Hydrogen peroxide-triggered gene silencing in mammalian cells through boronated antisense oligonucleotides

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.

Oncolytic Hairpin DNA Pair: Selective Cytotoxic Inducer through MicroRNA-Triggered DNA Self-Assembly

Artificial nucleic acids have attracted much attention as potential cancer immunotherapeutic materials because they are recognized by a variety of extracellular and intracellular nucleic acid sensors and can stimulate innate immune responses. However, their low selectivity for cancer cells causes severe systemic immunotoxicity, making it difficult to use artificial nucleic acid molecules for immune cancer therapy. To address this challenge, we herein introduce a hairpin DNA assembly technology that enables cancer-selective immune activation to induce cytotoxicity. The designed artificial DNA hairpins assemble into long nicked double-stranded DNA triggered by intracellular microRNA-21 (miR-21), which is overexpressed in various types of cancer cells. We found that the products from the hairpin DNA assembly selectively kill miR-21-abundant cancer cells in vitro and in vivo based on innate immune activation. Our approach is the first to allow selective oncolysis derived from intracellular DNA self-assembly, providing a powerful therapeutic modality to treat cancer.

Acetyl group assisted rapid intramolecular recognition of hydrogen peroxide: A novel promising approach for efficient hydrogen peroxide probe

As a vital biomolecule, hydrogen peroxide (H₂O₂) is involved in many physiological and pathological processes. Therefore, it is important to detect H₂O₂ in vivo conveniently and efficiently. In this paper, we report a new method of nucleophilic addition of H₂O₂ to the acetyl group to promote the rapid intramolecular reaction, which can be used to develop an efficient H₂O₂ probe. Based on this unique auxiliary recognition part, a fluorescent probe for H₂O₂ detection was designed and synthesized. This probe has the advantages of high sensitivity (limits of detection 7.0 × 10^-8 M or even lower.), fast response (within 3 min) and large Stokes shift (225 nm), which not only can monitor exogenous and endogenous H₂O₂ in cells but also successfully achieves the change of endogenous H₂O₂ level caused by drug sexual organ injury in zebrafish.

Ascorbate oxidase enabling glucometer readout for portable detection of hydrogen peroxide

A rapid, portable, and cost-effective method using personal glucose meter (PGM) for quantitative analysis of hydrogen peroxide (H₂O₂) was established based on ascorbate oxidase (AAO)-catalyzed reaction for the first time. Ascorbic acid (AA) can rapidly reduce ferricyanide (K₃[Fe(CN)₆]) to ferrocyanide (K₄[Fe(CN)₆]) in the glucose test strip and transfer electron to the electrode to generating a PGM detectable signal. Thus, the concentration of AA can be directly determined by the PGM as simple as measuring the blood glucose. On the other hand, AAO can catalyze the reduction of H₂O₂ and produce an enzyme-peroxide complex, which decreases the yields of dehydroascorbic acid formed by the oxidation of AA, resulting in the increase in PGM detectable signal of residual ascorbic acid (re-AA). Therefore, the concentration of H₂O₂ is proportional to the concentration of re-AA. After optimization of the experimental conditions, the developed method can be used to detect H₂O₂ at linear range of 2.5-5 × 10³ μM with the quantification limit of 2.5 μM. In addition, the satisfactory spiked recoveries (95.3-108.9 %) of real samples (i.e., tap water, contact lens solution, medical hydrogen peroxide, and normal human serum) confirm its feasibility for practical applications. In short, this study provides a feasible PGM-based method for H₂O₂ detection with simple operations.

Quantifying H2O2 by ratiometric fluorescence sensor platform of N-GQDs/rhodamine B in the presence of thioglycolic acid under the catalysis of Fe3

