Enhanced Light-Activated RNA Interference Using Phosphorothioate-Based dsRNA Precursors of siRNA

Copper-mediated siRNA activation for conditional control of gene expression

Copper plays a crucial role in maintaining biological redox balance in living organisms, with elevated levels observed in cancer cells. Short interfering RNAs (siRNAs) are effective in gene silencing and find applications as both research tools and therapeutic agents. A method to regulate RNA interference using copper is especially advantageous for cancer-specific therapy. We present a chemical approach of selective siRNA activation triggered by intracellular copper ions. We designed and synthesized nucleotides containing copper-responsive moieties, which were incorporated into siRNAs. These copper-responsive siRNAs effectively silenced the target cyclin B1 mRNA in living cells. This pioneering study introduces a novel method for conditionally controlling gene silencing using biologically relevant metal ions in human cells, thereby expanding the repertoire of chemical knockdown tools.

Translational control of gene function through optically regulated nucleic acids

Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.

Feasibility of cRGD conjugation at 5'-antisense strand of siRNA by phosphodiester linkage extension

Small interfering RNAs (siRNAs) are widely studied for their highly specific gene silencing activity. However, obstacles remain to the clinical application of siRNAs. Attaching conjugates to siRNAs can improve their stability and broaden their application, and most functional conjugates of siRNAs locate at the 3'-terminus of the sense or antisense strand. In this work, we found that conjugating a group at the 5'-terminus of the antisense strand via phosphodiester was practicable, especially when the group was a flexible moiety such as an alkyl linker. When conjugating a bulky ligand, such as cRGD, the length of the 5'-phosphodiester linker between the ligand and the 5'-terminus of the antisense strand was the key in terms of RNA interference (RNAi). With a relative longer linker, the conjugates showed potency similar to siRNA. A highly efficient transfection system composed of a neutral cytidinyl lipid (DNCA) and a gemini-like cationic lipid (CLD) was employed to deliver siRNAs or their conjugates. The cRGD conjugates showed superior targeting delivery and antitumor efficacy in vivo and also selective cellular uptake in vitro. This unity of encapsulation and conjugation strategy may provide potential strategies for siRNA-based gene therapy.

Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation

Previous work has shown that thiophosphate, a phosphate analogue, leads to a global shift in the distribution of cellular proteins in a variety of organisms. Thiophosphate, when added to culture media, gets incorporated into the nucleic acids of cells resulting in nuclease-resistant phosphorothioate linkages. Using Escherichia coli, as a model organism, it was found that the global changes in protein expression induced with thiophosphate could be accounted for by significant changes in the absolute transcription levels of more than 1500 genes detected via RNA seq analysis. In fact, 58% of transcripts detected in RNA seq studies using total RNA were increased an average of 44 × fold while the remaining 42% were decreased an average of 20 × fold in thiophosphate-treated cells. Furthermore, microarray results showed no correlation between the transcriptional changes observed and the known stability of the corresponding mRNAs measured. Overall, the total amount of non-ribosomal RNA accumulated in TP-treated cells was increased relative to rRNA ~ 4 × fold (1.5-6 ×). The results further indicated that metabolic changes may play a role in inducing the transcriptional profiles observed with thiophosphate. Indeed, pathway analysis of transcripts showed an increase in routes for phosphoribosyl pyrophosphate (PRPP) synthesis and related derivatives, presumably due to a reduction in RNA turnover. These results raise the possibility that the energy savings with reduced RNA turnover could lead to an increased energy charge in the cell that induces transcriptional changes leading to an increase in biosynthetic processes.

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.

Photomodulating Gene Expression by Using Caged siRNAs with Single-Aptamer Modification

Caged siRNAs incorporating terminal modification were rationally designed for photochemical regulation of gene silencing induced by RNA interference (RNAi). Through the conjugation of a single oligonucleotide aptamer at the 5' terminus of the antisense RNA strand, enhancement of the blocking effect for RNA-induced silencing complex (RISC) formation/processing was expected, due both/either to the aptamers themselves and/or to their interaction with large binding proteins. Two oligonucleotide aptamers (AS1411 and MUC-1) were chosen for aptamer-siRNA conjugation through a photolabile linker. This caging strategy was successfully used to photoregulate gene expression both of firefly luciferase and of green fluorescent protein (GFP) in cells. Further patterning experiments revealed that spatial regulation of GFP expression was successfully achieved by using the aptamer-modified caged siRNA and light activation. We expect that further optimized caged siRNAs featuring aptamer conjugation will be promising for practical applications to spatiotemporal photoregulation of gene expression in the future.

