cells and excitation with NIR laser at 100 mW power for 15 min provided the ideal interference efficiency and strongest induction of MB49 cell death. Our findings demonstrate the potential biological application of UCPs in treating bladder cancer by a novel therapeutic approach.

Hypoxic X-irradiation as an external stimulus for conformational change of oligodeoxynucleotides that possess disulfide bond and regulation of DNAzyme function

We achieved a conformational change of oligodeoxynucleotides and the regulation of DNAzyme function by means of a radiolytic strand exchange reaction of disulfide bond. We designed a system in which the DNAzyme function of RNA cleavage was suppressed by the hybridization of an inhibitor strand that possessed disulfide bond with an active DNAzyme. Hypoxic X-irradiation led to the recovery of RNA cleavage because the strand exchange reaction at the disulfide bond in inhibitor strand resulted in a release of inhibitor strand. This strategy may be applicable to gene regulation by hypoxic X-irradiation.

An intracellular buildup reaction of active siRNA species from short RNA fragments

Here we report a new strategy for the buildup reaction of active siRNA species from short RNA fragments in living cells using a chemical ligation reaction. This strategy could decrease undesired immune responses and provide more latitude for RNAi technology in the design and concentration of introduced RNA compared to traditional siRNA methods.

Polymerase synthesis of photocaged DNA resistant against cleavage by restriction endonucleases

5-[(2-Nitrobenzyl)oxymethyl]-2'-deoxyuridine 5'-O-triphosphate was used for polymerase (primer extension or PCR) synthesis of photocaged DNA that is resistant to the cleavage by restriction endonucleases. Photodeprotection of the caged DNA released 5-hydroxymethyluracil-modified nucleic acids, which were fully recognized and cleaved by restriction enzymes.

Synthesis and incorporation of the phosphoramidite derivative of 2'-O-photocaged 3'-s-thioguanosine into oligoribonucleotides: substrate for probing the mechanism of RNA catalysis

Oligoribonucleotides containing 3'-S-phosphorothiolate linkages possess properties that can reveal deep mechanistic insights into ribozyme-catalyzed reactions. "Photocaged" 3'-S- RNAs could provide a strategy to stall reactions at the chemical stage and release them after assembly steps have occurred. Toward this end, we describe here an approach for the synthesis of 2'-O-(o-nitrobenzyl)-3'-thioguanosine phosphoramidite starting from N(2)-isobutyrylguanosine in nine steps with 10.2% overall yield. Oligonucleotides containing the 2'-O-(o-nitrobenzyl)-3'-S-guanosine nucleotide were then constructed, characterized, and used in a nuclear pre-mRNA splicing reaction.

Cellular delivery and photochemical activation of antisense agents through a nucleobase caging strategy

Antisense oligonucleotides are powerful tools to regulate gene expression in cells and model organisms. However, a transfection or microinjection is typically needed for efficient delivery of the antisense agent. We report the conjugation of multiple HIV TAT peptides to a hairpin-protected antisense agent through a light-cleavable nucleobase caging group. This conjugation allows for the facile delivery of the antisense agent without a transfection reagent, and photochemical activation offers precise control over gene expression. The developed approach is highly modular, as demonstrated by the conjugation of folic acid to the caged antisense agent. This enabled targeted cell delivery through cell-surface folate receptors followed by photochemical triggering of antisense activity. Importantly, the presented strategy delivers native oligonucleotides after light-activation, devoid of any delivery functionalities or modifications that could otherwise impair their antisense activity.

Caged nucleotides/nucleosides and their photochemical biology

Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.