In the presence of thioglycolic acid (TGA) and under the catalysis of Fe³⁺, a simple, rapid, sensitive, selective and effective ratiometric fluorescence sensor platform based on the mixed physically blue nitrogen-doped graphene quantum dots (N-GQDs) as probe signals and orange rhodamine B as internal standard signals has been constructed for analysis of H₂O₂ in human serum. TGA is the key factor for fluorescence response toward H₂O₂ by N-GQDs and the mechanism is H₂O₂ reacts speedily with TGA under the catalysis of Fe³⁺, and produces intermediate of superoxide anions (O₂^-), which accepts electrons from N-GQDs, and generates graphene oxide, causing the fluorescence quench of N-GQDs. Compared with N-GQDs probe, the sensitivity of the ratiometric fluorescence sensor platform of N-GQDs/rhodamine B for analysis of H₂O₂ has been improved by nearly 5-folds. Under the optimum conditions, F_λ=580nm/F_λ=440nm has a good linear relationship with the concentration of H₂O₂ and the detection limit of H₂O₂ is 0.46 μmol/L with 3.5% RSD. The established sensor platform has been successfully used for probing H₂O₂ in human serum with satisfactory results. The superior performance of the probe lies in its high selectivity and can be directly employed in detecting H₂O₂ in serum samples without any sample pretreatment procedures.

Construction of a Reduction-responsive DNA Microsphere using a Reduction-cleavable Spacer based on a Nitrobenzene Scaffold

Here, we describe the design and synthesis of a new reduction-cleavable spacer (RCS) based on a nitrobenzene scaffold for constructing reduction-responsive oligonucleotides according to standard phosphoramidite chemistry. In addition, we demonstrate that the introduction of the RCS in the middle of an oligonucleotide (30 nt) enables the construction of a self-assembled microsphere capable of exhibiting a reduction-responsive disassembly.

2'-O-(N-(Aminoethyl)carbamoyl)methyl Modification Allows for Lower Phosphorothioate Content in Splice-Switching Oligonucleotides with Retained Activity

2′-O-(N-(Aminoethyl)carbamoyl)methyl (2′-O-AECM)-modified oligonucleotides (ONs) and their mixmers with 2′-O-methyl oligonucleotides (2′-OMe ONs) with phosphodiester linkers as well as with partial and full phosphorothioate (PS) inclusion were synthesized and functionally evaluated as splice-switching oligonucleotides in several different reporter cell lines originating from different tissues. This was enabled by first preparing the AECM-modified A, C, G and U, which required a different strategy for each building block. The AECM modification has previously been shown to provide high resistance to enzymatic degradation, even without PS linkages. It is therefore particularly interesting and unprecedented that the 2′-O-AECM ONs are shown to have efficient splice-switching activity even without inclusion of PS linkages and found to be as effective as 2′-OMe PS ONs. Importantly, the PS linkages can be partially included, without any significant reduction in splice-switching efficacy. This suggests that AECM modification has the potential to be used in balancing the PS content of ONs. Furthermore, conjugation of 2′-O-AECM ONs to an endosomal escape peptide significantly increased splice-switching suggesting that this effect could possibly be due to an increase in uptake of ON to the site of action.

Chemical synthesis of stimuli-responsive guide RNA for conditional control of CRISPR-Cas9 gene editing

CRISPR-Cas9 promotes changes in identity or abundance of nucleic acids in live cells and is a programmable modality of broad biotechnological and therapeutic interest. To reduce off-target effects, tools for conditional control of CRISPR-Cas9 functions are under active research, such as stimuli-responsive guide RNA (gRNA). However, the types of physiologically relevant stimuli that can trigger gRNA are largely limited due to the lack of a versatile synthetic approach in chemistry to introduce diverse labile modifications into gRNA. In this work, we developed such a general method to prepare stimuli-responsive gRNA based on site-specific derivatization of 2′-O-methylribonucleotide phosphorothioate (PS-2′-OMe). We demonstrated CRISPR-Cas9-mediated gene editing in human cells triggered by oxidative stress and visible light, respectively. Our study tackles the synthetic challenge and paves the way for chemically modified RNA to play more active roles in gene therapy.

Conditional control of CRISPR-Cas9 activity by reactive oxygen species and visible light is achieved using stimuli-responsive guide RNA synthesized by a general method based on RNA 2′-O-methylribonucleotide phosphorothioate.

Calcium-Mediated In Vitro Transfection Technique of Oligonucleotides with Broad Chemical Modification Compatibility

Oligonucleotide drugs (ODs) have gained increasing attention owing to their promising therapeutic potential. One major obstacle that ODs have been facing is the lack of appropriate in vitro validation systems that can predict in vivo activity and toxicity. We have devised a transfection method called CEM (Ca²⁺-enrichment method), where the simple enrichment of calcium ion with calcium chloride in culture medium potentiates the activity of various types of naked oligonucleotides including gapmers, siRNA, and phosphorodiamidate morpholino antisense oligonucleotides (PMO) in many cultured cell lines with limited cytotoxicity. We here describe a precise procedure of the method. Besides the benefit of the CEM's predictive power to accurately estimate in vivo activity of ODs of your interest in drug discovery and development settings, this cost-efficient, easy-to-access method can be a robust laboratory technique to modulate gene expressions with ODs with a variety of mechanisms of action.