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.

Light Control of Protein Solubility Through Isoelectric Point Modulation

We previously described the photoactivated depot or PAD approach that allows for the light control of therapeutic protein release. This approach relies on the ability to use light to change a protein's solubility. Traditionally this was accomplished by linking the protein to an insoluble but injectable polymer via a light cleaved linker. This allows the injected material to remain at the site of injection, until transcutaneous irradiation breaks the link between polymer and protein, permitting the protein to be absorbed. However, there are multiple problems associated with polymer based approaches: The polymer makes up a majority of the material, making it inefficient. In addition, after protein release, the polymer has to be cleared from the body, a significant design challenge. In this work, we create materials that form photoactivated depots of insulin without the need for polymers, by linking photolysis to an isoelectric point shift, which itself is linked to a solubility shift. Specifically, we linked basic groups to insulin via a light cleaved linker. These shift the normal pI of insulin from 5.4 to approximately 7. The result of this incorporation are materials that are completely soluble in mildly acidic solutions but precipitate upon injection into a pH 7 environment, i.e., the skin. We successfully synthesized four such modified insulins, demonstrating that their pI values were shifted in the expected manner. We then analyzed one of them, P2-insulin, in detail, demonstrating that it behaves as designed: It is soluble in a formulation pH of 4, but precipitates at pH 7.2, its approximate pI value. Upon irradiation, the photocleavable link to insulin is broken, and completely native and soluble insulin is released from the depot in a well behaved, first order fashion. These materials are 90% therapeutic, form completely soluble and injectable formulations in mildly acidic conditions, form insoluble depots at neutral pH, efficiently release soluble protein from these depots when irradiated, and leave behind only small easily absorbed molecules after irradiation. As such they approach ideality for photoactivated depot materials.

Alkaline-tolerant RNA aptamers useful to purify acid-sensitive antibodies in neutral conditions

Recently, several oligonucleotides have been launched for clinical use and a number of therapeutic oligonucleotides are under clinical trials. Aptamer is one of the oligonucleotide therapeutics and has received a lot of attention as a new technology and an efficacious pharmaceutical compound comparable to antibody. Aptamer could be used for various purposes, not only therapeutics but also diagnostics, and applicable to affinity chromatography as a carrier molecule to purify proteins of interest. Here we demonstrate the usage and advantages of RNA aptamer to Fc region of human IgG (i.e., IgG aptamer) for purification of human antibodies. IgG aptamer requires divalent cations for binding to IgG and bound IgG dissociates easily upon treatment with chelating reagent, such as EDTA, under neutral conditions. This elution step is very mild and advantageous for maintaining active conformations of therapeutic antibodies compared to the widely used affinity purification with Protein A/G, which requires acidic elution that often damages the active conformation of antibodies. In fact, of several monoclonal antibodies tested, three antibodies were prone to aggregate on acidic elution from the Protein A/G resin, while remained fully active upon neutral elution from the IgG aptamer resin. The IgG aptamer was fully manipulated to alkaline resistant by ribose 2'-modifications, and thereby reusable numerous times with 1 N NaOH washing. The capacity of the aptamer resin to bind IgG was equivalent to that of the Protein A/G resin. Therefore, the IgG aptamer will provide us with a unique tool to uncover and purify human monoclonal antibodies, which hold therapeutic potential but lose the activity upon acidic elution from Protein A/G-based affinity resin.

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.