Multicompartment micelle-structured peptide nanoparticles: a new biocompatible gene- and drug-delivery tool

Self-assembled, biodegradable materials that embed fragile, soluble, or insoluble compounds of therapeutic interest have potential use as drug delivery systems. The bead-forming peptide Ac-X3-gT can embed hydrophobic and hydrophilic payloads. Loaded peptide beads were internalized by human acute monocytic leukemia cell line (THP-1) macrophages, THP-1 monocytes, and hepatocellular carcinoma cells (Huh7). Furthermore, paclitaxel and doxorubicin coencapsulated in the peptide beads were delivered to THP-1 monocytes, causing a decrease in cell viability due to the activity of the anticancer drugs. In addition to the bead-forming peptide Ac-X3-gT, the use of a positively charged peptide analogue increased the RNA/DNA embedding efficiency to 99% by charge compensation and micellar complexation. Internalization of the resulting gene delivery systems by Huh7 cells led to specific gene silencing either by embedded small interfering RNA or by plasmid-encoding small hairpin RNA delivered in cells. The new class of purely peptidic material caused no measurable toxicity during in vitro experiments, thereby indicating potential use as a drug delivery system for multidrug delivery and gene therapy.

Silver nanoscale antisense drug delivery system for photoactivated gene silencing

The unique photophysical properties of noble metal nanoparticles contribute to their potential as photoactivated drug delivery vectors. Here we demonstrate the synthesis and characterization of 60-80 nm silver nanoparticles (SNPs) decorated with thiol-terminated photolabile DNA oligonucleotides. In vitro assays and fluorescent confocal microscopy of treated cell cultures show efficient UV-wavelength photoactivation of surface-tethered caged ISIS2302 antisense oligonucleotides possessing internal photocleavable linkers. As a demonstration of the advantages of these novel nanocarriers, we investigate properties including: enhanced stability to nucleases, increased hybridization activity upon photorelease, and efficient cellular uptake as compared to commercial transfection vectors. Their potential as multicomponent delivery agents for oligonucleotide therapeutics is shown through regulation of ICAM-1 (Intracellular Adhesion Molecule-1) silencing. Our results suggest a means to achieve light-triggered, spatiotemporally controlled gene silencing via nontoxic silver nanocarriers, which hold promise as tailorable platforms for nanomedicine, gene expression studies, and genetic therapies.

Design, synthesis, and photochemistry of modular caging groups for photoreleasable nucleotides

A modular approach to preparing caged nucleotides having additional properties has been achieved. The modular caging agent includes three components: an amine reactive NHS ester moiety, a photoactive Bhc group, and tosylhydrazone as a precursor of the diazomethyl group. Various amines including biotin and an Arg-Gly-Asp (RGD) peptide were introduced into the key intermediate via amide linkage. The Bio-Bhc-diazo thus synthesized enables the preparation of a photoreleasable siRNA with additional properties.

Caged circular antisense oligonucleotides for photomodulation of RNA digestion and gene expression in cells

We synthesized three 20mer caged circular antisense oligodeoxynucleotides (R20, R20B2 and R20B4) with a photocleavable linker and an amide bond linker between two 10mer oligodeoxynucleotides. With these caged circular antisense oligodeoxynucleotides, RNA-binding affinity and its digestion by ribonuclease H were readily photomodulated. RNA cleavage rates were upregulated ∼43-, 25- and 15-fold for R20, R20B2 and R20B4, respectively, upon light activation in vitro. R20B2 and R20B4 with 2- or 4-nt gaps in the target RNA lost their ability to bind the target RNA even though a small amount of RNA digestion was still observed. The loss of binding ability indicated promising gene photoregulation through a non-enzymatic strategy. To test this strategy, three caged circular antisense oligonucleotides (PS1, PS2 and PS3) with 2′-OMe RNA and phosphorothioate modifications were synthesized to target GFP expression. Upon light activation, photomodulation of target hybridization and GFP expression in cells was successfully achieved with PS1, PS2 and PS3. These caged circular antisense oligonucleotides show promising applications of photomodulating gene expression through both ribonuclease H and non-enzyme involved antisense strategies.

Manipulation of gene expression in zebrafish using caged circular morpholino oligomers

Morpholino oligomers (MOs) have been widely used to knock down specific genes in zebrafish, but their constitutive activities limit their experimental applications for studying a gene with multiple functions or within a gene network. We report herein a new design and synthesis of caged circular MOs (caged cMOs) with two ends linked by a photocleavable moiety. These caged cMOs were successfully used to photomodulate β-catenin-2 and no tail expression in zebrafish embryos.

Light-controlled tools

Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems--from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.