Conditionally Activated ("Caged") Oligonucleotides

Conditionally activated ("caged") oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.

Construction of a reduction-responsive oligonucleotide via a post-modification approach utilizing 4-nitrophenyl diazomethane

Herein, we describe the construction of a reduction-responsive oligonucleotide by post-modification of an oligonucleotide with a diazo compound bearing a 4-nitrobenzyl group as a reduction-responsive cleavable moiety. High-performance liquid chromatography and mass spectrometry were used to reveal the introduction of a 4-nitrobenzyl group to the 5′-phosphate group of an oligonucleotide, and the subsequent reduction-triggered recovery of the original oligonucleotide. The protocol used for the preparation of this reduction-responsive oligonucleotide is simple and it will have various applications in the fields of chemical and synthetic biology.

Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA

The function of CRISPR/Cas9 can be conditionally controlled by the rational engineering of guide RNA (gRNA) to target the gene of choice for precise manipulation of the genome. Particularly, chemically modified gRNA that can be activated by using specific stimuli provides a unique tool to expand the versatility of conditional control. Herein, unlike previous engineering of gRNA that generally focused on the RNA part only but neglected RNA-protein interactions, we aimed at the interactive sites between 2'-OH of ribose in the seed region of gRNA and the Cas9 protein and identified that chemical modifications at specific sites could be utilized to regulate the Cas9 activity. By introducing a photolabile group at these specific sites, we achieved optical control of Cas9 activity without disrupting the Watson-Crick base pairing. We further examined our design through CRISPR-mediated gene activation and nuclease cleavage in living cells and successfully manipulated the gene expression by using light irradiation. Our site-specific modification strategy exhibited a highly efficient and dynamic optical response and presented a new perspective for manipulating gRNA based on the RNA-protein interaction rather than the structure of RNA itself. In addition, these specific sites could also be potentially utilized for modification of other stimuli-responsive groups, which would further enrich the toolbox for conditional control of CRISPR/Cas9 function.

Caspase-Activated Oligonucleotide Probe

Light-activated ("caged") oligonucleotides provide a strategy for modulating the activity of antisense oligos, siRNA, miRNA, aptamers, DNAzymes, and mRNA-capturing probes with high spatiotemporal resolution. However, the near-UV and visible wavelengths that promote these bond-breaking reactions poorly penetrate living tissue, which limits some biological applications. To address this issue, we describe the first example of a protease-activated oligonucleotide probe, capable of reporting on caspase-3 during cellular apoptosis. The 2'-F RNA-peptide substrate-peptide nucleic acid (PNA) hairpin structure was generated in 30% yield in a single bioconjugation step.

Design of a facile fluorescent probe with a large Stokes shift for hydrogen peroxide imaging in vitro and in vivo

By modifying 4'‑hydroxybiphenyl‑4‑carbonitrile (BPN-OH) with 2‑(4‑(bromo‑methyl)phenyl)‑4,4,5,5‑tetramethyl‑1,3,2‑dioxaborolane group, a facile fluorescent probe, BPN-TOB, for sensitively tracing H₂O₂ was designed and synthesized. BPN-TOB displayed a low detection limit (67 nM), fast response time (10 min), low cytotoxicity, a mega Stokes shift (170 nm) and a remarkable fluorescence enhancement (72-fold) in the detection of H₂O₂. Additionally, probe BPN-TOB could monitor exogenous and endogenous H₂O₂ in living MGC-803 cells (human gastric cancer cells) and RAW264.7 cells (leukemia cellsin mouse macrophage). In particular, this probe BPN-TOB was successfully utilized for imaging H₂O₂ in zebrafish.