Photocontrolled nanoparticle delivery systems for biomedical applications

"Smart" stimuli-responsive nanomaterials are becoming popular as targeted delivery systems because they allow the use of internal or external stimuli to achieve spatial or temporal control over the delivery process. Among the stimuli that have been used, light is of special interest because it is not only noninvasive but also controllable both spatially and temporally, thus allowing unprecedented control over the delivery of bioactive molecules such as nucleic acids, proteins, drugs, etc. This is particularly advantageous for biomedical applications where specificity and selectivity are highly desired. Several strategies have evolved under the umbrella of light based delivery systems and can be classified into three main groups. The first strategy involves "caging" of the bioactive molecule using photolabile groups, loading these caged molecules onto a carrier and then "uncaging" or activating them at the targeted site upon irradiation with light of a particular wavelength. The second strategy makes use of nanocarriers that themselves are made photoresponsive either through modification with photosensitive groups or through the attachment of photolinkers on the carrier surface. These nanoparticles upon irradiation dissociate, releasing the cargo encapsulated within, or the photolinkers attaching the cargo to the surface get cleaved, resulting in release. The third approach makes use of the surface plasmon resonance of noble metal based nanoparticles. Upon irradiation with light at the plasmon resonant frequency, the resulting thermal or nonthermal field enhancement effects facilitate the release of bioactive molecules loaded onto the nanoparticles. In addition, other materials, certain metal sulfides, graphene oxide, etc., also exhibit photothermal transduction that can be exploited for targeted delivery. These approaches, though effective, are constrained by their predominant use of UV or visible light to which most photolabile groups are sensitive. Near infrared (NIR) excitation is preferred because NIR light is safer and can penetrate deeper in biological tissues. However, most photolabile groups cannot be excited by NIR light directly. So light conversion from NIR to UV/visible is required. Nanomaterials that display upconversion or two-photon-excitation properties have been developed that can serve as nanotransducers, converting NIR to UV/visible light to which the aforementioned photoresponsive moieties are sensitive. This Account will review the existing light-based nanoparticle delivery systems, their applications, the limitations they face, and the technologies that have emerged in an effort to overcome these limitations.

The synthesis of tetra-modified RNA for the multidimensional control of gene expression via light-activated RNA interference

Light-activated RNA interference (LARI) is an effective way to control gene expression with light. This, in turn, allows for the spacing, timing and degree of gene expression to be controlled by the spacing, timing and amount of light irradiation. The key mediators of this process are siRNA or dsRNA that have been modified with four photocleavable groups of dimethoxy nitro phenyl ethyl (DMNPE), located on the four terminal phosphate groups of the duplex RNA. These mediators can be easily synthesized and purified using two readily available products: synthetic RNA oligonucleotides and DMNPE-hydrazone. The synthesis of the tetra-DMNPE-modified duplex RNA is made possible by a remarkable regiospecificity of DMNPE for terminal phosphates (over internal phosphates or nucleobases) that we have previously identified. The four installed DMNPE groups effectively limit RNAi until irradiation cleaves them, releasing native, active siRNA. By using the described protocol, any process that is mediated by RNAi can be controlled with light. Although other methods exist to control gene expression with light by using specialized reagents, this method requires only two commercially available products. The protocol takes ∼3 d in total for the preparation of modified RNA.

Caged oligonucleotides for bidirectional photomodulation of let-7 miRNA in zebrafish embryos

Many biological functions of microRNA (miRNA) have been identified in the past decade. However, a single miRNA can regulate multiple gene targets, thus it has been a challenge to elucidate the specific functions of each miRNA in different locations and times. New chemical tools make it possible to modulate miRNA activity with higher spatiotemporal resolution. Here, we describe light-activated (caged) constructs for switching let-7 miRNA 'on' or 'off' with 365 nm light in developing zebrafish embryos.

Automated solid-phase synthesis of RNA oligonucleotides containing a nonbridging phosphorodithioate linkage via phosphorothioamidites

This work describes a general method for the synthesis of oligoribonucleotides containing a site-specific nonbridging phosphorodithioate linkage via automated solid-phase synthesis using 5'-O-DMTr-2'-O-TBS-ribonucleoside 3'-N,N-dimethyl-S-(2,4-dichlorobenzyl) phosphorothioamidites (2a-2d). The 3'-phosphorothioamidites (2a-2d) can be conveniently prepared in good yields (86-99%) via a one-pot reaction from the corresponding 5'-O-DMTr-2'-O-TBS-ribonucleosides (1a-1d).

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.