Hollow Mesoporous Bi@PEG-FA Nanoshell as a Novel Dual-Stimuli-Responsive Nanocarrier for Synergistic Chemo-Photothermal Cancer Therapy

The development of stimuli-responsive multifunctional nanocarriers for therapeutic drug delivery is extremely desirable for highly specific treatment of disease. Herein, thiol-polyethylene glycol-folate acid-modified hollow mesoporous bismuth nanoshells (HM-Bi@PEG-FA NSs) were developed as the new dual-stimuli-responsive single-"elemental" photothermal nanocarriers for synergistic chemo-photothermal therapy of tumor. The designed hollow-mesoporous-type nanocarriers present excellent photothermal conversion capacity (∼34.72%) and good biocompatibility. Meanwhile, acidic pH and near-infrared (NIR) laser dual-stimulated doxorubicin (DOX) release is successfully achieved. More importantly, the DOX-loaded HM-Bi@PEG-FA NSs hold an efficient in vitro/in vivo antitumor effect through the synergistic chemo-photothermal therapy. Therefore, our findings provide the possibility of designing a dual-stimuli-responsive hollow mesoporous Bi-based photothermal nanocarrier for synergistically enhanced antitumor therapy.

Ultra-Sensitive Hydrogen Peroxide Sensor Based on Peroxiredoxin and Fluorescence Resonance Energy Transfer

In this paper, a fluorescence resonance energy transfer (FRET)-based sensor for ultra-sensitive detection of H2O2 was developed by utilizing the unique enzymatic properties of peroxiredoxin (Prx) to H2O2. Cyan and yellow fluorescent protein (CFP and YFP) were fused to Prx and mutant thioredoxin (mTrx), respectively. In the presence of H2O2, Prx was oxidized into covalent homodimer through disulfide bonds, which were further reduced by mTrx to form a stable mixed disulfide bond intermediate between CFP-Prx and mTrx-YFP, inducing FRET. A linear quantification range of 10–320 nM was obtained according to the applied protein concentrations and the detection limit (LOD) was determined to be as low as 4 nM. By the assistance of glucose oxidase to transform glucose into H2O2, the CFP-Prx/mTrx-YFP system (CPmTY) was further exploited for the detection of glucose in real sample with good performance, suggesting this CPmTY protein sensor is highly practical.

DNA-AgNCs as a fluorescence turn-off probe for dual functional detection of H2O2 and Fe(II) ions

A novel fluorescence probe (DNA-AgNCs) was synthesized for dually detecting hydrogen peroxide (H₂O₂) and ferrous ion (Fe(II)) in water samples. The assay is carried out through a dramatic "turn-off" fluorescence response of AgNCs by hydroxyl radical (OH), which is produced when H₂O₂ and Fe(II) are present simultaneously. Under the optimal conditions, the degree of fluorescence quenching of the DNA-AgNCs at 525 nm is linearly related to the concentration of H₂O₂ in the range of 0.3 to 450 pM, and Fe(II) in the range of 0.2 to 6.0 μM. The limit of detection (LOD) of H₂O₂ and Fe(II) are as low as 99 fM and 60 nM, respectively. Moreover, this method has the advantages of good specificity, high sensitivity, and can be successfully applied for detecting H₂O₂ and Fe(II) in the real water samples.

Delivery of antisense oligonucleotide using polyethylenimine-based lipid nanoparticle modified with cell penetrating peptide

Efficient and stable delivery system of antisense oligonucleotide (ASO) is important and urgently needed. Here, an ASO delivery system, Lp-PPRP, which contains a cationic polymer based on PEI (branched, 25 kDa), named PEI-PC and a palmitic acid modified R8 (R8-PA) was prepared to deliver a kind of ASO, LOR-2501. The characteristics of the nanoparticles and the cellular uptake of LOR-2501 in HeLa cells and A549 cells were studied. Lp-PPRP showed suitable particle size and zeta potential to combine with LOR-2501; the particle size and zeta potential of Lp-PPRP/LOR were 276.87 ± 5.63 nm and 18.03 ± 0.25 mV. In vitro experiments suggested that Lp-PPRP had lower cytotoxic and higher transfection efficiency for delivering LOR-2501 compared with PEI. The addition of PEI-PC and R8-PA contributed to enhance the transfection efficiency of the nanoparticles. In HeLa cells and A549 cells, Lp-PPRP could transport LOR-2501 and down-regulate the level of R1 protein efficiently, and the R1 down regulations were 64.56% and 66.34%, respectively. Results suggested potential utility of Lp-PPRP in the development of ASO in tumor therapy.

Unprecedented green-emissive boranyl-hydrazone supramolecular assemblies and their in vitro diagnostic applications

This paper describes a novel symmetric N,N'-diethylsalicylaldehyde boranyl hydrazone (1) and its in situ-generated assemblies displaying opto-analytical capabilities for the diagnosis of nucleic acids under physiological conditions. The sensing capabilities of these unprecedented supramolecular assemblies were characterized using UV-Vis spectroscopy, fluorescence spectroscopy, 1D and 2D NMR spectroscopy, dynamic light scattering, and zeta potential measurements. Model compounds lacking boranyl units (2, 3) were prepared to correlate and evaluate the sensing mechanism. The rationally designed probe 1 displays unusual aggregation-induced emissive (AIE) properties, with an average particle size of 1096 nm exhibiting green emission upon excitation at 377 nm in pH-7.2 TRIZMA buffer. A selective switch on response toward organic PO₄^3- accompanied through specific nano-aggregations patterns and sizes, thereby causing a significant red-shift through AIE. Exploiting such switch on in green channel behavior has allowed the monitoring of DNase I activities and polymerase chain reactions.

UV cell stress induces oxidative cyclization of a protective reagent for DNA damage reduction in skin explants

UV irradiation is a major driver of DNA damage and ultimately skin cancer. UV exposure leads to persistent radicals that generate ROS over prolonged periods of time. Toward the goal of developing long-lasting antioxidants that can penetrate skin, we have designed a ROS-initiated protective (RIP) reagent that, upon reaction with ROS (antioxidant activity), self-cyclizes and then releases the natural product apocynin. Apocynin is a known antioxidant and inhibitor of NOX oxidase enzymes. A key phenol on the compound 1 controls ROS-initiated cyclization and makes 1 responsive to ROS with a EC50 comparable to common antioxidants in an ABTS assay. In an in vitro DNA nicking assay, the RIP reagent prevented DNA strand breaks. In cell-based assays, the reagent was not cytotoxic, apocynin was released only in cells treated with UVR, reduced UVR-induced cell death, and lowered DNA lesion formation. Finally, topical treatment of human skin explants with the RIP reagent reduced UV-induced DNA damage as monitored by quantification of cyclobutane dimer formation and DNA repair signaling via TP53. The reagent was more effective than administration of a catalase antioxidant on skin explants. This chemistry platform will expand the types of ROS-activated motifs and enable inhibitor release for potential use as a long-acting sunscreen.

A stimuli-responsive DNAzyme displaying Boolean logic-gate responses

Introducing a desired stimuli-responsive function into catalytically active biomacromolecules is potentially useful in developing molecular tools for various bio-applications. In this paper, we discuss the development of a stimuli-responsive DNAzyme (catalytic deoxyribozyme) capable of displaying Boolean logic-gate responses.

Aryl Azides as Phosphine-Activated Switches for Small Molecule Function

Engineered small molecule triggers are important tools for the control and investigation of biological processes, in particular protein function. Staudinger reductions of aryl azides to amines through the use of phosphines can trigger an elimination reaction, and thereby activation of a functional molecule, if an appropriately positioned leaving group is present. We conducted detailed investigations of the effect of aryl azide and phosphine structure on both the mechanism and kinetics of these reaction-induced eliminations and identified phosphine/azide pairs that enable complete activation within minutes under physiologically relevant conditions.

Reduction-Responsive DNA Duplex Containing O 6-Nitrobenzyl-Guanine

Stimuli-controlled structural transitions of nucleic acids have received growing attentions owing to their potential applications in the fields of chemical and synthetic biology. Here, we describe the development of reduction-responsive deoxyribonucleic acid (DNA) duplexes, in which guanine rings bearing a reduction-responsive cleavable nitrobenzyl (NB) group at the O ⁶ position (G^NB) are introduced at defined positions. We demonstrate that the artificial NB group can be removed in response to reduction stimulus without the dissociation of the intermolecular duplex structure, which comprises a G-quadruplex forming nucleic acid strand with one G^NB and its complementary sequence with one mismatch pair. Meanwhile, another duplex that comprised a G-quadruplex forming nucleic acid strand with two G^NB and its complementary sequence with three mismatch pairs exhibited reduction-responsive structural transitions from intermolecular duplex to intramolecular quadruplex. These findings might be useful for the development of DNA architectures endowed with reduction-responsive functions.